Starting phenix.real_space_refine on Sun Mar 10 14:20:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqt_25394/03_2024/7sqt_25394.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqt_25394/03_2024/7sqt_25394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqt_25394/03_2024/7sqt_25394.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqt_25394/03_2024/7sqt_25394.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqt_25394/03_2024/7sqt_25394.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sqt_25394/03_2024/7sqt_25394.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 504 5.16 5 C 67536 2.51 5 N 18624 2.21 5 O 20472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 107136 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4464 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 32, 'TRANS': 540} Chain breaks: 2 Chain: "B" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4464 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 32, 'TRANS': 540} Chain breaks: 2 Chain: "C" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4464 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 32, 'TRANS': 540} Chain breaks: 2 Chain: "D" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4464 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 32, 'TRANS': 540} Chain breaks: 2 Chain: "E" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4464 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 32, 'TRANS': 540} Chain breaks: 2 Chain: "F" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4464 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 32, 'TRANS': 540} Chain breaks: 2 Chain: "G" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4464 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 32, 'TRANS': 540} Chain breaks: 2 Chain: "H" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4464 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 32, 'TRANS': 540} Chain breaks: 2 Chain: "I" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4464 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 32, 'TRANS': 540} Chain breaks: 2 Chain: "J" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4464 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 32, 'TRANS': 540} Chain breaks: 2 Chain: "K" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4464 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 32, 'TRANS': 540} Chain breaks: 2 Chain: "L" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4464 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 32, 'TRANS': 540} Chain breaks: 2 Chain: "M" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4464 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 32, 'TRANS': 540} Chain breaks: 2 Chain: "N" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4464 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 32, 'TRANS': 540} Chain breaks: 2 Chain: "O" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4464 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 32, 'TRANS': 540} Chain breaks: 2 Chain: "P" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4464 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 32, 'TRANS': 540} Chain breaks: 2 Chain: "Q" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4464 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 32, 'TRANS': 540} Chain breaks: 2 Chain: "R" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4464 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 32, 'TRANS': 540} Chain breaks: 2 Chain: "S" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4464 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 32, 'TRANS': 540} Chain breaks: 2 Chain: "T" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4464 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 32, 'TRANS': 540} Chain breaks: 2 Chain: "V" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4464 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 32, 'TRANS': 540} Chain breaks: 2 Chain: "W" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4464 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 32, 'TRANS': 540} Chain breaks: 2 Chain: "X" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4464 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 32, 'TRANS': 540} Chain breaks: 2 Chain: "Y" Number of atoms: 4464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4464 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 32, 'TRANS': 540} Chain breaks: 2 Time building chain proxies: 40.70, per 1000 atoms: 0.38 Number of scatterers: 107136 At special positions: 0 Unit cell: (228.204, 228.204, 228.204, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 504 16.00 O 20472 8.00 N 18624 7.00 C 67536 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 29.65 Conformation dependent library (CDL) restraints added in 14.5 seconds 27216 Ramachandran restraints generated. 13608 Oldfield, 0 Emsley, 13608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 25440 Finding SS restraints... Secondary structure from input PDB file: 600 helices and 120 sheets defined 41.7% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.45 Creating SS restraints... Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 64 through 78 Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 154 through 170 Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.636A pdb=" N GLY A 175 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS A 219 " --> pdb=" O ARG A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA A 231 " --> pdb=" O GLY A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU A 360 " --> pdb=" O TRP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 372 through 375 removed outlier: 3.540A pdb=" N ALA A 375 " --> pdb=" O ASN A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 376 through 381 Processing helix chain 'A' and resid 394 through 403 Processing helix chain 'A' and resid 422 through 427 Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.500A pdb=" N ALA A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 462 " --> pdb=" O PHE A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 503 through 511 Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 529 through 546 Processing helix chain 'A' and resid 561 through 575 Processing helix chain 'A' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA A 600 " --> pdb=" O MET A 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 596 through 601' Processing helix chain 'A' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE A 610 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 611 " --> pdb=" O GLY A 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 611' Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 64 through 78 Processing helix chain 'B' and resid 148 through 153 Processing helix chain 'B' and resid 154 through 170 Processing helix chain 'B' and resid 171 through 175 removed outlier: 3.636A pdb=" N GLY B 175 " --> pdb=" O LYS B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP B 218 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS B 219 " --> pdb=" O ARG B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA B 231 " --> pdb=" O GLY B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 351 Processing helix chain 'B' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU B 360 " --> pdb=" O TRP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 367 No H-bonds generated for 'chain 'B' and resid 365 through 367' Processing helix chain 'B' and resid 372 through 375 removed outlier: 3.540A pdb=" N ALA B 375 " --> pdb=" O ASN B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 372 through 375' Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 394 through 403 Processing helix chain 'B' and resid 422 through 427 Processing helix chain 'B' and resid 427 through 432 removed outlier: 3.500A pdb=" N ALA B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 470 Processing helix chain 'B' and resid 500 through 502 No H-bonds generated for 'chain 'B' and resid 500 through 502' Processing helix chain 'B' and resid 503 through 511 Processing helix chain 'B' and resid 512 through 525 Processing helix chain 'B' and resid 529 through 546 Processing helix chain 'B' and resid 561 through 575 Processing helix chain 'B' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA B 600 " --> pdb=" O MET B 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 596 through 601' Processing helix chain 'B' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE B 610 " --> pdb=" O SER B 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR B 611 " --> pdb=" O GLY B 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 607 through 611' Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'C' and resid 48 through 53 Processing helix chain 'C' and resid 64 through 78 Processing helix chain 'C' and resid 148 through 153 Processing helix chain 'C' and resid 154 through 170 Processing helix chain 'C' and resid 171 through 175 removed outlier: 3.636A pdb=" N GLY C 175 " --> pdb=" O LYS C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS C 219 " --> pdb=" O ARG C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA C 231 " --> pdb=" O GLY C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 351 Processing helix chain 'C' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU C 360 " --> pdb=" O TRP C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 367 No H-bonds generated for 'chain 'C' and resid 365 through 367' Processing helix chain 'C' and resid 372 through 375 removed outlier: 3.540A pdb=" N ALA C 375 " --> pdb=" O ASN C 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 372 through 375' Processing helix chain 'C' and resid 376 through 381 Processing helix chain 'C' and resid 394 through 403 Processing helix chain 'C' and resid 422 through 427 Processing helix chain 'C' and resid 427 through 432 removed outlier: 3.500A pdb=" N ALA C 431 " --> pdb=" O ARG C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR C 462 " --> pdb=" O PHE C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 470 Processing helix chain 'C' and resid 500 through 502 No H-bonds generated for 'chain 'C' and resid 500 through 502' Processing helix chain 'C' and resid 503 through 511 Processing helix chain 'C' and resid 512 through 525 Processing helix chain 'C' and resid 529 through 546 Processing helix chain 'C' and resid 561 through 575 Processing helix chain 'C' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA C 600 " --> pdb=" O MET C 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG C 601 " --> pdb=" O ALA C 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 596 through 601' Processing helix chain 'C' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE C 610 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR C 611 " --> pdb=" O GLY C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 607 through 611' Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 64 through 78 Processing helix chain 'D' and resid 148 through 153 Processing helix chain 'D' and resid 154 through 170 Processing helix chain 'D' and resid 171 through 175 removed outlier: 3.636A pdb=" N GLY D 175 " --> pdb=" O LYS D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP D 218 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS D 219 " --> pdb=" O ARG D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA D 231 " --> pdb=" O GLY D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 351 Processing helix chain 'D' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU D 360 " --> pdb=" O TRP D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 367 No H-bonds generated for 'chain 'D' and resid 365 through 367' Processing helix chain 'D' and resid 372 through 375 removed outlier: 3.540A pdb=" N ALA D 375 " --> pdb=" O ASN D 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 372 through 375' Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 394 through 403 Processing helix chain 'D' and resid 422 through 427 Processing helix chain 'D' and resid 427 through 432 removed outlier: 3.500A pdb=" N ALA D 431 " --> pdb=" O ARG D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS D 452 " --> pdb=" O SER D 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR D 462 " --> pdb=" O PHE D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 470 Processing helix chain 'D' and resid 500 through 502 No H-bonds generated for 'chain 'D' and resid 500 through 502' Processing helix chain 'D' and resid 503 through 511 Processing helix chain 'D' and resid 512 through 525 Processing helix chain 'D' and resid 529 through 546 Processing helix chain 'D' and resid 561 through 575 Processing helix chain 'D' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA D 600 " --> pdb=" O MET D 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG D 601 " --> pdb=" O ALA D 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 596 through 601' Processing helix chain 'D' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE D 610 " --> pdb=" O SER D 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR D 611 " --> pdb=" O GLY D 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 607 through 611' Processing helix chain 'E' and resid 45 through 47 No H-bonds generated for 'chain 'E' and resid 45 through 47' Processing helix chain 'E' and resid 48 through 53 Processing helix chain 'E' and resid 64 through 78 Processing helix chain 'E' and resid 148 through 153 Processing helix chain 'E' and resid 154 through 170 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.636A pdb=" N GLY E 175 " --> pdb=" O LYS E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP E 218 " --> pdb=" O ILE E 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS E 219 " --> pdb=" O ARG E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA E 231 " --> pdb=" O GLY E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 351 Processing helix chain 'E' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU E 360 " --> pdb=" O TRP E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 367 No H-bonds generated for 'chain 'E' and resid 365 through 367' Processing helix chain 'E' and resid 372 through 375 removed outlier: 3.540A pdb=" N ALA E 375 " --> pdb=" O ASN E 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 372 through 375' Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 394 through 403 Processing helix chain 'E' and resid 422 through 427 Processing helix chain 'E' and resid 427 through 432 removed outlier: 3.500A pdb=" N ALA E 431 " --> pdb=" O ARG E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS E 452 " --> pdb=" O SER E 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR E 462 " --> pdb=" O PHE E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 470 Processing helix chain 'E' and resid 500 through 502 No H-bonds generated for 'chain 'E' and resid 500 through 502' Processing helix chain 'E' and resid 503 through 511 Processing helix chain 'E' and resid 512 through 525 Processing helix chain 'E' and resid 529 through 546 Processing helix chain 'E' and resid 561 through 575 Processing helix chain 'E' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA E 600 " --> pdb=" O MET E 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG E 601 " --> pdb=" O ALA E 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 596 through 601' Processing helix chain 'E' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE E 610 " --> pdb=" O SER E 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR E 611 " --> pdb=" O GLY E 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 607 through 611' Processing helix chain 'F' and resid 45 through 47 No H-bonds generated for 'chain 'F' and resid 45 through 47' Processing helix chain 'F' and resid 48 through 53 Processing helix chain 'F' and resid 64 through 78 Processing helix chain 'F' and resid 148 through 153 Processing helix chain 'F' and resid 154 through 170 Processing helix chain 'F' and resid 171 through 175 removed outlier: 3.636A pdb=" N GLY F 175 " --> pdb=" O LYS F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP F 218 " --> pdb=" O ILE F 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS F 219 " --> pdb=" O ARG F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA F 231 " --> pdb=" O GLY F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 351 Processing helix chain 'F' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU F 360 " --> pdb=" O TRP F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 367 No H-bonds generated for 'chain 'F' and resid 365 through 367' Processing helix chain 'F' and resid 372 through 375 removed outlier: 3.540A pdb=" N ALA F 375 " --> pdb=" O ASN F 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 372 through 375' Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 394 through 403 Processing helix chain 'F' and resid 422 through 427 Processing helix chain 'F' and resid 427 through 432 removed outlier: 3.500A pdb=" N ALA F 431 " --> pdb=" O ARG F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS F 452 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR F 462 " --> pdb=" O PHE F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 465 through 470 Processing helix chain 'F' and resid 500 through 502 No H-bonds generated for 'chain 'F' and resid 500 through 502' Processing helix chain 'F' and resid 503 through 511 Processing helix chain 'F' and resid 512 through 525 Processing helix chain 'F' and resid 529 through 546 Processing helix chain 'F' and resid 561 through 575 Processing helix chain 'F' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA F 600 " --> pdb=" O MET F 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG F 601 " --> pdb=" O ALA F 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 596 through 601' Processing helix chain 'F' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE F 610 " --> pdb=" O SER F 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR F 611 " --> pdb=" O GLY F 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 607 through 611' Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'G' and resid 48 through 53 Processing helix chain 'G' and resid 64 through 78 Processing helix chain 'G' and resid 148 through 153 Processing helix chain 'G' and resid 154 through 170 Processing helix chain 'G' and resid 171 through 175 removed outlier: 3.636A pdb=" N GLY G 175 " --> pdb=" O LYS G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP G 218 " --> pdb=" O ILE G 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS G 219 " --> pdb=" O ARG G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA G 231 " --> pdb=" O GLY G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 351 Processing helix chain 'G' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU G 360 " --> pdb=" O TRP G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 367 No H-bonds generated for 'chain 'G' and resid 365 through 367' Processing helix chain 'G' and resid 372 through 375 removed outlier: 3.540A pdb=" N ALA G 375 " --> pdb=" O ASN G 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 372 through 375' Processing helix chain 'G' and resid 376 through 381 Processing helix chain 'G' and resid 394 through 403 Processing helix chain 'G' and resid 422 through 427 Processing helix chain 'G' and resid 427 through 432 removed outlier: 3.500A pdb=" N ALA G 431 " --> pdb=" O ARG G 427 " (cutoff:3.500A) Processing helix chain 'G' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS G 452 " --> pdb=" O SER G 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR G 462 " --> pdb=" O PHE G 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 465 through 470 Processing helix chain 'G' and resid 500 through 502 No H-bonds generated for 'chain 'G' and resid 500 through 502' Processing helix chain 'G' and resid 503 through 511 Processing helix chain 'G' and resid 512 through 525 Processing helix chain 'G' and resid 529 through 546 Processing helix chain 'G' and resid 561 through 575 Processing helix chain 'G' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA G 600 " --> pdb=" O MET G 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG G 601 " --> pdb=" O ALA G 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 596 through 601' Processing helix chain 'G' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE G 610 " --> pdb=" O SER G 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR G 611 " --> pdb=" O GLY G 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 607 through 611' Processing helix chain 'H' and resid 45 through 47 No H-bonds generated for 'chain 'H' and resid 45 through 47' Processing helix chain 'H' and resid 48 through 53 Processing helix chain 'H' and resid 64 through 78 Processing helix chain 'H' and resid 148 through 153 Processing helix chain 'H' and resid 154 through 170 Processing helix chain 'H' and resid 171 through 175 removed outlier: 3.636A pdb=" N GLY H 175 " --> pdb=" O LYS H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP H 218 " --> pdb=" O ILE H 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS H 219 " --> pdb=" O ARG H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA H 231 " --> pdb=" O GLY H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 351 Processing helix chain 'H' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU H 360 " --> pdb=" O TRP H 356 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 367 No H-bonds generated for 'chain 'H' and resid 365 through 367' Processing helix chain 'H' and resid 372 through 375 removed outlier: 3.540A pdb=" N ALA H 375 " --> pdb=" O ASN H 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 372 through 375' Processing helix chain 'H' and resid 376 through 381 Processing helix chain 'H' and resid 394 through 403 Processing helix chain 'H' and resid 422 through 427 Processing helix chain 'H' and resid 427 through 432 removed outlier: 3.500A pdb=" N ALA H 431 " --> pdb=" O ARG H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS H 452 " --> pdb=" O SER H 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR H 462 " --> pdb=" O PHE H 458 " (cutoff:3.500A) Processing helix chain 'H' and resid 465 through 470 Processing helix chain 'H' and resid 500 through 502 No H-bonds generated for 'chain 'H' and resid 500 through 502' Processing helix chain 'H' and resid 503 through 511 Processing helix chain 'H' and resid 512 through 525 Processing helix chain 'H' and resid 529 through 546 Processing helix chain 'H' and resid 561 through 575 Processing helix chain 'H' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA H 600 " --> pdb=" O MET H 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG H 601 " --> pdb=" O ALA H 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 596 through 601' Processing helix chain 'H' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE H 610 " --> pdb=" O SER H 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR H 611 " --> pdb=" O GLY H 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 607 through 611' Processing helix chain 'I' and resid 45 through 47 No H-bonds generated for 'chain 'I' and resid 45 through 47' Processing helix chain 'I' and resid 48 through 53 Processing helix chain 'I' and resid 64 through 78 Processing helix chain 'I' and resid 148 through 153 Processing helix chain 'I' and resid 154 through 170 Processing helix chain 'I' and resid 171 through 175 removed outlier: 3.636A pdb=" N GLY I 175 " --> pdb=" O LYS I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP I 218 " --> pdb=" O ILE I 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS I 219 " --> pdb=" O ARG I 215 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA I 231 " --> pdb=" O GLY I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 351 Processing helix chain 'I' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU I 360 " --> pdb=" O TRP I 356 " (cutoff:3.500A) Processing helix chain 'I' and resid 365 through 367 No H-bonds generated for 'chain 'I' and resid 365 through 367' Processing helix chain 'I' and resid 372 through 375 removed outlier: 3.540A pdb=" N ALA I 375 " --> pdb=" O ASN I 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 372 through 375' Processing helix chain 'I' and resid 376 through 381 Processing helix chain 'I' and resid 394 through 403 Processing helix chain 'I' and resid 422 through 427 Processing helix chain 'I' and resid 427 through 432 removed outlier: 3.500A pdb=" N ALA I 431 " --> pdb=" O ARG I 427 " (cutoff:3.500A) Processing helix chain 'I' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS I 452 " --> pdb=" O SER I 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR I 462 " --> pdb=" O PHE I 458 " (cutoff:3.500A) Processing helix chain 'I' and resid 465 through 470 Processing helix chain 'I' and resid 500 through 502 No H-bonds generated for 'chain 'I' and resid 500 through 502' Processing helix chain 'I' and resid 503 through 511 Processing helix chain 'I' and resid 512 through 525 Processing helix chain 'I' and resid 529 through 546 Processing helix chain 'I' and resid 561 through 575 Processing helix chain 'I' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA I 600 " --> pdb=" O MET I 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG I 601 " --> pdb=" O ALA I 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 596 through 601' Processing helix chain 'I' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE I 610 " --> pdb=" O SER I 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR I 611 " --> pdb=" O GLY I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 607 through 611' Processing helix chain 'J' and resid 45 through 47 No H-bonds generated for 'chain 'J' and resid 45 through 47' Processing helix chain 'J' and resid 48 through 53 Processing helix chain 'J' and resid 64 through 78 Processing helix chain 'J' and resid 148 through 153 Processing helix chain 'J' and resid 154 through 170 Processing helix chain 'J' and resid 171 through 175 removed outlier: 3.636A pdb=" N GLY J 175 " --> pdb=" O LYS J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP J 218 " --> pdb=" O ILE J 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS J 219 " --> pdb=" O ARG J 215 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA J 231 " --> pdb=" O GLY J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 351 Processing helix chain 'J' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU J 360 " --> pdb=" O TRP J 356 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 367 No H-bonds generated for 'chain 'J' and resid 365 through 367' Processing helix chain 'J' and resid 372 through 375 removed outlier: 3.540A pdb=" N ALA J 375 " --> pdb=" O ASN J 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 372 through 375' Processing helix chain 'J' and resid 376 through 381 Processing helix chain 'J' and resid 394 through 403 Processing helix chain 'J' and resid 422 through 427 Processing helix chain 'J' and resid 427 through 432 removed outlier: 3.500A pdb=" N ALA J 431 " --> pdb=" O ARG J 427 " (cutoff:3.500A) Processing helix chain 'J' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS J 452 " --> pdb=" O SER J 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR J 462 " --> pdb=" O PHE J 458 " (cutoff:3.500A) Processing helix chain 'J' and resid 465 through 470 Processing helix chain 'J' and resid 500 through 502 No H-bonds generated for 'chain 'J' and resid 500 through 502' Processing helix chain 'J' and resid 503 through 511 Processing helix chain 'J' and resid 512 through 525 Processing helix chain 'J' and resid 529 through 546 Processing helix chain 'J' and resid 561 through 575 Processing helix chain 'J' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA J 600 " --> pdb=" O MET J 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG J 601 " --> pdb=" O ALA J 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 596 through 601' Processing helix chain 'J' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE J 610 " --> pdb=" O SER J 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR J 611 " --> pdb=" O GLY J 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 607 through 611' Processing helix chain 'K' and resid 45 through 47 No H-bonds generated for 'chain 'K' and resid 45 through 47' Processing helix chain 'K' and resid 48 through 53 Processing helix chain 'K' and resid 64 through 78 Processing helix chain 'K' and resid 148 through 153 Processing helix chain 'K' and resid 154 through 170 Processing helix chain 'K' and resid 171 through 175 removed outlier: 3.636A pdb=" N GLY K 175 " --> pdb=" O LYS K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP K 218 " --> pdb=" O ILE K 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS K 219 " --> pdb=" O ARG K 215 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA K 231 " --> pdb=" O GLY K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 351 Processing helix chain 'K' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU K 360 " --> pdb=" O TRP K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 365 through 367 No H-bonds generated for 'chain 'K' and resid 365 through 367' Processing helix chain 'K' and resid 372 through 375 removed outlier: 3.540A pdb=" N ALA K 375 " --> pdb=" O ASN K 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 372 through 375' Processing helix chain 'K' and resid 376 through 381 Processing helix chain 'K' and resid 394 through 403 Processing helix chain 'K' and resid 422 through 427 Processing helix chain 'K' and resid 427 through 432 removed outlier: 3.500A pdb=" N ALA K 431 " --> pdb=" O ARG K 427 " (cutoff:3.500A) Processing helix chain 'K' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS K 452 " --> pdb=" O SER K 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR K 462 " --> pdb=" O PHE K 458 " (cutoff:3.500A) Processing helix chain 'K' and resid 465 through 470 Processing helix chain 'K' and resid 500 through 502 No H-bonds generated for 'chain 'K' and resid 500 through 502' Processing helix chain 'K' and resid 503 through 511 Processing helix chain 'K' and resid 512 through 525 Processing helix chain 'K' and resid 529 through 546 Processing helix chain 'K' and resid 561 through 575 Processing helix chain 'K' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA K 600 " --> pdb=" O MET K 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG K 601 " --> pdb=" O ALA K 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 596 through 601' Processing helix chain 'K' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE K 610 " --> pdb=" O SER K 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR K 611 " --> pdb=" O GLY K 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 607 through 611' Processing helix chain 'L' and resid 45 through 47 No H-bonds generated for 'chain 'L' and resid 45 through 47' Processing helix chain 'L' and resid 48 through 53 Processing helix chain 'L' and resid 64 through 78 Processing helix chain 'L' and resid 148 through 153 Processing helix chain 'L' and resid 154 through 170 Processing helix chain 'L' and resid 171 through 175 removed outlier: 3.636A pdb=" N GLY L 175 " --> pdb=" O LYS L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP L 218 " --> pdb=" O ILE L 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS L 219 " --> pdb=" O ARG L 215 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA L 231 " --> pdb=" O GLY L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 335 through 351 Processing helix chain 'L' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU L 360 " --> pdb=" O TRP L 356 " (cutoff:3.500A) Processing helix chain 'L' and resid 365 through 367 No H-bonds generated for 'chain 'L' and resid 365 through 367' Processing helix chain 'L' and resid 372 through 375 removed outlier: 3.540A pdb=" N ALA L 375 " --> pdb=" O ASN L 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 372 through 375' Processing helix chain 'L' and resid 376 through 381 Processing helix chain 'L' and resid 394 through 403 Processing helix chain 'L' and resid 422 through 427 Processing helix chain 'L' and resid 427 through 432 removed outlier: 3.500A pdb=" N ALA L 431 " --> pdb=" O ARG L 427 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS L 452 " --> pdb=" O SER L 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR L 462 " --> pdb=" O PHE L 458 " (cutoff:3.500A) Processing helix chain 'L' and resid 465 through 470 Processing helix chain 'L' and resid 500 through 502 No H-bonds generated for 'chain 'L' and resid 500 through 502' Processing helix chain 'L' and resid 503 through 511 Processing helix chain 'L' and resid 512 through 525 Processing helix chain 'L' and resid 529 through 546 Processing helix chain 'L' and resid 561 through 575 Processing helix chain 'L' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA L 600 " --> pdb=" O MET L 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG L 601 " --> pdb=" O ALA L 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 596 through 601' Processing helix chain 'L' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE L 610 " --> pdb=" O SER L 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR L 611 " --> pdb=" O GLY L 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 607 through 611' Processing helix chain 'M' and resid 45 through 47 No H-bonds generated for 'chain 'M' and resid 45 through 47' Processing helix chain 'M' and resid 48 through 53 Processing helix chain 'M' and resid 64 through 78 Processing helix chain 'M' and resid 148 through 153 Processing helix chain 'M' and resid 154 through 170 Processing helix chain 'M' and resid 171 through 175 removed outlier: 3.636A pdb=" N GLY M 175 " --> pdb=" O LYS M 172 " (cutoff:3.500A) Processing helix chain 'M' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP M 218 " --> pdb=" O ILE M 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS M 219 " --> pdb=" O ARG M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA M 231 " --> pdb=" O GLY M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 351 Processing helix chain 'M' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU M 360 " --> pdb=" O TRP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 365 through 367 No H-bonds generated for 'chain 'M' and resid 365 through 367' Processing helix chain 'M' and resid 372 through 375 removed outlier: 3.540A pdb=" N ALA M 375 " --> pdb=" O ASN M 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 372 through 375' Processing helix chain 'M' and resid 376 through 381 Processing helix chain 'M' and resid 394 through 403 Processing helix chain 'M' and resid 422 through 427 Processing helix chain 'M' and resid 427 through 432 removed outlier: 3.500A pdb=" N ALA M 431 " --> pdb=" O ARG M 427 " (cutoff:3.500A) Processing helix chain 'M' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS M 452 " --> pdb=" O SER M 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR M 462 " --> pdb=" O PHE M 458 " (cutoff:3.500A) Processing helix chain 'M' and resid 465 through 470 Processing helix chain 'M' and resid 500 through 502 No H-bonds generated for 'chain 'M' and resid 500 through 502' Processing helix chain 'M' and resid 503 through 511 Processing helix chain 'M' and resid 512 through 525 Processing helix chain 'M' and resid 529 through 546 Processing helix chain 'M' and resid 561 through 575 Processing helix chain 'M' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA M 600 " --> pdb=" O MET M 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG M 601 " --> pdb=" O ALA M 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 596 through 601' Processing helix chain 'M' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE M 610 " --> pdb=" O SER M 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR M 611 " --> pdb=" O GLY M 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 607 through 611' Processing helix chain 'N' and resid 45 through 47 No H-bonds generated for 'chain 'N' and resid 45 through 47' Processing helix chain 'N' and resid 48 through 53 Processing helix chain 'N' and resid 64 through 78 Processing helix chain 'N' and resid 148 through 153 Processing helix chain 'N' and resid 154 through 170 Processing helix chain 'N' and resid 171 through 175 removed outlier: 3.636A pdb=" N GLY N 175 " --> pdb=" O LYS N 172 " (cutoff:3.500A) Processing helix chain 'N' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP N 218 " --> pdb=" O ILE N 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS N 219 " --> pdb=" O ARG N 215 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA N 231 " --> pdb=" O GLY N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 335 through 351 Processing helix chain 'N' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU N 360 " --> pdb=" O TRP N 356 " (cutoff:3.500A) Processing helix chain 'N' and resid 365 through 367 No H-bonds generated for 'chain 'N' and resid 365 through 367' Processing helix chain 'N' and resid 372 through 375 removed outlier: 3.540A pdb=" N ALA N 375 " --> pdb=" O ASN N 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 372 through 375' Processing helix chain 'N' and resid 376 through 381 Processing helix chain 'N' and resid 394 through 403 Processing helix chain 'N' and resid 422 through 427 Processing helix chain 'N' and resid 427 through 432 removed outlier: 3.500A pdb=" N ALA N 431 " --> pdb=" O ARG N 427 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS N 452 " --> pdb=" O SER N 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR N 462 " --> pdb=" O PHE N 458 " (cutoff:3.500A) Processing helix chain 'N' and resid 465 through 470 Processing helix chain 'N' and resid 500 through 502 No H-bonds generated for 'chain 'N' and resid 500 through 502' Processing helix chain 'N' and resid 503 through 511 Processing helix chain 'N' and resid 512 through 525 Processing helix chain 'N' and resid 529 through 546 Processing helix chain 'N' and resid 561 through 575 Processing helix chain 'N' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA N 600 " --> pdb=" O MET N 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG N 601 " --> pdb=" O ALA N 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 596 through 601' Processing helix chain 'N' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE N 610 " --> pdb=" O SER N 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR N 611 " --> pdb=" O GLY N 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 607 through 611' Processing helix chain 'O' and resid 45 through 47 No H-bonds generated for 'chain 'O' and resid 45 through 47' Processing helix chain 'O' and resid 48 through 53 Processing helix chain 'O' and resid 64 through 78 Processing helix chain 'O' and resid 148 through 153 Processing helix chain 'O' and resid 154 through 170 Processing helix chain 'O' and resid 171 through 175 removed outlier: 3.636A pdb=" N GLY O 175 " --> pdb=" O LYS O 172 " (cutoff:3.500A) Processing helix chain 'O' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP O 218 " --> pdb=" O ILE O 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS O 219 " --> pdb=" O ARG O 215 " (cutoff:3.500A) Processing helix chain 'O' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA O 231 " --> pdb=" O GLY O 228 " (cutoff:3.500A) Processing helix chain 'O' and resid 335 through 351 Processing helix chain 'O' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU O 360 " --> pdb=" O TRP O 356 " (cutoff:3.500A) Processing helix chain 'O' and resid 365 through 367 No H-bonds generated for 'chain 'O' and resid 365 through 367' Processing helix chain 'O' and resid 372 through 375 removed outlier: 3.540A pdb=" N ALA O 375 " --> pdb=" O ASN O 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 372 through 375' Processing helix chain 'O' and resid 376 through 381 Processing helix chain 'O' and resid 394 through 403 Processing helix chain 'O' and resid 422 through 427 Processing helix chain 'O' and resid 427 through 432 removed outlier: 3.500A pdb=" N ALA O 431 " --> pdb=" O ARG O 427 " (cutoff:3.500A) Processing helix chain 'O' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS O 452 " --> pdb=" O SER O 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR O 462 " --> pdb=" O PHE O 458 " (cutoff:3.500A) Processing helix chain 'O' and resid 465 through 470 Processing helix chain 'O' and resid 500 through 502 No H-bonds generated for 'chain 'O' and resid 500 through 502' Processing helix chain 'O' and resid 503 through 511 Processing helix chain 'O' and resid 512 through 525 Processing helix chain 'O' and resid 529 through 546 Processing helix chain 'O' and resid 561 through 575 Processing helix chain 'O' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA O 600 " --> pdb=" O MET O 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG O 601 " --> pdb=" O ALA O 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 596 through 601' Processing helix chain 'O' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE O 610 " --> pdb=" O SER O 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR O 611 " --> pdb=" O GLY O 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 607 through 611' Processing helix chain 'P' and resid 45 through 47 No H-bonds generated for 'chain 'P' and resid 45 through 47' Processing helix chain 'P' and resid 48 through 53 Processing helix chain 'P' and resid 64 through 78 Processing helix chain 'P' and resid 148 through 153 Processing helix chain 'P' and resid 154 through 170 Processing helix chain 'P' and resid 171 through 175 removed outlier: 3.636A pdb=" N GLY P 175 " --> pdb=" O LYS P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP P 218 " --> pdb=" O ILE P 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS P 219 " --> pdb=" O ARG P 215 " (cutoff:3.500A) Processing helix chain 'P' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA P 231 " --> pdb=" O GLY P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 335 through 351 Processing helix chain 'P' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU P 360 " --> pdb=" O TRP P 356 " (cutoff:3.500A) Processing helix chain 'P' and resid 365 through 367 No H-bonds generated for 'chain 'P' and resid 365 through 367' Processing helix chain 'P' and resid 372 through 375 removed outlier: 3.540A pdb=" N ALA P 375 " --> pdb=" O ASN P 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 372 through 375' Processing helix chain 'P' and resid 376 through 381 Processing helix chain 'P' and resid 394 through 403 Processing helix chain 'P' and resid 422 through 427 Processing helix chain 'P' and resid 427 through 432 removed outlier: 3.500A pdb=" N ALA P 431 " --> pdb=" O ARG P 427 " (cutoff:3.500A) Processing helix chain 'P' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS P 452 " --> pdb=" O SER P 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR P 462 " --> pdb=" O PHE P 458 " (cutoff:3.500A) Processing helix chain 'P' and resid 465 through 470 Processing helix chain 'P' and resid 500 through 502 No H-bonds generated for 'chain 'P' and resid 500 through 502' Processing helix chain 'P' and resid 503 through 511 Processing helix chain 'P' and resid 512 through 525 Processing helix chain 'P' and resid 529 through 546 Processing helix chain 'P' and resid 561 through 575 Processing helix chain 'P' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA P 600 " --> pdb=" O MET P 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG P 601 " --> pdb=" O ALA P 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 596 through 601' Processing helix chain 'P' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE P 610 " --> pdb=" O SER P 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR P 611 " --> pdb=" O GLY P 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 607 through 611' Processing helix chain 'Q' and resid 45 through 47 No H-bonds generated for 'chain 'Q' and resid 45 through 47' Processing helix chain 'Q' and resid 48 through 53 Processing helix chain 'Q' and resid 64 through 78 Processing helix chain 'Q' and resid 148 through 153 Processing helix chain 'Q' and resid 154 through 170 Processing helix chain 'Q' and resid 171 through 175 removed outlier: 3.636A pdb=" N GLY Q 175 " --> pdb=" O LYS Q 172 " (cutoff:3.500A) Processing helix chain 'Q' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP Q 218 " --> pdb=" O ILE Q 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS Q 219 " --> pdb=" O ARG Q 215 " (cutoff:3.500A) Processing helix chain 'Q' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA Q 231 " --> pdb=" O GLY Q 228 " (cutoff:3.500A) Processing helix chain 'Q' and resid 335 through 351 Processing helix chain 'Q' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU Q 360 " --> pdb=" O TRP Q 356 " (cutoff:3.500A) Processing helix chain 'Q' and resid 365 through 367 No H-bonds generated for 'chain 'Q' and resid 365 through 367' Processing helix chain 'Q' and resid 372 through 375 removed outlier: 3.540A pdb=" N ALA Q 375 " --> pdb=" O ASN Q 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 372 through 375' Processing helix chain 'Q' and resid 376 through 381 Processing helix chain 'Q' and resid 394 through 403 Processing helix chain 'Q' and resid 422 through 427 Processing helix chain 'Q' and resid 427 through 432 removed outlier: 3.500A pdb=" N ALA Q 431 " --> pdb=" O ARG Q 427 " (cutoff:3.500A) Processing helix chain 'Q' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS Q 452 " --> pdb=" O SER Q 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR Q 462 " --> pdb=" O PHE Q 458 " (cutoff:3.500A) Processing helix chain 'Q' and resid 465 through 470 Processing helix chain 'Q' and resid 500 through 502 No H-bonds generated for 'chain 'Q' and resid 500 through 502' Processing helix chain 'Q' and resid 503 through 511 Processing helix chain 'Q' and resid 512 through 525 Processing helix chain 'Q' and resid 529 through 546 Processing helix chain 'Q' and resid 561 through 575 Processing helix chain 'Q' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA Q 600 " --> pdb=" O MET Q 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG Q 601 " --> pdb=" O ALA Q 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 596 through 601' Processing helix chain 'Q' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE Q 610 " --> pdb=" O SER Q 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR Q 611 " --> pdb=" O GLY Q 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 607 through 611' Processing helix chain 'R' and resid 45 through 47 No H-bonds generated for 'chain 'R' and resid 45 through 47' Processing helix chain 'R' and resid 48 through 53 Processing helix chain 'R' and resid 64 through 78 Processing helix chain 'R' and resid 148 through 153 Processing helix chain 'R' and resid 154 through 170 Processing helix chain 'R' and resid 171 through 175 removed outlier: 3.636A pdb=" N GLY R 175 " --> pdb=" O LYS R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP R 218 " --> pdb=" O ILE R 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS R 219 " --> pdb=" O ARG R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA R 231 " --> pdb=" O GLY R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 351 Processing helix chain 'R' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU R 360 " --> pdb=" O TRP R 356 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 367 No H-bonds generated for 'chain 'R' and resid 365 through 367' Processing helix chain 'R' and resid 372 through 375 removed outlier: 3.540A pdb=" N ALA R 375 " --> pdb=" O ASN R 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 372 through 375' Processing helix chain 'R' and resid 376 through 381 Processing helix chain 'R' and resid 394 through 403 Processing helix chain 'R' and resid 422 through 427 Processing helix chain 'R' and resid 427 through 432 removed outlier: 3.500A pdb=" N ALA R 431 " --> pdb=" O ARG R 427 " (cutoff:3.500A) Processing helix chain 'R' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS R 452 " --> pdb=" O SER R 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR R 462 " --> pdb=" O PHE R 458 " (cutoff:3.500A) Processing helix chain 'R' and resid 465 through 470 Processing helix chain 'R' and resid 500 through 502 No H-bonds generated for 'chain 'R' and resid 500 through 502' Processing helix chain 'R' and resid 503 through 511 Processing helix chain 'R' and resid 512 through 525 Processing helix chain 'R' and resid 529 through 546 Processing helix chain 'R' and resid 561 through 575 Processing helix chain 'R' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA R 600 " --> pdb=" O MET R 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG R 601 " --> pdb=" O ALA R 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 596 through 601' Processing helix chain 'R' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE R 610 " --> pdb=" O SER R 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR R 611 " --> pdb=" O GLY R 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 607 through 611' Processing helix chain 'S' and resid 45 through 47 No H-bonds generated for 'chain 'S' and resid 45 through 47' Processing helix chain 'S' and resid 48 through 53 Processing helix chain 'S' and resid 64 through 78 Processing helix chain 'S' and resid 148 through 153 Processing helix chain 'S' and resid 154 through 170 Processing helix chain 'S' and resid 171 through 175 removed outlier: 3.636A pdb=" N GLY S 175 " --> pdb=" O LYS S 172 " (cutoff:3.500A) Processing helix chain 'S' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP S 218 " --> pdb=" O ILE S 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS S 219 " --> pdb=" O ARG S 215 " (cutoff:3.500A) Processing helix chain 'S' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA S 231 " --> pdb=" O GLY S 228 " (cutoff:3.500A) Processing helix chain 'S' and resid 335 through 351 Processing helix chain 'S' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU S 360 " --> pdb=" O TRP S 356 " (cutoff:3.500A) Processing helix chain 'S' and resid 365 through 367 No H-bonds generated for 'chain 'S' and resid 365 through 367' Processing helix chain 'S' and resid 372 through 375 removed outlier: 3.540A pdb=" N ALA S 375 " --> pdb=" O ASN S 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 372 through 375' Processing helix chain 'S' and resid 376 through 381 Processing helix chain 'S' and resid 394 through 403 Processing helix chain 'S' and resid 422 through 427 Processing helix chain 'S' and resid 427 through 432 removed outlier: 3.500A pdb=" N ALA S 431 " --> pdb=" O ARG S 427 " (cutoff:3.500A) Processing helix chain 'S' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS S 452 " --> pdb=" O SER S 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR S 462 " --> pdb=" O PHE S 458 " (cutoff:3.500A) Processing helix chain 'S' and resid 465 through 470 Processing helix chain 'S' and resid 500 through 502 No H-bonds generated for 'chain 'S' and resid 500 through 502' Processing helix chain 'S' and resid 503 through 511 Processing helix chain 'S' and resid 512 through 525 Processing helix chain 'S' and resid 529 through 546 Processing helix chain 'S' and resid 561 through 575 Processing helix chain 'S' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA S 600 " --> pdb=" O MET S 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG S 601 " --> pdb=" O ALA S 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 596 through 601' Processing helix chain 'S' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE S 610 " --> pdb=" O SER S 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR S 611 " --> pdb=" O GLY S 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 607 through 611' Processing helix chain 'T' and resid 45 through 47 No H-bonds generated for 'chain 'T' and resid 45 through 47' Processing helix chain 'T' and resid 48 through 53 Processing helix chain 'T' and resid 64 through 78 Processing helix chain 'T' and resid 148 through 153 Processing helix chain 'T' and resid 154 through 170 Processing helix chain 'T' and resid 171 through 175 removed outlier: 3.636A pdb=" N GLY T 175 " --> pdb=" O LYS T 172 " (cutoff:3.500A) Processing helix chain 'T' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP T 218 " --> pdb=" O ILE T 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS T 219 " --> pdb=" O ARG T 215 " (cutoff:3.500A) Processing helix chain 'T' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA T 231 " --> pdb=" O GLY T 228 " (cutoff:3.500A) Processing helix chain 'T' and resid 335 through 351 Processing helix chain 'T' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU T 360 " --> pdb=" O TRP T 356 " (cutoff:3.500A) Processing helix chain 'T' and resid 365 through 367 No H-bonds generated for 'chain 'T' and resid 365 through 367' Processing helix chain 'T' and resid 372 through 375 removed outlier: 3.540A pdb=" N ALA T 375 " --> pdb=" O ASN T 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 372 through 375' Processing helix chain 'T' and resid 376 through 381 Processing helix chain 'T' and resid 394 through 403 Processing helix chain 'T' and resid 422 through 427 Processing helix chain 'T' and resid 427 through 432 removed outlier: 3.500A pdb=" N ALA T 431 " --> pdb=" O ARG T 427 " (cutoff:3.500A) Processing helix chain 'T' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS T 452 " --> pdb=" O SER T 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR T 462 " --> pdb=" O PHE T 458 " (cutoff:3.500A) Processing helix chain 'T' and resid 465 through 470 Processing helix chain 'T' and resid 500 through 502 No H-bonds generated for 'chain 'T' and resid 500 through 502' Processing helix chain 'T' and resid 503 through 511 Processing helix chain 'T' and resid 512 through 525 Processing helix chain 'T' and resid 529 through 546 Processing helix chain 'T' and resid 561 through 575 Processing helix chain 'T' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA T 600 " --> pdb=" O MET T 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG T 601 " --> pdb=" O ALA T 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 596 through 601' Processing helix chain 'T' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE T 610 " --> pdb=" O SER T 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR T 611 " --> pdb=" O GLY T 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 607 through 611' Processing helix chain 'V' and resid 45 through 47 No H-bonds generated for 'chain 'V' and resid 45 through 47' Processing helix chain 'V' and resid 48 through 53 Processing helix chain 'V' and resid 64 through 78 Processing helix chain 'V' and resid 148 through 153 Processing helix chain 'V' and resid 154 through 170 Processing helix chain 'V' and resid 171 through 175 removed outlier: 3.636A pdb=" N GLY V 175 " --> pdb=" O LYS V 172 " (cutoff:3.500A) Processing helix chain 'V' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP V 218 " --> pdb=" O ILE V 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS V 219 " --> pdb=" O ARG V 215 " (cutoff:3.500A) Processing helix chain 'V' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA V 231 " --> pdb=" O GLY V 228 " (cutoff:3.500A) Processing helix chain 'V' and resid 335 through 351 Processing helix chain 'V' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU V 360 " --> pdb=" O TRP V 356 " (cutoff:3.500A) Processing helix chain 'V' and resid 365 through 367 No H-bonds generated for 'chain 'V' and resid 365 through 367' Processing helix chain 'V' and resid 372 through 375 removed outlier: 3.540A pdb=" N ALA V 375 " --> pdb=" O ASN V 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 372 through 375' Processing helix chain 'V' and resid 376 through 381 Processing helix chain 'V' and resid 394 through 403 Processing helix chain 'V' and resid 422 through 427 Processing helix chain 'V' and resid 427 through 432 removed outlier: 3.500A pdb=" N ALA V 431 " --> pdb=" O ARG V 427 " (cutoff:3.500A) Processing helix chain 'V' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS V 452 " --> pdb=" O SER V 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR V 462 " --> pdb=" O PHE V 458 " (cutoff:3.500A) Processing helix chain 'V' and resid 465 through 470 Processing helix chain 'V' and resid 500 through 502 No H-bonds generated for 'chain 'V' and resid 500 through 502' Processing helix chain 'V' and resid 503 through 511 Processing helix chain 'V' and resid 512 through 525 Processing helix chain 'V' and resid 529 through 546 Processing helix chain 'V' and resid 561 through 575 Processing helix chain 'V' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA V 600 " --> pdb=" O MET V 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG V 601 " --> pdb=" O ALA V 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 596 through 601' Processing helix chain 'V' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE V 610 " --> pdb=" O SER V 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR V 611 " --> pdb=" O GLY V 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 607 through 611' Processing helix chain 'W' and resid 45 through 47 No H-bonds generated for 'chain 'W' and resid 45 through 47' Processing helix chain 'W' and resid 48 through 53 Processing helix chain 'W' and resid 64 through 78 Processing helix chain 'W' and resid 148 through 153 Processing helix chain 'W' and resid 154 through 170 Processing helix chain 'W' and resid 171 through 175 removed outlier: 3.636A pdb=" N GLY W 175 " --> pdb=" O LYS W 172 " (cutoff:3.500A) Processing helix chain 'W' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP W 218 " --> pdb=" O ILE W 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS W 219 " --> pdb=" O ARG W 215 " (cutoff:3.500A) Processing helix chain 'W' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA W 231 " --> pdb=" O GLY W 228 " (cutoff:3.500A) Processing helix chain 'W' and resid 335 through 351 Processing helix chain 'W' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU W 360 " --> pdb=" O TRP W 356 " (cutoff:3.500A) Processing helix chain 'W' and resid 365 through 367 No H-bonds generated for 'chain 'W' and resid 365 through 367' Processing helix chain 'W' and resid 372 through 375 removed outlier: 3.540A pdb=" N ALA W 375 " --> pdb=" O ASN W 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 372 through 375' Processing helix chain 'W' and resid 376 through 381 Processing helix chain 'W' and resid 394 through 403 Processing helix chain 'W' and resid 422 through 427 Processing helix chain 'W' and resid 427 through 432 removed outlier: 3.500A pdb=" N ALA W 431 " --> pdb=" O ARG W 427 " (cutoff:3.500A) Processing helix chain 'W' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS W 452 " --> pdb=" O SER W 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR W 462 " --> pdb=" O PHE W 458 " (cutoff:3.500A) Processing helix chain 'W' and resid 465 through 470 Processing helix chain 'W' and resid 500 through 502 No H-bonds generated for 'chain 'W' and resid 500 through 502' Processing helix chain 'W' and resid 503 through 511 Processing helix chain 'W' and resid 512 through 525 Processing helix chain 'W' and resid 529 through 546 Processing helix chain 'W' and resid 561 through 575 Processing helix chain 'W' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA W 600 " --> pdb=" O MET W 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG W 601 " --> pdb=" O ALA W 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 596 through 601' Processing helix chain 'W' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE W 610 " --> pdb=" O SER W 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR W 611 " --> pdb=" O GLY W 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 607 through 611' Processing helix chain 'X' and resid 45 through 47 No H-bonds generated for 'chain 'X' and resid 45 through 47' Processing helix chain 'X' and resid 48 through 53 Processing helix chain 'X' and resid 64 through 78 Processing helix chain 'X' and resid 148 through 153 Processing helix chain 'X' and resid 154 through 170 Processing helix chain 'X' and resid 171 through 175 removed outlier: 3.636A pdb=" N GLY X 175 " --> pdb=" O LYS X 172 " (cutoff:3.500A) Processing helix chain 'X' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP X 218 " --> pdb=" O ILE X 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS X 219 " --> pdb=" O ARG X 215 " (cutoff:3.500A) Processing helix chain 'X' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA X 231 " --> pdb=" O GLY X 228 " (cutoff:3.500A) Processing helix chain 'X' and resid 335 through 351 Processing helix chain 'X' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU X 360 " --> pdb=" O TRP X 356 " (cutoff:3.500A) Processing helix chain 'X' and resid 365 through 367 No H-bonds generated for 'chain 'X' and resid 365 through 367' Processing helix chain 'X' and resid 372 through 375 removed outlier: 3.540A pdb=" N ALA X 375 " --> pdb=" O ASN X 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 372 through 375' Processing helix chain 'X' and resid 376 through 381 Processing helix chain 'X' and resid 394 through 403 Processing helix chain 'X' and resid 422 through 427 Processing helix chain 'X' and resid 427 through 432 removed outlier: 3.500A pdb=" N ALA X 431 " --> pdb=" O ARG X 427 " (cutoff:3.500A) Processing helix chain 'X' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS X 452 " --> pdb=" O SER X 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR X 462 " --> pdb=" O PHE X 458 " (cutoff:3.500A) Processing helix chain 'X' and resid 465 through 470 Processing helix chain 'X' and resid 500 through 502 No H-bonds generated for 'chain 'X' and resid 500 through 502' Processing helix chain 'X' and resid 503 through 511 Processing helix chain 'X' and resid 512 through 525 Processing helix chain 'X' and resid 529 through 546 Processing helix chain 'X' and resid 561 through 575 Processing helix chain 'X' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA X 600 " --> pdb=" O MET X 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG X 601 " --> pdb=" O ALA X 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 596 through 601' Processing helix chain 'X' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE X 610 " --> pdb=" O SER X 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR X 611 " --> pdb=" O GLY X 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 607 through 611' Processing helix chain 'Y' and resid 45 through 47 No H-bonds generated for 'chain 'Y' and resid 45 through 47' Processing helix chain 'Y' and resid 48 through 53 Processing helix chain 'Y' and resid 64 through 78 Processing helix chain 'Y' and resid 148 through 153 Processing helix chain 'Y' and resid 154 through 170 Processing helix chain 'Y' and resid 171 through 175 removed outlier: 3.636A pdb=" N GLY Y 175 " --> pdb=" O LYS Y 172 " (cutoff:3.500A) Processing helix chain 'Y' and resid 193 through 221 removed outlier: 6.278A pdb=" N ASP Y 218 " --> pdb=" O ILE Y 214 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LYS Y 219 " --> pdb=" O ARG Y 215 " (cutoff:3.500A) Processing helix chain 'Y' and resid 226 through 231 removed outlier: 3.567A pdb=" N ALA Y 231 " --> pdb=" O GLY Y 228 " (cutoff:3.500A) Processing helix chain 'Y' and resid 335 through 351 Processing helix chain 'Y' and resid 356 through 364 removed outlier: 4.319A pdb=" N LEU Y 360 " --> pdb=" O TRP Y 356 " (cutoff:3.500A) Processing helix chain 'Y' and resid 365 through 367 No H-bonds generated for 'chain 'Y' and resid 365 through 367' Processing helix chain 'Y' and resid 372 through 375 removed outlier: 3.540A pdb=" N ALA Y 375 " --> pdb=" O ASN Y 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 372 through 375' Processing helix chain 'Y' and resid 376 through 381 Processing helix chain 'Y' and resid 394 through 403 Processing helix chain 'Y' and resid 422 through 427 Processing helix chain 'Y' and resid 427 through 432 removed outlier: 3.500A pdb=" N ALA Y 431 " --> pdb=" O ARG Y 427 " (cutoff:3.500A) Processing helix chain 'Y' and resid 448 through 462 removed outlier: 3.541A pdb=" N LYS Y 452 " --> pdb=" O SER Y 448 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR Y 462 " --> pdb=" O PHE Y 458 " (cutoff:3.500A) Processing helix chain 'Y' and resid 465 through 470 Processing helix chain 'Y' and resid 500 through 502 No H-bonds generated for 'chain 'Y' and resid 500 through 502' Processing helix chain 'Y' and resid 503 through 511 Processing helix chain 'Y' and resid 512 through 525 Processing helix chain 'Y' and resid 529 through 546 Processing helix chain 'Y' and resid 561 through 575 Processing helix chain 'Y' and resid 596 through 601 removed outlier: 4.346A pdb=" N ALA Y 600 " --> pdb=" O MET Y 596 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG Y 601 " --> pdb=" O ALA Y 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 596 through 601' Processing helix chain 'Y' and resid 607 through 611 removed outlier: 3.857A pdb=" N ILE Y 610 " --> pdb=" O SER Y 607 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR Y 611 " --> pdb=" O GLY Y 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 607 through 611' Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN A 115 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG A 178 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE A 117 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA A 180 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY A 119 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU A 182 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A 121 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 137 Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 498 removed outlier: 7.187A pdb=" N THR A 480 " --> pdb=" O ASP A 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP A 559 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN A 482 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG A 557 " --> pdb=" O ASN A 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS A 488 " --> pdb=" O GLN A 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN A 551 " --> pdb=" O HIS A 488 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE A 412 " --> pdb=" O PHE A 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER A 325 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 14.476A pdb=" N TYR A 327 " --> pdb=" O PRO A 417 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR A 285 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA A 326 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA A 283 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU A 281 " --> pdb=" O PRO A 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN A 278 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE A 268 " --> pdb=" O GLN A 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG A 280 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN A 266 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 282 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN A 234 " --> pdb=" O ARG A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP A 248 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 305 through 306 Processing sheet with id=AA6, first strand: chain 'B' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN B 115 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG B 178 " --> pdb=" O ASN B 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE B 117 " --> pdb=" O ARG B 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA B 180 " --> pdb=" O PHE B 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY B 119 " --> pdb=" O ALA B 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B 182 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B 121 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 134 through 137 Processing sheet with id=AA8, first strand: chain 'B' and resid 496 through 498 removed outlier: 7.187A pdb=" N THR B 480 " --> pdb=" O ASP B 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP B 559 " --> pdb=" O THR B 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN B 482 " --> pdb=" O ARG B 557 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG B 557 " --> pdb=" O ASN B 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS B 488 " --> pdb=" O GLN B 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN B 551 " --> pdb=" O HIS B 488 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE B 412 " --> pdb=" O PHE B 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER B 325 " --> pdb=" O ASP B 415 " (cutoff:3.500A) removed outlier: 14.476A pdb=" N TYR B 327 " --> pdb=" O PRO B 417 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR B 285 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA B 326 " --> pdb=" O ALA B 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA B 283 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU B 281 " --> pdb=" O PRO B 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN B 278 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE B 268 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG B 280 " --> pdb=" O ASN B 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN B 266 " --> pdb=" O ARG B 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 282 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN B 234 " --> pdb=" O ARG B 267 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP B 248 " --> pdb=" O VAL B 256 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 305 through 306 Processing sheet with id=AB2, first strand: chain 'C' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN C 115 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG C 178 " --> pdb=" O ASN C 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE C 117 " --> pdb=" O ARG C 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA C 180 " --> pdb=" O PHE C 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY C 119 " --> pdb=" O ALA C 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU C 182 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL C 121 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 134 through 137 Processing sheet with id=AB4, first strand: chain 'C' and resid 496 through 498 removed outlier: 7.187A pdb=" N THR C 480 " --> pdb=" O ASP C 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP C 559 " --> pdb=" O THR C 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN C 482 " --> pdb=" O ARG C 557 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG C 557 " --> pdb=" O ASN C 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS C 488 " --> pdb=" O GLN C 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN C 551 " --> pdb=" O HIS C 488 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE C 412 " --> pdb=" O PHE C 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER C 325 " --> pdb=" O ASP C 415 " (cutoff:3.500A) removed outlier: 14.476A pdb=" N TYR C 327 " --> pdb=" O PRO C 417 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR C 285 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA C 326 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA C 283 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU C 281 " --> pdb=" O PRO C 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN C 278 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE C 268 " --> pdb=" O GLN C 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG C 280 " --> pdb=" O ASN C 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN C 266 " --> pdb=" O ARG C 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 282 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN C 234 " --> pdb=" O ARG C 267 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP C 248 " --> pdb=" O VAL C 256 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 305 through 306 Processing sheet with id=AB7, first strand: chain 'D' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN D 115 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG D 178 " --> pdb=" O ASN D 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE D 117 " --> pdb=" O ARG D 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA D 180 " --> pdb=" O PHE D 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY D 119 " --> pdb=" O ALA D 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU D 182 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL D 121 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 134 through 137 Processing sheet with id=AB9, first strand: chain 'D' and resid 496 through 498 removed outlier: 7.187A pdb=" N THR D 480 " --> pdb=" O ASP D 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP D 559 " --> pdb=" O THR D 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN D 482 " --> pdb=" O ARG D 557 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG D 557 " --> pdb=" O ASN D 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS D 488 " --> pdb=" O GLN D 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN D 551 " --> pdb=" O HIS D 488 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE D 412 " --> pdb=" O PHE D 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER D 325 " --> pdb=" O ASP D 415 " (cutoff:3.500A) removed outlier: 14.476A pdb=" N TYR D 327 " --> pdb=" O PRO D 417 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR D 285 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA D 326 " --> pdb=" O ALA D 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA D 283 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU D 281 " --> pdb=" O PRO D 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN D 278 " --> pdb=" O ILE D 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE D 268 " --> pdb=" O GLN D 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG D 280 " --> pdb=" O ASN D 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN D 266 " --> pdb=" O ARG D 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL D 282 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN D 234 " --> pdb=" O ARG D 267 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP D 248 " --> pdb=" O VAL D 256 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 305 through 306 Processing sheet with id=AC3, first strand: chain 'E' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN E 115 " --> pdb=" O THR E 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG E 178 " --> pdb=" O ASN E 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE E 117 " --> pdb=" O ARG E 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA E 180 " --> pdb=" O PHE E 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY E 119 " --> pdb=" O ALA E 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU E 182 " --> pdb=" O GLY E 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL E 121 " --> pdb=" O LEU E 182 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 134 through 137 Processing sheet with id=AC5, first strand: chain 'E' and resid 496 through 498 removed outlier: 7.187A pdb=" N THR E 480 " --> pdb=" O ASP E 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP E 559 " --> pdb=" O THR E 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN E 482 " --> pdb=" O ARG E 557 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG E 557 " --> pdb=" O ASN E 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS E 488 " --> pdb=" O GLN E 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN E 551 " --> pdb=" O HIS E 488 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE E 412 " --> pdb=" O PHE E 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER E 325 " --> pdb=" O ASP E 415 " (cutoff:3.500A) removed outlier: 14.476A pdb=" N TYR E 327 " --> pdb=" O PRO E 417 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR E 285 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA E 326 " --> pdb=" O ALA E 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA E 283 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU E 281 " --> pdb=" O PRO E 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN E 278 " --> pdb=" O ILE E 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE E 268 " --> pdb=" O GLN E 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG E 280 " --> pdb=" O ASN E 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN E 266 " --> pdb=" O ARG E 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL E 282 " --> pdb=" O ILE E 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN E 234 " --> pdb=" O ARG E 267 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP E 248 " --> pdb=" O VAL E 256 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 305 through 306 Processing sheet with id=AC8, first strand: chain 'F' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN F 115 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG F 178 " --> pdb=" O ASN F 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE F 117 " --> pdb=" O ARG F 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA F 180 " --> pdb=" O PHE F 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY F 119 " --> pdb=" O ALA F 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU F 182 " --> pdb=" O GLY F 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL F 121 " --> pdb=" O LEU F 182 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 134 through 137 Processing sheet with id=AD1, first strand: chain 'F' and resid 496 through 498 removed outlier: 7.187A pdb=" N THR F 480 " --> pdb=" O ASP F 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP F 559 " --> pdb=" O THR F 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN F 482 " --> pdb=" O ARG F 557 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG F 557 " --> pdb=" O ASN F 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS F 488 " --> pdb=" O GLN F 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN F 551 " --> pdb=" O HIS F 488 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE F 412 " --> pdb=" O PHE F 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER F 325 " --> pdb=" O ASP F 415 " (cutoff:3.500A) removed outlier: 14.476A pdb=" N TYR F 327 " --> pdb=" O PRO F 417 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR F 285 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA F 326 " --> pdb=" O ALA F 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA F 283 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU F 281 " --> pdb=" O PRO F 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN F 278 " --> pdb=" O ILE F 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE F 268 " --> pdb=" O GLN F 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG F 280 " --> pdb=" O ASN F 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN F 266 " --> pdb=" O ARG F 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL F 282 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN F 234 " --> pdb=" O ARG F 267 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP F 248 " --> pdb=" O VAL F 256 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 305 through 306 Processing sheet with id=AD4, first strand: chain 'G' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN G 115 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG G 178 " --> pdb=" O ASN G 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE G 117 " --> pdb=" O ARG G 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA G 180 " --> pdb=" O PHE G 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY G 119 " --> pdb=" O ALA G 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU G 182 " --> pdb=" O GLY G 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL G 121 " --> pdb=" O LEU G 182 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 134 through 137 Processing sheet with id=AD6, first strand: chain 'G' and resid 496 through 498 removed outlier: 7.187A pdb=" N THR G 480 " --> pdb=" O ASP G 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP G 559 " --> pdb=" O THR G 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN G 482 " --> pdb=" O ARG G 557 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG G 557 " --> pdb=" O ASN G 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS G 488 " --> pdb=" O GLN G 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN G 551 " --> pdb=" O HIS G 488 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE G 412 " --> pdb=" O PHE G 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER G 325 " --> pdb=" O ASP G 415 " (cutoff:3.500A) removed outlier: 14.476A pdb=" N TYR G 327 " --> pdb=" O PRO G 417 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR G 285 " --> pdb=" O THR G 324 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA G 326 " --> pdb=" O ALA G 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA G 283 " --> pdb=" O ALA G 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU G 281 " --> pdb=" O PRO G 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN G 278 " --> pdb=" O ILE G 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE G 268 " --> pdb=" O GLN G 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG G 280 " --> pdb=" O ASN G 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN G 266 " --> pdb=" O ARG G 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL G 282 " --> pdb=" O ILE G 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN G 234 " --> pdb=" O ARG G 267 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP G 248 " --> pdb=" O VAL G 256 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 305 through 306 Processing sheet with id=AD9, first strand: chain 'H' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN H 115 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG H 178 " --> pdb=" O ASN H 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE H 117 " --> pdb=" O ARG H 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA H 180 " --> pdb=" O PHE H 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY H 119 " --> pdb=" O ALA H 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU H 182 " --> pdb=" O GLY H 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL H 121 " --> pdb=" O LEU H 182 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 134 through 137 Processing sheet with id=AE2, first strand: chain 'H' and resid 496 through 498 removed outlier: 7.187A pdb=" N THR H 480 " --> pdb=" O ASP H 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP H 559 " --> pdb=" O THR H 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN H 482 " --> pdb=" O ARG H 557 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG H 557 " --> pdb=" O ASN H 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS H 488 " --> pdb=" O GLN H 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN H 551 " --> pdb=" O HIS H 488 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE H 412 " --> pdb=" O PHE H 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER H 325 " --> pdb=" O ASP H 415 " (cutoff:3.500A) removed outlier: 14.476A pdb=" N TYR H 327 " --> pdb=" O PRO H 417 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR H 285 " --> pdb=" O THR H 324 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA H 326 " --> pdb=" O ALA H 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA H 283 " --> pdb=" O ALA H 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU H 281 " --> pdb=" O PRO H 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN H 278 " --> pdb=" O ILE H 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE H 268 " --> pdb=" O GLN H 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG H 280 " --> pdb=" O ASN H 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN H 266 " --> pdb=" O ARG H 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL H 282 " --> pdb=" O ILE H 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN H 234 " --> pdb=" O ARG H 267 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP H 248 " --> pdb=" O VAL H 256 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 305 through 306 Processing sheet with id=AE5, first strand: chain 'I' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN I 115 " --> pdb=" O THR I 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG I 178 " --> pdb=" O ASN I 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE I 117 " --> pdb=" O ARG I 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA I 180 " --> pdb=" O PHE I 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY I 119 " --> pdb=" O ALA I 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU I 182 " --> pdb=" O GLY I 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL I 121 " --> pdb=" O LEU I 182 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 134 through 137 Processing sheet with id=AE7, first strand: chain 'I' and resid 496 through 498 removed outlier: 7.187A pdb=" N THR I 480 " --> pdb=" O ASP I 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP I 559 " --> pdb=" O THR I 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN I 482 " --> pdb=" O ARG I 557 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG I 557 " --> pdb=" O ASN I 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS I 488 " --> pdb=" O GLN I 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN I 551 " --> pdb=" O HIS I 488 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE I 412 " --> pdb=" O PHE I 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER I 325 " --> pdb=" O ASP I 415 " (cutoff:3.500A) removed outlier: 14.476A pdb=" N TYR I 327 " --> pdb=" O PRO I 417 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR I 285 " --> pdb=" O THR I 324 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA I 326 " --> pdb=" O ALA I 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA I 283 " --> pdb=" O ALA I 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU I 281 " --> pdb=" O PRO I 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN I 278 " --> pdb=" O ILE I 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE I 268 " --> pdb=" O GLN I 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG I 280 " --> pdb=" O ASN I 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN I 266 " --> pdb=" O ARG I 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL I 282 " --> pdb=" O ILE I 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN I 234 " --> pdb=" O ARG I 267 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP I 248 " --> pdb=" O VAL I 256 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 305 through 306 Processing sheet with id=AF1, first strand: chain 'J' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN J 115 " --> pdb=" O THR J 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG J 178 " --> pdb=" O ASN J 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE J 117 " --> pdb=" O ARG J 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA J 180 " --> pdb=" O PHE J 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY J 119 " --> pdb=" O ALA J 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU J 182 " --> pdb=" O GLY J 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL J 121 " --> pdb=" O LEU J 182 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 134 through 137 Processing sheet with id=AF3, first strand: chain 'J' and resid 496 through 498 removed outlier: 7.187A pdb=" N THR J 480 " --> pdb=" O ASP J 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP J 559 " --> pdb=" O THR J 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN J 482 " --> pdb=" O ARG J 557 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG J 557 " --> pdb=" O ASN J 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS J 488 " --> pdb=" O GLN J 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN J 551 " --> pdb=" O HIS J 488 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE J 412 " --> pdb=" O PHE J 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER J 325 " --> pdb=" O ASP J 415 " (cutoff:3.500A) removed outlier: 14.476A pdb=" N TYR J 327 " --> pdb=" O PRO J 417 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR J 285 " --> pdb=" O THR J 324 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA J 326 " --> pdb=" O ALA J 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA J 283 " --> pdb=" O ALA J 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU J 281 " --> pdb=" O PRO J 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN J 278 " --> pdb=" O ILE J 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE J 268 " --> pdb=" O GLN J 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG J 280 " --> pdb=" O ASN J 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN J 266 " --> pdb=" O ARG J 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL J 282 " --> pdb=" O ILE J 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN J 234 " --> pdb=" O ARG J 267 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP J 248 " --> pdb=" O VAL J 256 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 305 through 306 Processing sheet with id=AF6, first strand: chain 'K' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN K 115 " --> pdb=" O THR K 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG K 178 " --> pdb=" O ASN K 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE K 117 " --> pdb=" O ARG K 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA K 180 " --> pdb=" O PHE K 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY K 119 " --> pdb=" O ALA K 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU K 182 " --> pdb=" O GLY K 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL K 121 " --> pdb=" O LEU K 182 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 134 through 137 Processing sheet with id=AF8, first strand: chain 'K' and resid 496 through 498 removed outlier: 7.187A pdb=" N THR K 480 " --> pdb=" O ASP K 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP K 559 " --> pdb=" O THR K 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN K 482 " --> pdb=" O ARG K 557 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG K 557 " --> pdb=" O ASN K 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS K 488 " --> pdb=" O GLN K 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN K 551 " --> pdb=" O HIS K 488 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE K 412 " --> pdb=" O PHE K 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER K 325 " --> pdb=" O ASP K 415 " (cutoff:3.500A) removed outlier: 14.476A pdb=" N TYR K 327 " --> pdb=" O PRO K 417 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR K 285 " --> pdb=" O THR K 324 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA K 326 " --> pdb=" O ALA K 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA K 283 " --> pdb=" O ALA K 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU K 281 " --> pdb=" O PRO K 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN K 278 " --> pdb=" O ILE K 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE K 268 " --> pdb=" O GLN K 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG K 280 " --> pdb=" O ASN K 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN K 266 " --> pdb=" O ARG K 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL K 282 " --> pdb=" O ILE K 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN K 234 " --> pdb=" O ARG K 267 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP K 248 " --> pdb=" O VAL K 256 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 305 through 306 Processing sheet with id=AG2, first strand: chain 'L' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN L 115 " --> pdb=" O THR L 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG L 178 " --> pdb=" O ASN L 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE L 117 " --> pdb=" O ARG L 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA L 180 " --> pdb=" O PHE L 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY L 119 " --> pdb=" O ALA L 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU L 182 " --> pdb=" O GLY L 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL L 121 " --> pdb=" O LEU L 182 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 134 through 137 Processing sheet with id=AG4, first strand: chain 'L' and resid 496 through 498 removed outlier: 7.187A pdb=" N THR L 480 " --> pdb=" O ASP L 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP L 559 " --> pdb=" O THR L 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN L 482 " --> pdb=" O ARG L 557 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG L 557 " --> pdb=" O ASN L 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS L 488 " --> pdb=" O GLN L 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN L 551 " --> pdb=" O HIS L 488 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE L 412 " --> pdb=" O PHE L 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER L 325 " --> pdb=" O ASP L 415 " (cutoff:3.500A) removed outlier: 14.476A pdb=" N TYR L 327 " --> pdb=" O PRO L 417 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR L 285 " --> pdb=" O THR L 324 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA L 326 " --> pdb=" O ALA L 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA L 283 " --> pdb=" O ALA L 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU L 281 " --> pdb=" O PRO L 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN L 278 " --> pdb=" O ILE L 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE L 268 " --> pdb=" O GLN L 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG L 280 " --> pdb=" O ASN L 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN L 266 " --> pdb=" O ARG L 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL L 282 " --> pdb=" O ILE L 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN L 234 " --> pdb=" O ARG L 267 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP L 248 " --> pdb=" O VAL L 256 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 305 through 306 Processing sheet with id=AG7, first strand: chain 'M' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN M 115 " --> pdb=" O THR M 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG M 178 " --> pdb=" O ASN M 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE M 117 " --> pdb=" O ARG M 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA M 180 " --> pdb=" O PHE M 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY M 119 " --> pdb=" O ALA M 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU M 182 " --> pdb=" O GLY M 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL M 121 " --> pdb=" O LEU M 182 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 134 through 137 Processing sheet with id=AG9, first strand: chain 'M' and resid 496 through 498 removed outlier: 7.187A pdb=" N THR M 480 " --> pdb=" O ASP M 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP M 559 " --> pdb=" O THR M 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN M 482 " --> pdb=" O ARG M 557 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG M 557 " --> pdb=" O ASN M 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS M 488 " --> pdb=" O GLN M 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN M 551 " --> pdb=" O HIS M 488 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE M 412 " --> pdb=" O PHE M 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER M 325 " --> pdb=" O ASP M 415 " (cutoff:3.500A) removed outlier: 14.476A pdb=" N TYR M 327 " --> pdb=" O PRO M 417 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR M 285 " --> pdb=" O THR M 324 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA M 326 " --> pdb=" O ALA M 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA M 283 " --> pdb=" O ALA M 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU M 281 " --> pdb=" O PRO M 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN M 278 " --> pdb=" O ILE M 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE M 268 " --> pdb=" O GLN M 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG M 280 " --> pdb=" O ASN M 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN M 266 " --> pdb=" O ARG M 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL M 282 " --> pdb=" O ILE M 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN M 234 " --> pdb=" O ARG M 267 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'M' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP M 248 " --> pdb=" O VAL M 256 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'M' and resid 305 through 306 Processing sheet with id=AH3, first strand: chain 'N' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN N 115 " --> pdb=" O THR N 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG N 178 " --> pdb=" O ASN N 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE N 117 " --> pdb=" O ARG N 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA N 180 " --> pdb=" O PHE N 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY N 119 " --> pdb=" O ALA N 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU N 182 " --> pdb=" O GLY N 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL N 121 " --> pdb=" O LEU N 182 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 134 through 137 Processing sheet with id=AH5, first strand: chain 'N' and resid 496 through 498 removed outlier: 7.187A pdb=" N THR N 480 " --> pdb=" O ASP N 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP N 559 " --> pdb=" O THR N 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN N 482 " --> pdb=" O ARG N 557 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG N 557 " --> pdb=" O ASN N 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS N 488 " --> pdb=" O GLN N 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN N 551 " --> pdb=" O HIS N 488 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE N 412 " --> pdb=" O PHE N 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER N 325 " --> pdb=" O ASP N 415 " (cutoff:3.500A) removed outlier: 14.476A pdb=" N TYR N 327 " --> pdb=" O PRO N 417 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR N 285 " --> pdb=" O THR N 324 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA N 326 " --> pdb=" O ALA N 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA N 283 " --> pdb=" O ALA N 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU N 281 " --> pdb=" O PRO N 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN N 278 " --> pdb=" O ILE N 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE N 268 " --> pdb=" O GLN N 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG N 280 " --> pdb=" O ASN N 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN N 266 " --> pdb=" O ARG N 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL N 282 " --> pdb=" O ILE N 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN N 234 " --> pdb=" O ARG N 267 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'N' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP N 248 " --> pdb=" O VAL N 256 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'N' and resid 305 through 306 Processing sheet with id=AH8, first strand: chain 'O' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN O 115 " --> pdb=" O THR O 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG O 178 " --> pdb=" O ASN O 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE O 117 " --> pdb=" O ARG O 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA O 180 " --> pdb=" O PHE O 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY O 119 " --> pdb=" O ALA O 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU O 182 " --> pdb=" O GLY O 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL O 121 " --> pdb=" O LEU O 182 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'O' and resid 134 through 137 Processing sheet with id=AI1, first strand: chain 'O' and resid 496 through 498 removed outlier: 7.187A pdb=" N THR O 480 " --> pdb=" O ASP O 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP O 559 " --> pdb=" O THR O 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN O 482 " --> pdb=" O ARG O 557 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG O 557 " --> pdb=" O ASN O 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS O 488 " --> pdb=" O GLN O 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN O 551 " --> pdb=" O HIS O 488 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE O 412 " --> pdb=" O PHE O 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER O 325 " --> pdb=" O ASP O 415 " (cutoff:3.500A) removed outlier: 14.476A pdb=" N TYR O 327 " --> pdb=" O PRO O 417 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR O 285 " --> pdb=" O THR O 324 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA O 326 " --> pdb=" O ALA O 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA O 283 " --> pdb=" O ALA O 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU O 281 " --> pdb=" O PRO O 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN O 278 " --> pdb=" O ILE O 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE O 268 " --> pdb=" O GLN O 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG O 280 " --> pdb=" O ASN O 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN O 266 " --> pdb=" O ARG O 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL O 282 " --> pdb=" O ILE O 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN O 234 " --> pdb=" O ARG O 267 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'O' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP O 248 " --> pdb=" O VAL O 256 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'O' and resid 305 through 306 Processing sheet with id=AI4, first strand: chain 'P' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN P 115 " --> pdb=" O THR P 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG P 178 " --> pdb=" O ASN P 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE P 117 " --> pdb=" O ARG P 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA P 180 " --> pdb=" O PHE P 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY P 119 " --> pdb=" O ALA P 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU P 182 " --> pdb=" O GLY P 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL P 121 " --> pdb=" O LEU P 182 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'P' and resid 134 through 137 Processing sheet with id=AI6, first strand: chain 'P' and resid 496 through 498 removed outlier: 7.187A pdb=" N THR P 480 " --> pdb=" O ASP P 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP P 559 " --> pdb=" O THR P 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN P 482 " --> pdb=" O ARG P 557 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG P 557 " --> pdb=" O ASN P 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS P 488 " --> pdb=" O GLN P 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN P 551 " --> pdb=" O HIS P 488 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE P 412 " --> pdb=" O PHE P 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER P 325 " --> pdb=" O ASP P 415 " (cutoff:3.500A) removed outlier: 14.476A pdb=" N TYR P 327 " --> pdb=" O PRO P 417 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR P 285 " --> pdb=" O THR P 324 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA P 326 " --> pdb=" O ALA P 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA P 283 " --> pdb=" O ALA P 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU P 281 " --> pdb=" O PRO P 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN P 278 " --> pdb=" O ILE P 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE P 268 " --> pdb=" O GLN P 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG P 280 " --> pdb=" O ASN P 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN P 266 " --> pdb=" O ARG P 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL P 282 " --> pdb=" O ILE P 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN P 234 " --> pdb=" O ARG P 267 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'P' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP P 248 " --> pdb=" O VAL P 256 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'P' and resid 305 through 306 Processing sheet with id=AI9, first strand: chain 'Q' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN Q 115 " --> pdb=" O THR Q 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG Q 178 " --> pdb=" O ASN Q 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE Q 117 " --> pdb=" O ARG Q 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA Q 180 " --> pdb=" O PHE Q 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY Q 119 " --> pdb=" O ALA Q 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU Q 182 " --> pdb=" O GLY Q 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL Q 121 " --> pdb=" O LEU Q 182 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'Q' and resid 134 through 137 Processing sheet with id=AJ2, first strand: chain 'Q' and resid 496 through 498 removed outlier: 7.187A pdb=" N THR Q 480 " --> pdb=" O ASP Q 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP Q 559 " --> pdb=" O THR Q 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN Q 482 " --> pdb=" O ARG Q 557 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG Q 557 " --> pdb=" O ASN Q 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS Q 488 " --> pdb=" O GLN Q 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN Q 551 " --> pdb=" O HIS Q 488 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE Q 412 " --> pdb=" O PHE Q 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER Q 325 " --> pdb=" O ASP Q 415 " (cutoff:3.500A) removed outlier: 14.476A pdb=" N TYR Q 327 " --> pdb=" O PRO Q 417 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR Q 285 " --> pdb=" O THR Q 324 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA Q 326 " --> pdb=" O ALA Q 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA Q 283 " --> pdb=" O ALA Q 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU Q 281 " --> pdb=" O PRO Q 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN Q 278 " --> pdb=" O ILE Q 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE Q 268 " --> pdb=" O GLN Q 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG Q 280 " --> pdb=" O ASN Q 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN Q 266 " --> pdb=" O ARG Q 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL Q 282 " --> pdb=" O ILE Q 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN Q 234 " --> pdb=" O ARG Q 267 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'Q' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP Q 248 " --> pdb=" O VAL Q 256 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'Q' and resid 305 through 306 Processing sheet with id=AJ5, first strand: chain 'R' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN R 115 " --> pdb=" O THR R 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG R 178 " --> pdb=" O ASN R 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE R 117 " --> pdb=" O ARG R 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA R 180 " --> pdb=" O PHE R 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY R 119 " --> pdb=" O ALA R 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU R 182 " --> pdb=" O GLY R 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL R 121 " --> pdb=" O LEU R 182 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'R' and resid 134 through 137 Processing sheet with id=AJ7, first strand: chain 'R' and resid 496 through 498 removed outlier: 7.187A pdb=" N THR R 480 " --> pdb=" O ASP R 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP R 559 " --> pdb=" O THR R 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN R 482 " --> pdb=" O ARG R 557 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG R 557 " --> pdb=" O ASN R 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS R 488 " --> pdb=" O GLN R 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN R 551 " --> pdb=" O HIS R 488 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE R 412 " --> pdb=" O PHE R 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER R 325 " --> pdb=" O ASP R 415 " (cutoff:3.500A) removed outlier: 14.476A pdb=" N TYR R 327 " --> pdb=" O PRO R 417 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR R 285 " --> pdb=" O THR R 324 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA R 326 " --> pdb=" O ALA R 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA R 283 " --> pdb=" O ALA R 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU R 281 " --> pdb=" O PRO R 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN R 278 " --> pdb=" O ILE R 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE R 268 " --> pdb=" O GLN R 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG R 280 " --> pdb=" O ASN R 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN R 266 " --> pdb=" O ARG R 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL R 282 " --> pdb=" O ILE R 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN R 234 " --> pdb=" O ARG R 267 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'R' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP R 248 " --> pdb=" O VAL R 256 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'R' and resid 305 through 306 Processing sheet with id=AK1, first strand: chain 'S' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN S 115 " --> pdb=" O THR S 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG S 178 " --> pdb=" O ASN S 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE S 117 " --> pdb=" O ARG S 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA S 180 " --> pdb=" O PHE S 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY S 119 " --> pdb=" O ALA S 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU S 182 " --> pdb=" O GLY S 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL S 121 " --> pdb=" O LEU S 182 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'S' and resid 134 through 137 Processing sheet with id=AK3, first strand: chain 'S' and resid 496 through 498 removed outlier: 7.187A pdb=" N THR S 480 " --> pdb=" O ASP S 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP S 559 " --> pdb=" O THR S 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN S 482 " --> pdb=" O ARG S 557 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG S 557 " --> pdb=" O ASN S 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS S 488 " --> pdb=" O GLN S 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN S 551 " --> pdb=" O HIS S 488 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE S 412 " --> pdb=" O PHE S 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER S 325 " --> pdb=" O ASP S 415 " (cutoff:3.500A) removed outlier: 14.476A pdb=" N TYR S 327 " --> pdb=" O PRO S 417 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR S 285 " --> pdb=" O THR S 324 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA S 326 " --> pdb=" O ALA S 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA S 283 " --> pdb=" O ALA S 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU S 281 " --> pdb=" O PRO S 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN S 278 " --> pdb=" O ILE S 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE S 268 " --> pdb=" O GLN S 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG S 280 " --> pdb=" O ASN S 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN S 266 " --> pdb=" O ARG S 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL S 282 " --> pdb=" O ILE S 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN S 234 " --> pdb=" O ARG S 267 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'S' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP S 248 " --> pdb=" O VAL S 256 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'S' and resid 305 through 306 Processing sheet with id=AK6, first strand: chain 'T' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN T 115 " --> pdb=" O THR T 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG T 178 " --> pdb=" O ASN T 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE T 117 " --> pdb=" O ARG T 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA T 180 " --> pdb=" O PHE T 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY T 119 " --> pdb=" O ALA T 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU T 182 " --> pdb=" O GLY T 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL T 121 " --> pdb=" O LEU T 182 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'T' and resid 134 through 137 Processing sheet with id=AK8, first strand: chain 'T' and resid 496 through 498 removed outlier: 7.187A pdb=" N THR T 480 " --> pdb=" O ASP T 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP T 559 " --> pdb=" O THR T 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN T 482 " --> pdb=" O ARG T 557 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG T 557 " --> pdb=" O ASN T 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS T 488 " --> pdb=" O GLN T 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN T 551 " --> pdb=" O HIS T 488 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE T 412 " --> pdb=" O PHE T 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER T 325 " --> pdb=" O ASP T 415 " (cutoff:3.500A) removed outlier: 14.476A pdb=" N TYR T 327 " --> pdb=" O PRO T 417 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR T 285 " --> pdb=" O THR T 324 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA T 326 " --> pdb=" O ALA T 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA T 283 " --> pdb=" O ALA T 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU T 281 " --> pdb=" O PRO T 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN T 278 " --> pdb=" O ILE T 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE T 268 " --> pdb=" O GLN T 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG T 280 " --> pdb=" O ASN T 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN T 266 " --> pdb=" O ARG T 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL T 282 " --> pdb=" O ILE T 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN T 234 " --> pdb=" O ARG T 267 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'T' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP T 248 " --> pdb=" O VAL T 256 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'T' and resid 305 through 306 Processing sheet with id=AL2, first strand: chain 'V' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN V 115 " --> pdb=" O THR V 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG V 178 " --> pdb=" O ASN V 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE V 117 " --> pdb=" O ARG V 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA V 180 " --> pdb=" O PHE V 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY V 119 " --> pdb=" O ALA V 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU V 182 " --> pdb=" O GLY V 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL V 121 " --> pdb=" O LEU V 182 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'V' and resid 134 through 137 Processing sheet with id=AL4, first strand: chain 'V' and resid 496 through 498 removed outlier: 7.187A pdb=" N THR V 480 " --> pdb=" O ASP V 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP V 559 " --> pdb=" O THR V 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN V 482 " --> pdb=" O ARG V 557 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG V 557 " --> pdb=" O ASN V 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS V 488 " --> pdb=" O GLN V 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN V 551 " --> pdb=" O HIS V 488 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE V 412 " --> pdb=" O PHE V 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER V 325 " --> pdb=" O ASP V 415 " (cutoff:3.500A) removed outlier: 14.476A pdb=" N TYR V 327 " --> pdb=" O PRO V 417 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR V 285 " --> pdb=" O THR V 324 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA V 326 " --> pdb=" O ALA V 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA V 283 " --> pdb=" O ALA V 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU V 281 " --> pdb=" O PRO V 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN V 278 " --> pdb=" O ILE V 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE V 268 " --> pdb=" O GLN V 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG V 280 " --> pdb=" O ASN V 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN V 266 " --> pdb=" O ARG V 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL V 282 " --> pdb=" O ILE V 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN V 234 " --> pdb=" O ARG V 267 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'V' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP V 248 " --> pdb=" O VAL V 256 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'V' and resid 305 through 306 Processing sheet with id=AL7, first strand: chain 'W' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN W 115 " --> pdb=" O THR W 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG W 178 " --> pdb=" O ASN W 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE W 117 " --> pdb=" O ARG W 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA W 180 " --> pdb=" O PHE W 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY W 119 " --> pdb=" O ALA W 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU W 182 " --> pdb=" O GLY W 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL W 121 " --> pdb=" O LEU W 182 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'W' and resid 134 through 137 Processing sheet with id=AL9, first strand: chain 'W' and resid 496 through 498 removed outlier: 7.187A pdb=" N THR W 480 " --> pdb=" O ASP W 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP W 559 " --> pdb=" O THR W 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN W 482 " --> pdb=" O ARG W 557 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG W 557 " --> pdb=" O ASN W 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS W 488 " --> pdb=" O GLN W 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN W 551 " --> pdb=" O HIS W 488 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE W 412 " --> pdb=" O PHE W 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER W 325 " --> pdb=" O ASP W 415 " (cutoff:3.500A) removed outlier: 14.476A pdb=" N TYR W 327 " --> pdb=" O PRO W 417 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR W 285 " --> pdb=" O THR W 324 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA W 326 " --> pdb=" O ALA W 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA W 283 " --> pdb=" O ALA W 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU W 281 " --> pdb=" O PRO W 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN W 278 " --> pdb=" O ILE W 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE W 268 " --> pdb=" O GLN W 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG W 280 " --> pdb=" O ASN W 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN W 266 " --> pdb=" O ARG W 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL W 282 " --> pdb=" O ILE W 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN W 234 " --> pdb=" O ARG W 267 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'W' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP W 248 " --> pdb=" O VAL W 256 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'W' and resid 305 through 306 Processing sheet with id=AM3, first strand: chain 'X' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN X 115 " --> pdb=" O THR X 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG X 178 " --> pdb=" O ASN X 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE X 117 " --> pdb=" O ARG X 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA X 180 " --> pdb=" O PHE X 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY X 119 " --> pdb=" O ALA X 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU X 182 " --> pdb=" O GLY X 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL X 121 " --> pdb=" O LEU X 182 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'X' and resid 134 through 137 Processing sheet with id=AM5, first strand: chain 'X' and resid 496 through 498 removed outlier: 7.187A pdb=" N THR X 480 " --> pdb=" O ASP X 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP X 559 " --> pdb=" O THR X 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN X 482 " --> pdb=" O ARG X 557 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG X 557 " --> pdb=" O ASN X 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS X 488 " --> pdb=" O GLN X 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN X 551 " --> pdb=" O HIS X 488 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE X 412 " --> pdb=" O PHE X 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER X 325 " --> pdb=" O ASP X 415 " (cutoff:3.500A) removed outlier: 14.476A pdb=" N TYR X 327 " --> pdb=" O PRO X 417 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR X 285 " --> pdb=" O THR X 324 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA X 326 " --> pdb=" O ALA X 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA X 283 " --> pdb=" O ALA X 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU X 281 " --> pdb=" O PRO X 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN X 278 " --> pdb=" O ILE X 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE X 268 " --> pdb=" O GLN X 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG X 280 " --> pdb=" O ASN X 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN X 266 " --> pdb=" O ARG X 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL X 282 " --> pdb=" O ILE X 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN X 234 " --> pdb=" O ARG X 267 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'X' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP X 248 " --> pdb=" O VAL X 256 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'X' and resid 305 through 306 Processing sheet with id=AM8, first strand: chain 'Y' and resid 87 through 91 removed outlier: 6.948A pdb=" N ASN Y 115 " --> pdb=" O THR Y 176 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ARG Y 178 " --> pdb=" O ASN Y 115 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE Y 117 " --> pdb=" O ARG Y 178 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA Y 180 " --> pdb=" O PHE Y 117 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY Y 119 " --> pdb=" O ALA Y 180 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU Y 182 " --> pdb=" O GLY Y 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL Y 121 " --> pdb=" O LEU Y 182 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'Y' and resid 134 through 137 Processing sheet with id=AN1, first strand: chain 'Y' and resid 496 through 498 removed outlier: 7.187A pdb=" N THR Y 480 " --> pdb=" O ASP Y 559 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASP Y 559 " --> pdb=" O THR Y 480 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN Y 482 " --> pdb=" O ARG Y 557 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG Y 557 " --> pdb=" O ASN Y 482 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N HIS Y 488 " --> pdb=" O GLN Y 551 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN Y 551 " --> pdb=" O HIS Y 488 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ILE Y 412 " --> pdb=" O PHE Y 560 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER Y 325 " --> pdb=" O ASP Y 415 " (cutoff:3.500A) removed outlier: 14.476A pdb=" N TYR Y 327 " --> pdb=" O PRO Y 417 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR Y 285 " --> pdb=" O THR Y 324 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA Y 326 " --> pdb=" O ALA Y 283 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA Y 283 " --> pdb=" O ALA Y 326 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU Y 281 " --> pdb=" O PRO Y 328 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN Y 278 " --> pdb=" O ILE Y 268 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE Y 268 " --> pdb=" O GLN Y 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG Y 280 " --> pdb=" O ASN Y 266 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN Y 266 " --> pdb=" O ARG Y 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL Y 282 " --> pdb=" O ILE Y 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN Y 234 " --> pdb=" O ARG Y 267 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'Y' and resid 248 through 249 removed outlier: 3.516A pdb=" N ASP Y 248 " --> pdb=" O VAL Y 256 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'Y' and resid 305 through 306 4608 hydrogen bonds defined for protein. 12888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 47.12 Time building geometry restraints manager: 33.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 35520 1.34 - 1.45: 14880 1.45 - 1.57: 58056 1.57 - 1.69: 0 1.69 - 1.81: 984 Bond restraints: 109440 Sorted by residual: bond pdb=" N VAL F 66 " pdb=" CA VAL F 66 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.55e+00 bond pdb=" N VAL J 66 " pdb=" CA VAL J 66 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.55e+00 bond pdb=" N VAL R 66 " pdb=" CA VAL R 66 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.55e+00 bond pdb=" N VAL V 66 " pdb=" CA VAL V 66 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.55e+00 bond pdb=" N VAL C 66 " pdb=" CA VAL C 66 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.55e+00 ... (remaining 109435 not shown) Histogram of bond angle deviations from ideal: 99.55 - 106.48: 3336 106.48 - 113.41: 59160 113.41 - 120.34: 41376 120.34 - 127.28: 43848 127.28 - 134.21: 1248 Bond angle restraints: 148968 Sorted by residual: angle pdb=" N THR N 437 " pdb=" CA THR N 437 " pdb=" C THR N 437 " ideal model delta sigma weight residual 110.20 104.01 6.19 1.58e+00 4.01e-01 1.54e+01 angle pdb=" N THR B 437 " pdb=" CA THR B 437 " pdb=" C THR B 437 " ideal model delta sigma weight residual 110.20 104.01 6.19 1.58e+00 4.01e-01 1.54e+01 angle pdb=" N THR G 437 " pdb=" CA THR G 437 " pdb=" C THR G 437 " ideal model delta sigma weight residual 110.20 104.01 6.19 1.58e+00 4.01e-01 1.54e+01 angle pdb=" N THR P 437 " pdb=" CA THR P 437 " pdb=" C THR P 437 " ideal model delta sigma weight residual 110.20 104.01 6.19 1.58e+00 4.01e-01 1.54e+01 angle pdb=" N THR R 437 " pdb=" CA THR R 437 " pdb=" C THR R 437 " ideal model delta sigma weight residual 110.20 104.01 6.19 1.58e+00 4.01e-01 1.54e+01 ... (remaining 148963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.09: 56712 16.09 - 32.18: 6432 32.18 - 48.27: 1848 48.27 - 64.36: 384 64.36 - 80.44: 216 Dihedral angle restraints: 65592 sinusoidal: 25848 harmonic: 39744 Sorted by residual: dihedral pdb=" N GLU Q 570 " pdb=" CA GLU Q 570 " pdb=" CB GLU Q 570 " pdb=" CG GLU Q 570 " ideal model delta sinusoidal sigma weight residual -180.00 -122.28 -57.72 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" N GLU N 570 " pdb=" CA GLU N 570 " pdb=" CB GLU N 570 " pdb=" CG GLU N 570 " ideal model delta sinusoidal sigma weight residual -180.00 -122.28 -57.72 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" N GLU B 570 " pdb=" CA GLU B 570 " pdb=" CB GLU B 570 " pdb=" CG GLU B 570 " ideal model delta sinusoidal sigma weight residual -180.00 -122.28 -57.72 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 65589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 7464 0.033 - 0.066: 5184 0.066 - 0.098: 2784 0.098 - 0.131: 960 0.131 - 0.164: 288 Chirality restraints: 16680 Sorted by residual: chirality pdb=" CA PRO A 513 " pdb=" N PRO A 513 " pdb=" C PRO A 513 " pdb=" CB PRO A 513 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CA PRO O 513 " pdb=" N PRO O 513 " pdb=" C PRO O 513 " pdb=" CB PRO O 513 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CA PRO L 513 " pdb=" N PRO L 513 " pdb=" C PRO L 513 " pdb=" CB PRO L 513 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.72e-01 ... (remaining 16677 not shown) Planarity restraints: 19632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 335 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO H 336 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO H 336 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 336 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR O 335 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO O 336 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO O 336 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO O 336 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 335 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO A 336 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 336 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 336 " 0.030 5.00e-02 4.00e+02 ... (remaining 19629 not shown) Histogram of nonbonded interaction distances: 0.90 - 1.70: 120 1.70 - 2.50: 576 2.50 - 3.30: 111312 3.30 - 4.10: 246216 4.10 - 4.90: 457440 Warning: very small nonbonded interaction distances. Nonbonded interactions: 815664 Sorted by model distance: nonbonded pdb=" CE2 TYR L 309 " pdb=" CA GLY R 302 " model vdw 0.902 3.740 nonbonded pdb=" CA GLY K 302 " pdb=" CE2 TYR Q 309 " model vdw 0.902 3.740 nonbonded pdb=" CA GLY F 302 " pdb=" CE2 TYR H 309 " model vdw 0.902 3.740 nonbonded pdb=" CE2 TYR D 309 " pdb=" CA GLY G 302 " model vdw 0.902 3.740 nonbonded pdb=" CA GLY E 302 " pdb=" CE2 TYR W 309 " model vdw 0.902 3.740 ... (remaining 815659 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 6.770 Check model and map are aligned: 1.180 Set scattering table: 0.710 Process input model: 212.940 Find NCS groups from input model: 5.030 Set up NCS constraints: 0.690 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 230.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.052 109440 Z= 0.639 Angle : 0.699 6.192 148968 Z= 0.406 Chirality : 0.055 0.164 16680 Planarity : 0.005 0.054 19632 Dihedral : 15.781 80.444 40152 Min Nonbonded Distance : 0.902 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.25 % Allowed : 15.45 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.07), residues: 13608 helix: 1.96 (0.08), residues: 4632 sheet: 1.14 (0.09), residues: 3216 loop : -0.01 (0.08), residues: 5760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP L 424 HIS 0.006 0.002 HIS P 491 PHE 0.011 0.002 PHE T 339 TYR 0.016 0.002 TYR K 455 ARG 0.008 0.001 ARG L 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27216 Ramachandran restraints generated. 13608 Oldfield, 0 Emsley, 13608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27216 Ramachandran restraints generated. 13608 Oldfield, 0 Emsley, 13608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 11496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 744 time to evaluate : 8.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 MET cc_start: 0.9561 (mtm) cc_final: 0.9141 (tpp) REVERT: A 165 MET cc_start: 0.9842 (mtp) cc_final: 0.9485 (tpp) REVERT: A 323 MET cc_start: 0.9202 (ttm) cc_final: 0.8455 (tmm) REVERT: A 507 MET cc_start: 0.9449 (mmt) cc_final: 0.8411 (ttm) REVERT: A 528 MET cc_start: 0.9124 (mtp) cc_final: 0.8891 (ptt) REVERT: B 106 MET cc_start: 0.9564 (mtm) cc_final: 0.9106 (tpp) REVERT: B 165 MET cc_start: 0.9846 (mtp) cc_final: 0.9481 (tpp) REVERT: B 323 MET cc_start: 0.9178 (ttm) cc_final: 0.8445 (tmm) REVERT: B 507 MET cc_start: 0.9448 (mmt) cc_final: 0.8415 (ttm) REVERT: C 106 MET cc_start: 0.9578 (mtm) cc_final: 0.9099 (tpp) REVERT: C 165 MET cc_start: 0.9841 (mtp) cc_final: 0.9476 (tpp) REVERT: C 323 MET cc_start: 0.9177 (ttm) cc_final: 0.8433 (tmm) REVERT: C 507 MET cc_start: 0.9453 (mmt) cc_final: 0.8403 (ttm) REVERT: C 528 MET cc_start: 0.9113 (mtp) cc_final: 0.8910 (ptt) REVERT: D 106 MET cc_start: 0.9573 (mtm) cc_final: 0.9137 (tpp) REVERT: D 165 MET cc_start: 0.9842 (mtp) cc_final: 0.9479 (tpp) REVERT: D 323 MET cc_start: 0.9200 (ttm) cc_final: 0.8450 (tmm) REVERT: D 507 MET cc_start: 0.9442 (mmt) cc_final: 0.8400 (ttm) REVERT: D 528 MET cc_start: 0.9101 (mtp) cc_final: 0.8880 (ptt) REVERT: E 106 MET cc_start: 0.9560 (mtm) cc_final: 0.9127 (tpp) REVERT: E 165 MET cc_start: 0.9844 (mtp) cc_final: 0.9473 (tpp) REVERT: E 323 MET cc_start: 0.9206 (ttm) cc_final: 0.8462 (tmm) REVERT: E 507 MET cc_start: 0.9451 (mmt) cc_final: 0.8413 (ttm) REVERT: E 528 MET cc_start: 0.9123 (mtp) cc_final: 0.8901 (ptt) REVERT: F 106 MET cc_start: 0.9566 (mtm) cc_final: 0.9104 (tpp) REVERT: F 165 MET cc_start: 0.9842 (mtp) cc_final: 0.9466 (tpp) REVERT: F 323 MET cc_start: 0.9194 (ttm) cc_final: 0.8445 (tmm) REVERT: F 507 MET cc_start: 0.9445 (mmt) cc_final: 0.8402 (ttm) REVERT: F 528 MET cc_start: 0.9131 (mtp) cc_final: 0.8902 (ptt) REVERT: G 106 MET cc_start: 0.9545 (mtm) cc_final: 0.9119 (tpp) REVERT: G 165 MET cc_start: 0.9843 (mtp) cc_final: 0.9475 (tpp) REVERT: G 323 MET cc_start: 0.9218 (ttm) cc_final: 0.8463 (tmm) REVERT: G 507 MET cc_start: 0.9440 (mmt) cc_final: 0.8404 (ttm) REVERT: G 528 MET cc_start: 0.9118 (mtp) cc_final: 0.8887 (ptt) REVERT: H 106 MET cc_start: 0.9579 (mtm) cc_final: 0.9137 (tpp) REVERT: H 165 MET cc_start: 0.9835 (mtp) cc_final: 0.9479 (tpp) REVERT: H 323 MET cc_start: 0.9193 (ttm) cc_final: 0.8447 (tmm) REVERT: H 507 MET cc_start: 0.9455 (mmt) cc_final: 0.8403 (ttm) REVERT: I 106 MET cc_start: 0.9578 (mtm) cc_final: 0.9099 (tpp) REVERT: I 165 MET cc_start: 0.9841 (mtp) cc_final: 0.9476 (tpp) REVERT: I 323 MET cc_start: 0.9178 (ttm) cc_final: 0.8434 (tmm) REVERT: I 507 MET cc_start: 0.9453 (mmt) cc_final: 0.8403 (ttm) REVERT: I 528 MET cc_start: 0.9113 (mtp) cc_final: 0.8910 (ptt) REVERT: J 106 MET cc_start: 0.9579 (mtm) cc_final: 0.9137 (tpp) REVERT: J 165 MET cc_start: 0.9835 (mtp) cc_final: 0.9479 (tpp) REVERT: J 323 MET cc_start: 0.9193 (ttm) cc_final: 0.8447 (tmm) REVERT: J 507 MET cc_start: 0.9455 (mmt) cc_final: 0.8403 (ttm) REVERT: K 106 MET cc_start: 0.9579 (mtm) cc_final: 0.9137 (tpp) REVERT: K 165 MET cc_start: 0.9835 (mtp) cc_final: 0.9479 (tpp) REVERT: K 323 MET cc_start: 0.9193 (ttm) cc_final: 0.8447 (tmm) REVERT: K 507 MET cc_start: 0.9455 (mmt) cc_final: 0.8403 (ttm) REVERT: L 106 MET cc_start: 0.9561 (mtm) cc_final: 0.9141 (tpp) REVERT: L 165 MET cc_start: 0.9842 (mtp) cc_final: 0.9485 (tpp) REVERT: L 323 MET cc_start: 0.9202 (ttm) cc_final: 0.8455 (tmm) REVERT: L 507 MET cc_start: 0.9449 (mmt) cc_final: 0.8411 (ttm) REVERT: L 528 MET cc_start: 0.9124 (mtp) cc_final: 0.8891 (ptt) REVERT: M 106 MET cc_start: 0.9566 (mtm) cc_final: 0.9104 (tpp) REVERT: M 165 MET cc_start: 0.9842 (mtp) cc_final: 0.9466 (tpp) REVERT: M 323 MET cc_start: 0.9194 (ttm) cc_final: 0.8445 (tmm) REVERT: M 507 MET cc_start: 0.9445 (mmt) cc_final: 0.8402 (ttm) REVERT: M 528 MET cc_start: 0.9131 (mtp) cc_final: 0.8902 (ptt) REVERT: N 106 MET cc_start: 0.9545 (mtm) cc_final: 0.9119 (tpp) REVERT: N 165 MET cc_start: 0.9843 (mtp) cc_final: 0.9475 (tpp) REVERT: N 323 MET cc_start: 0.9218 (ttm) cc_final: 0.8463 (tmm) REVERT: N 507 MET cc_start: 0.9440 (mmt) cc_final: 0.8404 (ttm) REVERT: N 528 MET cc_start: 0.9118 (mtp) cc_final: 0.8887 (ptt) REVERT: O 106 MET cc_start: 0.9561 (mtm) cc_final: 0.9141 (tpp) REVERT: O 165 MET cc_start: 0.9842 (mtp) cc_final: 0.9485 (tpp) REVERT: O 323 MET cc_start: 0.9202 (ttm) cc_final: 0.8455 (tmm) REVERT: O 507 MET cc_start: 0.9449 (mmt) cc_final: 0.8411 (ttm) REVERT: O 528 MET cc_start: 0.9123 (mtp) cc_final: 0.8891 (ptt) REVERT: P 106 MET cc_start: 0.9578 (mtm) cc_final: 0.9099 (tpp) REVERT: P 165 MET cc_start: 0.9841 (mtp) cc_final: 0.9476 (tpp) REVERT: P 323 MET cc_start: 0.9178 (ttm) cc_final: 0.8434 (tmm) REVERT: P 507 MET cc_start: 0.9453 (mmt) cc_final: 0.8403 (ttm) REVERT: P 528 MET cc_start: 0.9113 (mtp) cc_final: 0.8910 (ptt) REVERT: Q 106 MET cc_start: 0.9564 (mtm) cc_final: 0.9106 (tpp) REVERT: Q 165 MET cc_start: 0.9846 (mtp) cc_final: 0.9481 (tpp) REVERT: Q 323 MET cc_start: 0.9178 (ttm) cc_final: 0.8445 (tmm) REVERT: Q 507 MET cc_start: 0.9448 (mmt) cc_final: 0.8415 (ttm) REVERT: R 106 MET cc_start: 0.9573 (mtm) cc_final: 0.9137 (tpp) REVERT: R 165 MET cc_start: 0.9842 (mtp) cc_final: 0.9479 (tpp) REVERT: R 323 MET cc_start: 0.9200 (ttm) cc_final: 0.8450 (tmm) REVERT: R 507 MET cc_start: 0.9442 (mmt) cc_final: 0.8400 (ttm) REVERT: R 528 MET cc_start: 0.9101 (mtp) cc_final: 0.8880 (ptt) REVERT: S 106 MET cc_start: 0.9560 (mtm) cc_final: 0.9127 (tpp) REVERT: S 165 MET cc_start: 0.9844 (mtp) cc_final: 0.9473 (tpp) REVERT: S 323 MET cc_start: 0.9206 (ttm) cc_final: 0.8462 (tmm) REVERT: S 507 MET cc_start: 0.9451 (mmt) cc_final: 0.8412 (ttm) REVERT: S 528 MET cc_start: 0.9123 (mtp) cc_final: 0.8901 (ptt) REVERT: T 106 MET cc_start: 0.9545 (mtm) cc_final: 0.9119 (tpp) REVERT: T 165 MET cc_start: 0.9843 (mtp) cc_final: 0.9475 (tpp) REVERT: T 323 MET cc_start: 0.9218 (ttm) cc_final: 0.8463 (tmm) REVERT: T 507 MET cc_start: 0.9440 (mmt) cc_final: 0.8404 (ttm) REVERT: T 528 MET cc_start: 0.9118 (mtp) cc_final: 0.8887 (ptt) REVERT: V 106 MET cc_start: 0.9566 (mtm) cc_final: 0.9104 (tpp) REVERT: V 165 MET cc_start: 0.9842 (mtp) cc_final: 0.9466 (tpp) REVERT: V 323 MET cc_start: 0.9194 (ttm) cc_final: 0.8445 (tmm) REVERT: V 507 MET cc_start: 0.9445 (mmt) cc_final: 0.8402 (ttm) REVERT: V 528 MET cc_start: 0.9131 (mtp) cc_final: 0.8902 (ptt) REVERT: W 106 MET cc_start: 0.9560 (mtm) cc_final: 0.9127 (tpp) REVERT: W 165 MET cc_start: 0.9844 (mtp) cc_final: 0.9473 (tpp) REVERT: W 323 MET cc_start: 0.9206 (ttm) cc_final: 0.8462 (tmm) REVERT: W 507 MET cc_start: 0.9451 (mmt) cc_final: 0.8413 (ttm) REVERT: W 528 MET cc_start: 0.9123 (mtp) cc_final: 0.8901 (ptt) REVERT: X 106 MET cc_start: 0.9564 (mtm) cc_final: 0.9106 (tpp) REVERT: X 165 MET cc_start: 0.9846 (mtp) cc_final: 0.9481 (tpp) REVERT: X 323 MET cc_start: 0.9178 (ttm) cc_final: 0.8445 (tmm) REVERT: X 507 MET cc_start: 0.9448 (mmt) cc_final: 0.8415 (ttm) REVERT: Y 106 MET cc_start: 0.9573 (mtm) cc_final: 0.9137 (tpp) REVERT: Y 165 MET cc_start: 0.9842 (mtp) cc_final: 0.9479 (tpp) REVERT: Y 323 MET cc_start: 0.9200 (ttm) cc_final: 0.8450 (tmm) REVERT: Y 507 MET cc_start: 0.9442 (mmt) cc_final: 0.8400 (ttm) REVERT: Y 528 MET cc_start: 0.9101 (mtp) cc_final: 0.8880 (ptt) outliers start: 144 outliers final: 48 residues processed: 840 average time/residue: 0.7956 time to fit residues: 1209.3493 Evaluate side-chains 624 residues out of total 11496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 576 time to evaluate : 8.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain G residue 46 MET Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain H residue 46 MET Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain J residue 46 MET Chi-restraints excluded: chain J residue 60 ASN Chi-restraints excluded: chain K residue 46 MET Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain M residue 46 MET Chi-restraints excluded: chain M residue 60 ASN Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain O residue 46 MET Chi-restraints excluded: chain O residue 60 ASN Chi-restraints excluded: chain P residue 46 MET Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain Q residue 46 MET Chi-restraints excluded: chain Q residue 60 ASN Chi-restraints excluded: chain R residue 46 MET Chi-restraints excluded: chain R residue 60 ASN Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 60 ASN Chi-restraints excluded: chain T residue 46 MET Chi-restraints excluded: chain T residue 60 ASN Chi-restraints excluded: chain V residue 46 MET Chi-restraints excluded: chain V residue 60 ASN Chi-restraints excluded: chain W residue 46 MET Chi-restraints excluded: chain W residue 60 ASN Chi-restraints excluded: chain X residue 46 MET Chi-restraints excluded: chain X residue 60 ASN Chi-restraints excluded: chain Y residue 46 MET Chi-restraints excluded: chain Y residue 60 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 1155 optimal weight: 7.9990 chunk 1036 optimal weight: 20.0000 chunk 575 optimal weight: 10.0000 chunk 354 optimal weight: 30.0000 chunk 699 optimal weight: 7.9990 chunk 553 optimal weight: 6.9990 chunk 1072 optimal weight: 8.9990 chunk 414 optimal weight: 7.9990 chunk 651 optimal weight: 9.9990 chunk 798 optimal weight: 40.0000 chunk 1242 optimal weight: 4.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 109440 Z= 0.225 Angle : 0.577 7.223 148968 Z= 0.302 Chirality : 0.042 0.146 16680 Planarity : 0.005 0.046 19632 Dihedral : 4.570 35.633 15264 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.09 % Allowed : 14.87 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.07), residues: 13608 helix: 1.91 (0.08), residues: 4632 sheet: 1.04 (0.09), residues: 3096 loop : 0.09 (0.08), residues: 5880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 149 HIS 0.006 0.001 HIS T 538 PHE 0.011 0.001 PHE J 157 TYR 0.041 0.001 TYR B 309 ARG 0.004 0.000 ARG D 599 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27216 Ramachandran restraints generated. 13608 Oldfield, 0 Emsley, 13608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27216 Ramachandran restraints generated. 13608 Oldfield, 0 Emsley, 13608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 11496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 600 time to evaluate : 8.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7209 (mpp) cc_final: 0.6611 (mpp) REVERT: A 323 MET cc_start: 0.9269 (ttm) cc_final: 0.8633 (tmm) REVERT: A 411 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9156 (mt) REVERT: A 507 MET cc_start: 0.9298 (mmt) cc_final: 0.8159 (ttm) REVERT: B 229 MET cc_start: 0.7230 (mpp) cc_final: 0.6627 (mpp) REVERT: B 323 MET cc_start: 0.9251 (ttm) cc_final: 0.8624 (tmm) REVERT: B 411 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9124 (mt) REVERT: B 507 MET cc_start: 0.9302 (mmt) cc_final: 0.8167 (ttm) REVERT: C 229 MET cc_start: 0.7247 (mpp) cc_final: 0.6636 (mpp) REVERT: C 323 MET cc_start: 0.9250 (ttm) cc_final: 0.8614 (tmm) REVERT: C 411 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9148 (mt) REVERT: C 507 MET cc_start: 0.9303 (mmt) cc_final: 0.8154 (ttm) REVERT: D 229 MET cc_start: 0.7294 (mpp) cc_final: 0.6667 (mpp) REVERT: D 323 MET cc_start: 0.9269 (ttm) cc_final: 0.8630 (tmm) REVERT: D 411 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9174 (mt) REVERT: D 507 MET cc_start: 0.9301 (mmt) cc_final: 0.8157 (ttm) REVERT: E 229 MET cc_start: 0.7325 (mpp) cc_final: 0.6681 (mpp) REVERT: E 323 MET cc_start: 0.9272 (ttm) cc_final: 0.8638 (tmm) REVERT: E 411 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9150 (mt) REVERT: E 507 MET cc_start: 0.9309 (mmt) cc_final: 0.8169 (ttm) REVERT: F 229 MET cc_start: 0.7307 (mpp) cc_final: 0.6677 (mpp) REVERT: F 323 MET cc_start: 0.9266 (ttm) cc_final: 0.8625 (tmm) REVERT: F 411 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9160 (mt) REVERT: F 507 MET cc_start: 0.9298 (mmt) cc_final: 0.8154 (ttm) REVERT: G 229 MET cc_start: 0.7298 (mpp) cc_final: 0.6669 (mpp) REVERT: G 323 MET cc_start: 0.9278 (ttm) cc_final: 0.8637 (tmm) REVERT: G 411 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9156 (mt) REVERT: G 507 MET cc_start: 0.9289 (mmt) cc_final: 0.8157 (ttm) REVERT: H 229 MET cc_start: 0.7308 (mpp) cc_final: 0.6678 (mpp) REVERT: H 323 MET cc_start: 0.9265 (ttm) cc_final: 0.8626 (tmm) REVERT: H 411 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9138 (mt) REVERT: H 507 MET cc_start: 0.9317 (mmt) cc_final: 0.8158 (ttm) REVERT: I 229 MET cc_start: 0.7247 (mpp) cc_final: 0.6636 (mpp) REVERT: I 323 MET cc_start: 0.9250 (ttm) cc_final: 0.8614 (tmm) REVERT: I 411 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9148 (mt) REVERT: I 507 MET cc_start: 0.9303 (mmt) cc_final: 0.8154 (ttm) REVERT: J 229 MET cc_start: 0.7308 (mpp) cc_final: 0.6678 (mpp) REVERT: J 323 MET cc_start: 0.9264 (ttm) cc_final: 0.8626 (tmm) REVERT: J 411 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9138 (mt) REVERT: J 507 MET cc_start: 0.9317 (mmt) cc_final: 0.8158 (ttm) REVERT: K 229 MET cc_start: 0.7308 (mpp) cc_final: 0.6678 (mpp) REVERT: K 323 MET cc_start: 0.9264 (ttm) cc_final: 0.8626 (tmm) REVERT: K 411 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9138 (mt) REVERT: K 507 MET cc_start: 0.9317 (mmt) cc_final: 0.8158 (ttm) REVERT: L 229 MET cc_start: 0.7209 (mpp) cc_final: 0.6611 (mpp) REVERT: L 323 MET cc_start: 0.9269 (ttm) cc_final: 0.8633 (tmm) REVERT: L 411 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9156 (mt) REVERT: L 507 MET cc_start: 0.9298 (mmt) cc_final: 0.8159 (ttm) REVERT: M 229 MET cc_start: 0.7307 (mpp) cc_final: 0.6677 (mpp) REVERT: M 323 MET cc_start: 0.9266 (ttm) cc_final: 0.8625 (tmm) REVERT: M 411 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9160 (mt) REVERT: M 507 MET cc_start: 0.9298 (mmt) cc_final: 0.8154 (ttm) REVERT: N 229 MET cc_start: 0.7298 (mpp) cc_final: 0.6669 (mpp) REVERT: N 323 MET cc_start: 0.9278 (ttm) cc_final: 0.8637 (tmm) REVERT: N 411 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9156 (mt) REVERT: N 507 MET cc_start: 0.9289 (mmt) cc_final: 0.8157 (ttm) REVERT: O 229 MET cc_start: 0.7209 (mpp) cc_final: 0.6611 (mpp) REVERT: O 323 MET cc_start: 0.9269 (ttm) cc_final: 0.8633 (tmm) REVERT: O 411 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9156 (mt) REVERT: O 507 MET cc_start: 0.9298 (mmt) cc_final: 0.8159 (ttm) REVERT: P 229 MET cc_start: 0.7247 (mpp) cc_final: 0.6636 (mpp) REVERT: P 323 MET cc_start: 0.9250 (ttm) cc_final: 0.8614 (tmm) REVERT: P 411 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9148 (mt) REVERT: P 507 MET cc_start: 0.9303 (mmt) cc_final: 0.8154 (ttm) REVERT: Q 229 MET cc_start: 0.7230 (mpp) cc_final: 0.6627 (mpp) REVERT: Q 323 MET cc_start: 0.9251 (ttm) cc_final: 0.8624 (tmm) REVERT: Q 411 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9124 (mt) REVERT: Q 507 MET cc_start: 0.9302 (mmt) cc_final: 0.8168 (ttm) REVERT: R 229 MET cc_start: 0.7294 (mpp) cc_final: 0.6667 (mpp) REVERT: R 323 MET cc_start: 0.9269 (ttm) cc_final: 0.8630 (tmm) REVERT: R 411 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9174 (mt) REVERT: R 507 MET cc_start: 0.9301 (mmt) cc_final: 0.8157 (ttm) REVERT: S 229 MET cc_start: 0.7325 (mpp) cc_final: 0.6681 (mpp) REVERT: S 323 MET cc_start: 0.9271 (ttm) cc_final: 0.8638 (tmm) REVERT: S 411 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9150 (mt) REVERT: S 507 MET cc_start: 0.9309 (mmt) cc_final: 0.8169 (ttm) REVERT: T 229 MET cc_start: 0.7298 (mpp) cc_final: 0.6669 (mpp) REVERT: T 323 MET cc_start: 0.9278 (ttm) cc_final: 0.8637 (tmm) REVERT: T 411 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9156 (mt) REVERT: T 507 MET cc_start: 0.9289 (mmt) cc_final: 0.8157 (ttm) REVERT: V 229 MET cc_start: 0.7307 (mpp) cc_final: 0.6677 (mpp) REVERT: V 323 MET cc_start: 0.9266 (ttm) cc_final: 0.8625 (tmm) REVERT: V 411 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9160 (mt) REVERT: V 507 MET cc_start: 0.9298 (mmt) cc_final: 0.8154 (ttm) REVERT: W 229 MET cc_start: 0.7325 (mpp) cc_final: 0.6681 (mpp) REVERT: W 323 MET cc_start: 0.9272 (ttm) cc_final: 0.8638 (tmm) REVERT: W 411 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9150 (mt) REVERT: W 507 MET cc_start: 0.9309 (mmt) cc_final: 0.8170 (ttm) REVERT: X 229 MET cc_start: 0.7230 (mpp) cc_final: 0.6627 (mpp) REVERT: X 323 MET cc_start: 0.9251 (ttm) cc_final: 0.8624 (tmm) REVERT: X 411 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9124 (mt) REVERT: X 507 MET cc_start: 0.9302 (mmt) cc_final: 0.8168 (ttm) REVERT: Y 229 MET cc_start: 0.7294 (mpp) cc_final: 0.6667 (mpp) REVERT: Y 323 MET cc_start: 0.9269 (ttm) cc_final: 0.8630 (tmm) REVERT: Y 411 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9174 (mt) REVERT: Y 507 MET cc_start: 0.9301 (mmt) cc_final: 0.8157 (ttm) outliers start: 240 outliers final: 72 residues processed: 792 average time/residue: 0.8318 time to fit residues: 1180.5717 Evaluate side-chains 672 residues out of total 11496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 576 time to evaluate : 8.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 388 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain G residue 46 MET Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 388 LEU Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain H residue 46 MET Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 388 LEU Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 411 LEU Chi-restraints excluded: chain J residue 46 MET Chi-restraints excluded: chain J residue 60 ASN Chi-restraints excluded: chain J residue 388 LEU Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain K residue 46 MET Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain K residue 388 LEU Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 388 LEU Chi-restraints excluded: chain L residue 411 LEU Chi-restraints excluded: chain M residue 46 MET Chi-restraints excluded: chain M residue 60 ASN Chi-restraints excluded: chain M residue 388 LEU Chi-restraints excluded: chain M residue 411 LEU Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 388 LEU Chi-restraints excluded: chain N residue 411 LEU Chi-restraints excluded: chain O residue 46 MET Chi-restraints excluded: chain O residue 60 ASN Chi-restraints excluded: chain O residue 388 LEU Chi-restraints excluded: chain O residue 411 LEU Chi-restraints excluded: chain P residue 46 MET Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain P residue 388 LEU Chi-restraints excluded: chain P residue 411 LEU Chi-restraints excluded: chain Q residue 46 MET Chi-restraints excluded: chain Q residue 60 ASN Chi-restraints excluded: chain Q residue 388 LEU Chi-restraints excluded: chain Q residue 411 LEU Chi-restraints excluded: chain R residue 46 MET Chi-restraints excluded: chain R residue 60 ASN Chi-restraints excluded: chain R residue 388 LEU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 60 ASN Chi-restraints excluded: chain S residue 388 LEU Chi-restraints excluded: chain S residue 411 LEU Chi-restraints excluded: chain T residue 46 MET Chi-restraints excluded: chain T residue 60 ASN Chi-restraints excluded: chain T residue 388 LEU Chi-restraints excluded: chain T residue 411 LEU Chi-restraints excluded: chain V residue 46 MET Chi-restraints excluded: chain V residue 60 ASN Chi-restraints excluded: chain V residue 388 LEU Chi-restraints excluded: chain V residue 411 LEU Chi-restraints excluded: chain W residue 46 MET Chi-restraints excluded: chain W residue 60 ASN Chi-restraints excluded: chain W residue 388 LEU Chi-restraints excluded: chain W residue 411 LEU Chi-restraints excluded: chain X residue 46 MET Chi-restraints excluded: chain X residue 60 ASN Chi-restraints excluded: chain X residue 388 LEU Chi-restraints excluded: chain X residue 411 LEU Chi-restraints excluded: chain Y residue 46 MET Chi-restraints excluded: chain Y residue 60 ASN Chi-restraints excluded: chain Y residue 388 LEU Chi-restraints excluded: chain Y residue 411 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 690 optimal weight: 10.0000 chunk 385 optimal weight: 40.0000 chunk 1033 optimal weight: 40.0000 chunk 845 optimal weight: 7.9990 chunk 342 optimal weight: 50.0000 chunk 1244 optimal weight: 20.0000 chunk 1344 optimal weight: 0.7980 chunk 1108 optimal weight: 30.0000 chunk 1234 optimal weight: 40.0000 chunk 424 optimal weight: 6.9990 chunk 998 optimal weight: 8.9990 overall best weight: 6.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 109440 Z= 0.216 Angle : 0.543 9.322 148968 Z= 0.276 Chirality : 0.041 0.153 16680 Planarity : 0.004 0.042 19632 Dihedral : 4.234 37.151 15264 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.25 % Allowed : 16.13 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.07), residues: 13608 helix: 1.99 (0.08), residues: 4656 sheet: 1.24 (0.09), residues: 3096 loop : 0.40 (0.08), residues: 5856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 549 HIS 0.006 0.001 HIS X 538 PHE 0.008 0.001 PHE W 88 TYR 0.015 0.001 TYR O 309 ARG 0.004 0.001 ARG Y 537 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27216 Ramachandran restraints generated. 13608 Oldfield, 0 Emsley, 13608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27216 Ramachandran restraints generated. 13608 Oldfield, 0 Emsley, 13608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 11496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 600 time to evaluate : 9.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7012 (mpp) cc_final: 0.6527 (mpp) REVERT: A 323 MET cc_start: 0.9343 (ttm) cc_final: 0.8745 (tmm) REVERT: A 411 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9186 (mt) REVERT: A 507 MET cc_start: 0.9196 (mmt) cc_final: 0.7931 (ttm) REVERT: A 530 MET cc_start: 0.9206 (ppp) cc_final: 0.8594 (ppp) REVERT: B 229 MET cc_start: 0.7029 (mpp) cc_final: 0.6541 (mpp) REVERT: B 323 MET cc_start: 0.9323 (ttm) cc_final: 0.8732 (tmm) REVERT: B 411 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9164 (mt) REVERT: B 507 MET cc_start: 0.9168 (mmt) cc_final: 0.7922 (ttm) REVERT: C 229 MET cc_start: 0.7051 (mpp) cc_final: 0.6554 (mpp) REVERT: C 323 MET cc_start: 0.9322 (ttm) cc_final: 0.8723 (tmm) REVERT: C 411 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9184 (mt) REVERT: C 507 MET cc_start: 0.9171 (mmt) cc_final: 0.7905 (ttm) REVERT: C 530 MET cc_start: 0.9164 (ppp) cc_final: 0.8564 (ppp) REVERT: D 229 MET cc_start: 0.7090 (mpp) cc_final: 0.6581 (mpp) REVERT: D 323 MET cc_start: 0.9346 (ttm) cc_final: 0.8746 (tmm) REVERT: D 411 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9191 (mt) REVERT: D 507 MET cc_start: 0.9193 (mmt) cc_final: 0.7923 (ttm) REVERT: D 530 MET cc_start: 0.9194 (ppp) cc_final: 0.8587 (ppp) REVERT: E 229 MET cc_start: 0.7119 (mpp) cc_final: 0.6595 (mpp) REVERT: E 323 MET cc_start: 0.9346 (ttm) cc_final: 0.8749 (tmm) REVERT: E 411 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9174 (mt) REVERT: E 507 MET cc_start: 0.9189 (mmt) cc_final: 0.7928 (ttm) REVERT: E 530 MET cc_start: 0.9204 (ppp) cc_final: 0.8595 (ppp) REVERT: F 229 MET cc_start: 0.7111 (mpp) cc_final: 0.6598 (mpp) REVERT: F 323 MET cc_start: 0.9340 (ttm) cc_final: 0.8736 (tmm) REVERT: F 411 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9181 (mt) REVERT: F 507 MET cc_start: 0.9184 (mmt) cc_final: 0.7916 (ttm) REVERT: F 530 MET cc_start: 0.9204 (ppp) cc_final: 0.8591 (ppp) REVERT: G 229 MET cc_start: 0.7104 (mpp) cc_final: 0.6590 (mpp) REVERT: G 323 MET cc_start: 0.9352 (ttm) cc_final: 0.8748 (tmm) REVERT: G 411 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9182 (mt) REVERT: G 507 MET cc_start: 0.9172 (mmt) cc_final: 0.7920 (ttm) REVERT: G 530 MET cc_start: 0.9252 (ppp) cc_final: 0.8614 (ppp) REVERT: H 229 MET cc_start: 0.7105 (mpp) cc_final: 0.6594 (mpp) REVERT: H 323 MET cc_start: 0.9337 (ttm) cc_final: 0.8736 (tmm) REVERT: H 411 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9168 (mt) REVERT: H 507 MET cc_start: 0.9179 (mmt) cc_final: 0.7907 (ttm) REVERT: I 229 MET cc_start: 0.7051 (mpp) cc_final: 0.6554 (mpp) REVERT: I 323 MET cc_start: 0.9322 (ttm) cc_final: 0.8723 (tmm) REVERT: I 411 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9184 (mt) REVERT: I 507 MET cc_start: 0.9171 (mmt) cc_final: 0.7905 (ttm) REVERT: I 530 MET cc_start: 0.9164 (ppp) cc_final: 0.8564 (ppp) REVERT: J 229 MET cc_start: 0.7105 (mpp) cc_final: 0.6594 (mpp) REVERT: J 323 MET cc_start: 0.9337 (ttm) cc_final: 0.8736 (tmm) REVERT: J 411 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9167 (mt) REVERT: J 507 MET cc_start: 0.9179 (mmt) cc_final: 0.7907 (ttm) REVERT: K 229 MET cc_start: 0.7105 (mpp) cc_final: 0.6594 (mpp) REVERT: K 323 MET cc_start: 0.9337 (ttm) cc_final: 0.8736 (tmm) REVERT: K 411 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9167 (mt) REVERT: K 507 MET cc_start: 0.9179 (mmt) cc_final: 0.7907 (ttm) REVERT: L 229 MET cc_start: 0.7012 (mpp) cc_final: 0.6527 (mpp) REVERT: L 323 MET cc_start: 0.9343 (ttm) cc_final: 0.8745 (tmm) REVERT: L 411 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9186 (mt) REVERT: L 507 MET cc_start: 0.9196 (mmt) cc_final: 0.7931 (ttm) REVERT: L 530 MET cc_start: 0.9206 (ppp) cc_final: 0.8594 (ppp) REVERT: M 229 MET cc_start: 0.7111 (mpp) cc_final: 0.6598 (mpp) REVERT: M 323 MET cc_start: 0.9340 (ttm) cc_final: 0.8736 (tmm) REVERT: M 411 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9181 (mt) REVERT: M 507 MET cc_start: 0.9184 (mmt) cc_final: 0.7916 (ttm) REVERT: M 530 MET cc_start: 0.9204 (ppp) cc_final: 0.8591 (ppp) REVERT: N 229 MET cc_start: 0.7104 (mpp) cc_final: 0.6590 (mpp) REVERT: N 323 MET cc_start: 0.9352 (ttm) cc_final: 0.8748 (tmm) REVERT: N 411 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9182 (mt) REVERT: N 507 MET cc_start: 0.9172 (mmt) cc_final: 0.7920 (ttm) REVERT: N 530 MET cc_start: 0.9252 (ppp) cc_final: 0.8614 (ppp) REVERT: O 229 MET cc_start: 0.7012 (mpp) cc_final: 0.6527 (mpp) REVERT: O 323 MET cc_start: 0.9343 (ttm) cc_final: 0.8745 (tmm) REVERT: O 411 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9186 (mt) REVERT: O 507 MET cc_start: 0.9196 (mmt) cc_final: 0.7931 (ttm) REVERT: O 530 MET cc_start: 0.9206 (ppp) cc_final: 0.8594 (ppp) REVERT: P 229 MET cc_start: 0.7051 (mpp) cc_final: 0.6554 (mpp) REVERT: P 323 MET cc_start: 0.9322 (ttm) cc_final: 0.8723 (tmm) REVERT: P 411 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9184 (mt) REVERT: P 507 MET cc_start: 0.9171 (mmt) cc_final: 0.7905 (ttm) REVERT: P 530 MET cc_start: 0.9164 (ppp) cc_final: 0.8564 (ppp) REVERT: Q 229 MET cc_start: 0.7029 (mpp) cc_final: 0.6541 (mpp) REVERT: Q 323 MET cc_start: 0.9323 (ttm) cc_final: 0.8732 (tmm) REVERT: Q 411 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9164 (mt) REVERT: Q 507 MET cc_start: 0.9168 (mmt) cc_final: 0.7922 (ttm) REVERT: R 229 MET cc_start: 0.7090 (mpp) cc_final: 0.6581 (mpp) REVERT: R 323 MET cc_start: 0.9346 (ttm) cc_final: 0.8745 (tmm) REVERT: R 411 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9191 (mt) REVERT: R 507 MET cc_start: 0.9193 (mmt) cc_final: 0.7923 (ttm) REVERT: R 530 MET cc_start: 0.9194 (ppp) cc_final: 0.8587 (ppp) REVERT: S 229 MET cc_start: 0.7119 (mpp) cc_final: 0.6595 (mpp) REVERT: S 323 MET cc_start: 0.9346 (ttm) cc_final: 0.8749 (tmm) REVERT: S 411 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9174 (mt) REVERT: S 507 MET cc_start: 0.9189 (mmt) cc_final: 0.7928 (ttm) REVERT: S 530 MET cc_start: 0.9204 (ppp) cc_final: 0.8595 (ppp) REVERT: T 229 MET cc_start: 0.7104 (mpp) cc_final: 0.6590 (mpp) REVERT: T 323 MET cc_start: 0.9352 (ttm) cc_final: 0.8748 (tmm) REVERT: T 411 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9182 (mt) REVERT: T 507 MET cc_start: 0.9172 (mmt) cc_final: 0.7920 (ttm) REVERT: T 530 MET cc_start: 0.9252 (ppp) cc_final: 0.8614 (ppp) REVERT: V 229 MET cc_start: 0.7111 (mpp) cc_final: 0.6598 (mpp) REVERT: V 323 MET cc_start: 0.9340 (ttm) cc_final: 0.8736 (tmm) REVERT: V 411 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9181 (mt) REVERT: V 507 MET cc_start: 0.9184 (mmt) cc_final: 0.7916 (ttm) REVERT: V 530 MET cc_start: 0.9204 (ppp) cc_final: 0.8591 (ppp) REVERT: W 229 MET cc_start: 0.7119 (mpp) cc_final: 0.6595 (mpp) REVERT: W 323 MET cc_start: 0.9346 (ttm) cc_final: 0.8749 (tmm) REVERT: W 411 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9174 (mt) REVERT: W 507 MET cc_start: 0.9189 (mmt) cc_final: 0.7928 (ttm) REVERT: W 530 MET cc_start: 0.9204 (ppp) cc_final: 0.8595 (ppp) REVERT: X 229 MET cc_start: 0.7029 (mpp) cc_final: 0.6541 (mpp) REVERT: X 323 MET cc_start: 0.9323 (ttm) cc_final: 0.8732 (tmm) REVERT: X 411 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9164 (mt) REVERT: X 507 MET cc_start: 0.9168 (mmt) cc_final: 0.7922 (ttm) REVERT: Y 229 MET cc_start: 0.7090 (mpp) cc_final: 0.6581 (mpp) REVERT: Y 323 MET cc_start: 0.9346 (ttm) cc_final: 0.8745 (tmm) REVERT: Y 411 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9191 (mt) REVERT: Y 507 MET cc_start: 0.9193 (mmt) cc_final: 0.7923 (ttm) REVERT: Y 530 MET cc_start: 0.9194 (ppp) cc_final: 0.8587 (ppp) outliers start: 144 outliers final: 48 residues processed: 696 average time/residue: 0.8166 time to fit residues: 1030.8326 Evaluate side-chains 672 residues out of total 11496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 600 time to evaluate : 8.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain G residue 46 MET Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain H residue 46 MET Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain I residue 411 LEU Chi-restraints excluded: chain J residue 46 MET Chi-restraints excluded: chain J residue 60 ASN Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain K residue 46 MET Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 411 LEU Chi-restraints excluded: chain M residue 46 MET Chi-restraints excluded: chain M residue 60 ASN Chi-restraints excluded: chain M residue 411 LEU Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 411 LEU Chi-restraints excluded: chain O residue 46 MET Chi-restraints excluded: chain O residue 60 ASN Chi-restraints excluded: chain O residue 411 LEU Chi-restraints excluded: chain P residue 46 MET Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain P residue 411 LEU Chi-restraints excluded: chain Q residue 46 MET Chi-restraints excluded: chain Q residue 60 ASN Chi-restraints excluded: chain Q residue 411 LEU Chi-restraints excluded: chain R residue 46 MET Chi-restraints excluded: chain R residue 60 ASN Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 60 ASN Chi-restraints excluded: chain S residue 411 LEU Chi-restraints excluded: chain T residue 46 MET Chi-restraints excluded: chain T residue 60 ASN Chi-restraints excluded: chain T residue 411 LEU Chi-restraints excluded: chain V residue 46 MET Chi-restraints excluded: chain V residue 60 ASN Chi-restraints excluded: chain V residue 411 LEU Chi-restraints excluded: chain W residue 46 MET Chi-restraints excluded: chain W residue 60 ASN Chi-restraints excluded: chain W residue 411 LEU Chi-restraints excluded: chain X residue 46 MET Chi-restraints excluded: chain X residue 60 ASN Chi-restraints excluded: chain X residue 411 LEU Chi-restraints excluded: chain Y residue 46 MET Chi-restraints excluded: chain Y residue 60 ASN Chi-restraints excluded: chain Y residue 411 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 1229 optimal weight: 30.0000 chunk 935 optimal weight: 7.9990 chunk 645 optimal weight: 30.0000 chunk 137 optimal weight: 9.9990 chunk 593 optimal weight: 10.0000 chunk 835 optimal weight: 30.0000 chunk 1248 optimal weight: 6.9990 chunk 1322 optimal weight: 20.0000 chunk 652 optimal weight: 40.0000 chunk 1183 optimal weight: 50.0000 chunk 356 optimal weight: 30.0000 overall best weight: 10.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN B 240 GLN C 240 GLN ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 GLN E 240 GLN F 240 GLN G 240 GLN H 240 GLN I 240 GLN J 240 GLN K 240 GLN L 240 GLN M 240 GLN ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 240 GLN ** O 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 240 GLN P 240 GLN Q 240 GLN R 240 GLN S 240 GLN T 240 GLN V 240 GLN W 240 GLN X 240 GLN Y 240 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 109440 Z= 0.302 Angle : 0.608 7.735 148968 Z= 0.312 Chirality : 0.042 0.149 16680 Planarity : 0.004 0.038 19632 Dihedral : 4.411 36.781 15264 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.09 % Allowed : 15.81 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.07), residues: 13608 helix: 1.44 (0.08), residues: 4632 sheet: 1.10 (0.09), residues: 3096 loop : 0.65 (0.08), residues: 5880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 549 HIS 0.005 0.002 HIS N 195 PHE 0.026 0.002 PHE J 157 TYR 0.012 0.001 TYR C 309 ARG 0.005 0.001 ARG Q 533 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27216 Ramachandran restraints generated. 13608 Oldfield, 0 Emsley, 13608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27216 Ramachandran restraints generated. 13608 Oldfield, 0 Emsley, 13608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 11496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 582 time to evaluate : 9.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7399 (mpp) cc_final: 0.6912 (mpp) REVERT: A 323 MET cc_start: 0.9400 (ttm) cc_final: 0.8798 (tmm) REVERT: A 354 MET cc_start: 0.9220 (ppp) cc_final: 0.8755 (ppp) REVERT: A 411 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9219 (mt) REVERT: A 507 MET cc_start: 0.9105 (mmt) cc_final: 0.7686 (ttm) REVERT: B 229 MET cc_start: 0.7411 (mpp) cc_final: 0.6922 (mpp) REVERT: B 323 MET cc_start: 0.9381 (ttm) cc_final: 0.8784 (tmm) REVERT: B 354 MET cc_start: 0.9183 (ppp) cc_final: 0.8679 (ppp) REVERT: B 411 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9196 (mt) REVERT: B 507 MET cc_start: 0.9071 (mmt) cc_final: 0.7673 (ttm) REVERT: C 229 MET cc_start: 0.7431 (mpp) cc_final: 0.6933 (mpp) REVERT: C 323 MET cc_start: 0.9377 (ttm) cc_final: 0.8771 (tmm) REVERT: C 354 MET cc_start: 0.9215 (ppp) cc_final: 0.8726 (ppp) REVERT: C 411 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9215 (mt) REVERT: C 507 MET cc_start: 0.9080 (mmt) cc_final: 0.7658 (ttm) REVERT: D 229 MET cc_start: 0.7477 (mpp) cc_final: 0.6966 (mpp) REVERT: D 323 MET cc_start: 0.9408 (ttm) cc_final: 0.8801 (tmm) REVERT: D 354 MET cc_start: 0.9205 (ppp) cc_final: 0.8747 (ppp) REVERT: D 411 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9230 (mt) REVERT: D 507 MET cc_start: 0.9106 (mmt) cc_final: 0.7678 (ttm) REVERT: E 229 MET cc_start: 0.7507 (mpp) cc_final: 0.6981 (mpp) REVERT: E 323 MET cc_start: 0.9407 (ttm) cc_final: 0.8802 (tmm) REVERT: E 354 MET cc_start: 0.9200 (ppp) cc_final: 0.8750 (ppp) REVERT: E 411 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9212 (mt) REVERT: E 507 MET cc_start: 0.9100 (mmt) cc_final: 0.7683 (ttm) REVERT: F 229 MET cc_start: 0.7483 (mpp) cc_final: 0.6971 (mpp) REVERT: F 323 MET cc_start: 0.9400 (ttm) cc_final: 0.8787 (tmm) REVERT: F 354 MET cc_start: 0.9219 (ppp) cc_final: 0.8751 (ppp) REVERT: F 411 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9220 (mt) REVERT: F 507 MET cc_start: 0.9093 (mmt) cc_final: 0.7669 (ttm) REVERT: G 229 MET cc_start: 0.7479 (mpp) cc_final: 0.6966 (mpp) REVERT: G 323 MET cc_start: 0.9408 (ttm) cc_final: 0.8797 (tmm) REVERT: G 354 MET cc_start: 0.9217 (ppp) cc_final: 0.8748 (ppp) REVERT: G 411 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9216 (mt) REVERT: G 507 MET cc_start: 0.9078 (mmt) cc_final: 0.7675 (ttm) REVERT: H 229 MET cc_start: 0.7490 (mpp) cc_final: 0.6977 (mpp) REVERT: H 323 MET cc_start: 0.9394 (ttm) cc_final: 0.8786 (tmm) REVERT: H 354 MET cc_start: 0.9224 (ppp) cc_final: 0.8756 (ppp) REVERT: H 411 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9206 (mt) REVERT: H 507 MET cc_start: 0.9084 (mmt) cc_final: 0.7653 (ttm) REVERT: I 229 MET cc_start: 0.7431 (mpp) cc_final: 0.6933 (mpp) REVERT: I 323 MET cc_start: 0.9376 (ttm) cc_final: 0.8772 (tmm) REVERT: I 354 MET cc_start: 0.9215 (ppp) cc_final: 0.8726 (ppp) REVERT: I 411 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9215 (mt) REVERT: I 507 MET cc_start: 0.9080 (mmt) cc_final: 0.7658 (ttm) REVERT: J 229 MET cc_start: 0.7490 (mpp) cc_final: 0.6977 (mpp) REVERT: J 323 MET cc_start: 0.9394 (ttm) cc_final: 0.8786 (tmm) REVERT: J 354 MET cc_start: 0.9224 (ppp) cc_final: 0.8756 (ppp) REVERT: J 411 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9206 (mt) REVERT: J 507 MET cc_start: 0.9084 (mmt) cc_final: 0.7653 (ttm) REVERT: K 229 MET cc_start: 0.7490 (mpp) cc_final: 0.6977 (mpp) REVERT: K 323 MET cc_start: 0.9394 (ttm) cc_final: 0.8786 (tmm) REVERT: K 354 MET cc_start: 0.9224 (ppp) cc_final: 0.8756 (ppp) REVERT: K 411 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9206 (mt) REVERT: K 507 MET cc_start: 0.9084 (mmt) cc_final: 0.7653 (ttm) REVERT: L 229 MET cc_start: 0.7399 (mpp) cc_final: 0.6912 (mpp) REVERT: L 323 MET cc_start: 0.9401 (ttm) cc_final: 0.8798 (tmm) REVERT: L 354 MET cc_start: 0.9220 (ppp) cc_final: 0.8755 (ppp) REVERT: L 411 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9219 (mt) REVERT: L 507 MET cc_start: 0.9105 (mmt) cc_final: 0.7686 (ttm) REVERT: M 229 MET cc_start: 0.7483 (mpp) cc_final: 0.6971 (mpp) REVERT: M 323 MET cc_start: 0.9400 (ttm) cc_final: 0.8787 (tmm) REVERT: M 354 MET cc_start: 0.9219 (ppp) cc_final: 0.8751 (ppp) REVERT: M 411 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9220 (mt) REVERT: M 507 MET cc_start: 0.9093 (mmt) cc_final: 0.7669 (ttm) REVERT: N 229 MET cc_start: 0.7479 (mpp) cc_final: 0.6966 (mpp) REVERT: N 323 MET cc_start: 0.9408 (ttm) cc_final: 0.8797 (tmm) REVERT: N 354 MET cc_start: 0.9217 (ppp) cc_final: 0.8748 (ppp) REVERT: N 411 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9216 (mt) REVERT: N 507 MET cc_start: 0.9078 (mmt) cc_final: 0.7675 (ttm) REVERT: O 229 MET cc_start: 0.7399 (mpp) cc_final: 0.6912 (mpp) REVERT: O 323 MET cc_start: 0.9401 (ttm) cc_final: 0.8798 (tmm) REVERT: O 354 MET cc_start: 0.9220 (ppp) cc_final: 0.8755 (ppp) REVERT: O 411 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9219 (mt) REVERT: O 507 MET cc_start: 0.9105 (mmt) cc_final: 0.7686 (ttm) REVERT: P 229 MET cc_start: 0.7431 (mpp) cc_final: 0.6933 (mpp) REVERT: P 323 MET cc_start: 0.9376 (ttm) cc_final: 0.8772 (tmm) REVERT: P 354 MET cc_start: 0.9215 (ppp) cc_final: 0.8727 (ppp) REVERT: P 411 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9215 (mt) REVERT: P 507 MET cc_start: 0.9080 (mmt) cc_final: 0.7658 (ttm) REVERT: Q 229 MET cc_start: 0.7411 (mpp) cc_final: 0.6922 (mpp) REVERT: Q 323 MET cc_start: 0.9381 (ttm) cc_final: 0.8784 (tmm) REVERT: Q 354 MET cc_start: 0.9183 (ppp) cc_final: 0.8679 (ppp) REVERT: Q 411 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9196 (mt) REVERT: Q 507 MET cc_start: 0.9071 (mmt) cc_final: 0.7673 (ttm) REVERT: R 229 MET cc_start: 0.7477 (mpp) cc_final: 0.6966 (mpp) REVERT: R 323 MET cc_start: 0.9408 (ttm) cc_final: 0.8801 (tmm) REVERT: R 354 MET cc_start: 0.9205 (ppp) cc_final: 0.8747 (ppp) REVERT: R 411 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9230 (mt) REVERT: R 507 MET cc_start: 0.9106 (mmt) cc_final: 0.7678 (ttm) REVERT: S 229 MET cc_start: 0.7507 (mpp) cc_final: 0.6981 (mpp) REVERT: S 323 MET cc_start: 0.9407 (ttm) cc_final: 0.8802 (tmm) REVERT: S 354 MET cc_start: 0.9200 (ppp) cc_final: 0.8750 (ppp) REVERT: S 411 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9212 (mt) REVERT: S 507 MET cc_start: 0.9100 (mmt) cc_final: 0.7683 (ttm) REVERT: T 229 MET cc_start: 0.7479 (mpp) cc_final: 0.6966 (mpp) REVERT: T 323 MET cc_start: 0.9408 (ttm) cc_final: 0.8797 (tmm) REVERT: T 354 MET cc_start: 0.9217 (ppp) cc_final: 0.8748 (ppp) REVERT: T 411 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9216 (mt) REVERT: T 507 MET cc_start: 0.9078 (mmt) cc_final: 0.7675 (ttm) REVERT: V 229 MET cc_start: 0.7483 (mpp) cc_final: 0.6971 (mpp) REVERT: V 323 MET cc_start: 0.9400 (ttm) cc_final: 0.8787 (tmm) REVERT: V 354 MET cc_start: 0.9219 (ppp) cc_final: 0.8751 (ppp) REVERT: V 411 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9220 (mt) REVERT: V 507 MET cc_start: 0.9093 (mmt) cc_final: 0.7669 (ttm) REVERT: W 229 MET cc_start: 0.7507 (mpp) cc_final: 0.6981 (mpp) REVERT: W 323 MET cc_start: 0.9407 (ttm) cc_final: 0.8802 (tmm) REVERT: W 354 MET cc_start: 0.9200 (ppp) cc_final: 0.8750 (ppp) REVERT: W 411 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9212 (mt) REVERT: W 507 MET cc_start: 0.9100 (mmt) cc_final: 0.7683 (ttm) REVERT: X 229 MET cc_start: 0.7411 (mpp) cc_final: 0.6922 (mpp) REVERT: X 323 MET cc_start: 0.9381 (ttm) cc_final: 0.8784 (tmm) REVERT: X 354 MET cc_start: 0.9183 (ppp) cc_final: 0.8679 (ppp) REVERT: X 411 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9196 (mt) REVERT: X 507 MET cc_start: 0.9071 (mmt) cc_final: 0.7673 (ttm) REVERT: Y 229 MET cc_start: 0.7477 (mpp) cc_final: 0.6966 (mpp) REVERT: Y 323 MET cc_start: 0.9408 (ttm) cc_final: 0.8801 (tmm) REVERT: Y 354 MET cc_start: 0.9205 (ppp) cc_final: 0.8747 (ppp) REVERT: Y 411 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9230 (mt) REVERT: Y 507 MET cc_start: 0.9106 (mmt) cc_final: 0.7678 (ttm) outliers start: 240 outliers final: 96 residues processed: 774 average time/residue: 0.8197 time to fit residues: 1141.3045 Evaluate side-chains 672 residues out of total 11496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 552 time to evaluate : 8.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 596 MET Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 596 MET Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 596 MET Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 596 MET Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 596 MET Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 596 MET Chi-restraints excluded: chain G residue 46 MET Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 596 MET Chi-restraints excluded: chain H residue 46 MET Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 596 MET Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain I residue 252 VAL Chi-restraints excluded: chain I residue 411 LEU Chi-restraints excluded: chain I residue 596 MET Chi-restraints excluded: chain J residue 46 MET Chi-restraints excluded: chain J residue 60 ASN Chi-restraints excluded: chain J residue 252 VAL Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain J residue 596 MET Chi-restraints excluded: chain K residue 46 MET Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain K residue 596 MET Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 252 VAL Chi-restraints excluded: chain L residue 411 LEU Chi-restraints excluded: chain L residue 596 MET Chi-restraints excluded: chain M residue 46 MET Chi-restraints excluded: chain M residue 60 ASN Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 411 LEU Chi-restraints excluded: chain M residue 596 MET Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 252 VAL Chi-restraints excluded: chain N residue 411 LEU Chi-restraints excluded: chain N residue 596 MET Chi-restraints excluded: chain O residue 46 MET Chi-restraints excluded: chain O residue 60 ASN Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 411 LEU Chi-restraints excluded: chain O residue 596 MET Chi-restraints excluded: chain P residue 46 MET Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain P residue 411 LEU Chi-restraints excluded: chain P residue 596 MET Chi-restraints excluded: chain Q residue 46 MET Chi-restraints excluded: chain Q residue 60 ASN Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain Q residue 411 LEU Chi-restraints excluded: chain Q residue 596 MET Chi-restraints excluded: chain R residue 46 MET Chi-restraints excluded: chain R residue 60 ASN Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 596 MET Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 60 ASN Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain S residue 411 LEU Chi-restraints excluded: chain S residue 596 MET Chi-restraints excluded: chain T residue 46 MET Chi-restraints excluded: chain T residue 60 ASN Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain T residue 411 LEU Chi-restraints excluded: chain T residue 596 MET Chi-restraints excluded: chain V residue 46 MET Chi-restraints excluded: chain V residue 60 ASN Chi-restraints excluded: chain V residue 252 VAL Chi-restraints excluded: chain V residue 411 LEU Chi-restraints excluded: chain V residue 596 MET Chi-restraints excluded: chain W residue 46 MET Chi-restraints excluded: chain W residue 60 ASN Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain W residue 411 LEU Chi-restraints excluded: chain W residue 596 MET Chi-restraints excluded: chain X residue 46 MET Chi-restraints excluded: chain X residue 60 ASN Chi-restraints excluded: chain X residue 252 VAL Chi-restraints excluded: chain X residue 411 LEU Chi-restraints excluded: chain X residue 596 MET Chi-restraints excluded: chain Y residue 46 MET Chi-restraints excluded: chain Y residue 60 ASN Chi-restraints excluded: chain Y residue 252 VAL Chi-restraints excluded: chain Y residue 411 LEU Chi-restraints excluded: chain Y residue 596 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 1101 optimal weight: 40.0000 chunk 750 optimal weight: 9.9990 chunk 19 optimal weight: 40.0000 chunk 984 optimal weight: 20.0000 chunk 545 optimal weight: 40.0000 chunk 1128 optimal weight: 20.0000 chunk 914 optimal weight: 8.9990 chunk 1 optimal weight: 30.0000 chunk 675 optimal weight: 10.0000 chunk 1186 optimal weight: 4.9990 chunk 333 optimal weight: 0.7980 overall best weight: 6.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 109440 Z= 0.195 Angle : 0.532 8.118 148968 Z= 0.273 Chirality : 0.041 0.140 16680 Planarity : 0.004 0.038 19632 Dihedral : 4.269 37.929 15264 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.04 % Allowed : 16.28 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.07), residues: 13608 helix: 1.79 (0.08), residues: 4680 sheet: 1.05 (0.09), residues: 3192 loop : 0.86 (0.08), residues: 5736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP T 554 HIS 0.003 0.001 HIS X 538 PHE 0.011 0.001 PHE M 157 TYR 0.011 0.001 TYR S 309 ARG 0.003 0.000 ARG X 366 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27216 Ramachandran restraints generated. 13608 Oldfield, 0 Emsley, 13608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27216 Ramachandran restraints generated. 13608 Oldfield, 0 Emsley, 13608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 11496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 552 time to evaluate : 9.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7522 (mpp) cc_final: 0.7099 (mpp) REVERT: A 323 MET cc_start: 0.9395 (ttm) cc_final: 0.8838 (tmm) REVERT: A 354 MET cc_start: 0.9243 (ppp) cc_final: 0.8830 (ppp) REVERT: A 411 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9199 (mt) REVERT: B 229 MET cc_start: 0.7533 (mpp) cc_final: 0.7108 (mpp) REVERT: B 323 MET cc_start: 0.9377 (ttm) cc_final: 0.8825 (tmm) REVERT: B 354 MET cc_start: 0.9204 (ppp) cc_final: 0.8754 (ppp) REVERT: B 411 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9174 (mt) REVERT: C 229 MET cc_start: 0.7551 (mpp) cc_final: 0.7118 (mpp) REVERT: C 323 MET cc_start: 0.9373 (ttm) cc_final: 0.8815 (tmm) REVERT: C 354 MET cc_start: 0.9238 (ppp) cc_final: 0.8800 (ppp) REVERT: C 411 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9196 (mt) REVERT: D 229 MET cc_start: 0.7590 (mpp) cc_final: 0.7145 (mpp) REVERT: D 323 MET cc_start: 0.9399 (ttm) cc_final: 0.8839 (tmm) REVERT: D 354 MET cc_start: 0.9228 (ppp) cc_final: 0.8820 (ppp) REVERT: D 411 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9211 (mt) REVERT: E 229 MET cc_start: 0.7611 (mpp) cc_final: 0.7157 (mpp) REVERT: E 323 MET cc_start: 0.9398 (ttm) cc_final: 0.8841 (tmm) REVERT: E 354 MET cc_start: 0.9221 (ppp) cc_final: 0.8820 (ppp) REVERT: E 411 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9192 (mt) REVERT: F 229 MET cc_start: 0.7591 (mpp) cc_final: 0.7147 (mpp) REVERT: F 323 MET cc_start: 0.9393 (ttm) cc_final: 0.8827 (tmm) REVERT: F 354 MET cc_start: 0.9241 (ppp) cc_final: 0.8825 (ppp) REVERT: F 411 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9204 (mt) REVERT: G 229 MET cc_start: 0.7590 (mpp) cc_final: 0.7144 (mpp) REVERT: G 323 MET cc_start: 0.9401 (ttm) cc_final: 0.8837 (tmm) REVERT: G 354 MET cc_start: 0.9239 (ppp) cc_final: 0.8821 (ppp) REVERT: G 411 LEU cc_start: 0.9628 (OUTLIER) cc_final: 0.9195 (mt) REVERT: H 229 MET cc_start: 0.7598 (mpp) cc_final: 0.7152 (mpp) REVERT: H 323 MET cc_start: 0.9389 (ttm) cc_final: 0.8827 (tmm) REVERT: H 341 LEU cc_start: 0.9876 (OUTLIER) cc_final: 0.9676 (pp) REVERT: H 354 MET cc_start: 0.9248 (ppp) cc_final: 0.8830 (ppp) REVERT: H 411 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9188 (mt) REVERT: I 229 MET cc_start: 0.7551 (mpp) cc_final: 0.7118 (mpp) REVERT: I 323 MET cc_start: 0.9373 (ttm) cc_final: 0.8815 (tmm) REVERT: I 354 MET cc_start: 0.9238 (ppp) cc_final: 0.8800 (ppp) REVERT: I 411 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9196 (mt) REVERT: J 229 MET cc_start: 0.7598 (mpp) cc_final: 0.7152 (mpp) REVERT: J 323 MET cc_start: 0.9389 (ttm) cc_final: 0.8827 (tmm) REVERT: J 341 LEU cc_start: 0.9876 (OUTLIER) cc_final: 0.9676 (pp) REVERT: J 354 MET cc_start: 0.9248 (ppp) cc_final: 0.8830 (ppp) REVERT: J 411 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9188 (mt) REVERT: K 229 MET cc_start: 0.7598 (mpp) cc_final: 0.7152 (mpp) REVERT: K 323 MET cc_start: 0.9389 (ttm) cc_final: 0.8827 (tmm) REVERT: K 341 LEU cc_start: 0.9876 (OUTLIER) cc_final: 0.9676 (pp) REVERT: K 354 MET cc_start: 0.9248 (ppp) cc_final: 0.8830 (ppp) REVERT: K 411 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9188 (mt) REVERT: L 229 MET cc_start: 0.7522 (mpp) cc_final: 0.7099 (mpp) REVERT: L 323 MET cc_start: 0.9395 (ttm) cc_final: 0.8838 (tmm) REVERT: L 354 MET cc_start: 0.9244 (ppp) cc_final: 0.8831 (ppp) REVERT: L 411 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9199 (mt) REVERT: M 229 MET cc_start: 0.7591 (mpp) cc_final: 0.7147 (mpp) REVERT: M 323 MET cc_start: 0.9393 (ttm) cc_final: 0.8827 (tmm) REVERT: M 354 MET cc_start: 0.9241 (ppp) cc_final: 0.8824 (ppp) REVERT: M 411 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9204 (mt) REVERT: N 229 MET cc_start: 0.7590 (mpp) cc_final: 0.7144 (mpp) REVERT: N 323 MET cc_start: 0.9401 (ttm) cc_final: 0.8837 (tmm) REVERT: N 354 MET cc_start: 0.9239 (ppp) cc_final: 0.8821 (ppp) REVERT: N 411 LEU cc_start: 0.9628 (OUTLIER) cc_final: 0.9196 (mt) REVERT: O 229 MET cc_start: 0.7522 (mpp) cc_final: 0.7099 (mpp) REVERT: O 323 MET cc_start: 0.9395 (ttm) cc_final: 0.8838 (tmm) REVERT: O 354 MET cc_start: 0.9244 (ppp) cc_final: 0.8830 (ppp) REVERT: O 411 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9199 (mt) REVERT: P 229 MET cc_start: 0.7551 (mpp) cc_final: 0.7118 (mpp) REVERT: P 323 MET cc_start: 0.9373 (ttm) cc_final: 0.8815 (tmm) REVERT: P 354 MET cc_start: 0.9238 (ppp) cc_final: 0.8800 (ppp) REVERT: P 411 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9196 (mt) REVERT: Q 229 MET cc_start: 0.7533 (mpp) cc_final: 0.7108 (mpp) REVERT: Q 323 MET cc_start: 0.9377 (ttm) cc_final: 0.8825 (tmm) REVERT: Q 354 MET cc_start: 0.9204 (ppp) cc_final: 0.8754 (ppp) REVERT: Q 411 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9174 (mt) REVERT: R 229 MET cc_start: 0.7590 (mpp) cc_final: 0.7145 (mpp) REVERT: R 323 MET cc_start: 0.9399 (ttm) cc_final: 0.8839 (tmm) REVERT: R 354 MET cc_start: 0.9228 (ppp) cc_final: 0.8820 (ppp) REVERT: R 411 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9211 (mt) REVERT: S 229 MET cc_start: 0.7611 (mpp) cc_final: 0.7157 (mpp) REVERT: S 323 MET cc_start: 0.9398 (ttm) cc_final: 0.8841 (tmm) REVERT: S 354 MET cc_start: 0.9221 (ppp) cc_final: 0.8820 (ppp) REVERT: S 411 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9192 (mt) REVERT: T 229 MET cc_start: 0.7590 (mpp) cc_final: 0.7144 (mpp) REVERT: T 323 MET cc_start: 0.9401 (ttm) cc_final: 0.8837 (tmm) REVERT: T 354 MET cc_start: 0.9239 (ppp) cc_final: 0.8821 (ppp) REVERT: T 411 LEU cc_start: 0.9628 (OUTLIER) cc_final: 0.9196 (mt) REVERT: V 229 MET cc_start: 0.7591 (mpp) cc_final: 0.7147 (mpp) REVERT: V 323 MET cc_start: 0.9393 (ttm) cc_final: 0.8827 (tmm) REVERT: V 354 MET cc_start: 0.9241 (ppp) cc_final: 0.8824 (ppp) REVERT: V 411 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9204 (mt) REVERT: W 229 MET cc_start: 0.7611 (mpp) cc_final: 0.7157 (mpp) REVERT: W 323 MET cc_start: 0.9398 (ttm) cc_final: 0.8841 (tmm) REVERT: W 354 MET cc_start: 0.9221 (ppp) cc_final: 0.8820 (ppp) REVERT: W 411 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9192 (mt) REVERT: X 229 MET cc_start: 0.7533 (mpp) cc_final: 0.7108 (mpp) REVERT: X 323 MET cc_start: 0.9377 (ttm) cc_final: 0.8825 (tmm) REVERT: X 354 MET cc_start: 0.9204 (ppp) cc_final: 0.8754 (ppp) REVERT: X 411 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9174 (mt) REVERT: Y 229 MET cc_start: 0.7590 (mpp) cc_final: 0.7145 (mpp) REVERT: Y 323 MET cc_start: 0.9399 (ttm) cc_final: 0.8839 (tmm) REVERT: Y 354 MET cc_start: 0.9228 (ppp) cc_final: 0.8820 (ppp) REVERT: Y 411 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9211 (mt) outliers start: 120 outliers final: 48 residues processed: 624 average time/residue: 0.8238 time to fit residues: 929.3128 Evaluate side-chains 627 residues out of total 11496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 552 time to evaluate : 8.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain G residue 46 MET Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain H residue 46 MET Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 341 LEU Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain I residue 411 LEU Chi-restraints excluded: chain J residue 46 MET Chi-restraints excluded: chain J residue 60 ASN Chi-restraints excluded: chain J residue 341 LEU Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain K residue 46 MET Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain K residue 341 LEU Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 411 LEU Chi-restraints excluded: chain M residue 46 MET Chi-restraints excluded: chain M residue 60 ASN Chi-restraints excluded: chain M residue 411 LEU Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 411 LEU Chi-restraints excluded: chain O residue 46 MET Chi-restraints excluded: chain O residue 60 ASN Chi-restraints excluded: chain O residue 411 LEU Chi-restraints excluded: chain P residue 46 MET Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain P residue 411 LEU Chi-restraints excluded: chain Q residue 46 MET Chi-restraints excluded: chain Q residue 60 ASN Chi-restraints excluded: chain Q residue 411 LEU Chi-restraints excluded: chain R residue 46 MET Chi-restraints excluded: chain R residue 60 ASN Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 60 ASN Chi-restraints excluded: chain S residue 411 LEU Chi-restraints excluded: chain T residue 46 MET Chi-restraints excluded: chain T residue 60 ASN Chi-restraints excluded: chain T residue 411 LEU Chi-restraints excluded: chain V residue 46 MET Chi-restraints excluded: chain V residue 60 ASN Chi-restraints excluded: chain V residue 411 LEU Chi-restraints excluded: chain W residue 46 MET Chi-restraints excluded: chain W residue 60 ASN Chi-restraints excluded: chain W residue 411 LEU Chi-restraints excluded: chain X residue 46 MET Chi-restraints excluded: chain X residue 60 ASN Chi-restraints excluded: chain X residue 411 LEU Chi-restraints excluded: chain Y residue 46 MET Chi-restraints excluded: chain Y residue 60 ASN Chi-restraints excluded: chain Y residue 411 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 444 optimal weight: 10.0000 chunk 1190 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 776 optimal weight: 6.9990 chunk 326 optimal weight: 9.9990 chunk 1323 optimal weight: 20.0000 chunk 1098 optimal weight: 0.0370 chunk 612 optimal weight: 30.0000 chunk 110 optimal weight: 0.0570 chunk 437 optimal weight: 2.9990 chunk 694 optimal weight: 6.9990 overall best weight: 3.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 109440 Z= 0.144 Angle : 0.570 16.083 148968 Z= 0.281 Chirality : 0.042 0.141 16680 Planarity : 0.003 0.039 19632 Dihedral : 4.099 38.225 15264 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.33 % Allowed : 16.41 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.07), residues: 13608 helix: 1.83 (0.08), residues: 4704 sheet: 1.17 (0.09), residues: 3192 loop : 0.88 (0.09), residues: 5712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 554 HIS 0.003 0.000 HIS G 538 PHE 0.016 0.001 PHE O 225 TYR 0.011 0.001 TYR I 309 ARG 0.003 0.000 ARG B 366 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27216 Ramachandran restraints generated. 13608 Oldfield, 0 Emsley, 13608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27216 Ramachandran restraints generated. 13608 Oldfield, 0 Emsley, 13608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 11496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 576 time to evaluate : 9.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7252 (mpt) REVERT: A 323 MET cc_start: 0.9357 (ttm) cc_final: 0.8799 (tmm) REVERT: A 354 MET cc_start: 0.9250 (ppp) cc_final: 0.8820 (ppp) REVERT: A 411 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9144 (mt) REVERT: A 507 MET cc_start: 0.9260 (mmm) cc_final: 0.8923 (mtt) REVERT: B 229 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7262 (mpt) REVERT: B 323 MET cc_start: 0.9339 (ttm) cc_final: 0.8787 (tmm) REVERT: B 354 MET cc_start: 0.9209 (ppp) cc_final: 0.8744 (ppp) REVERT: B 411 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9128 (mt) REVERT: B 507 MET cc_start: 0.9262 (mmm) cc_final: 0.8927 (mtt) REVERT: C 229 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7271 (mpt) REVERT: C 323 MET cc_start: 0.9335 (ttm) cc_final: 0.8775 (tmm) REVERT: C 354 MET cc_start: 0.9244 (ppp) cc_final: 0.8792 (ppp) REVERT: C 411 LEU cc_start: 0.9612 (OUTLIER) cc_final: 0.9146 (mt) REVERT: C 507 MET cc_start: 0.9268 (mmm) cc_final: 0.8925 (mtt) REVERT: D 229 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7302 (mpt) REVERT: D 323 MET cc_start: 0.9359 (ttm) cc_final: 0.8800 (tmm) REVERT: D 354 MET cc_start: 0.9235 (ppp) cc_final: 0.8810 (ppp) REVERT: D 411 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9153 (mt) REVERT: D 507 MET cc_start: 0.9259 (mmm) cc_final: 0.8919 (mtt) REVERT: E 229 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7318 (mpt) REVERT: E 323 MET cc_start: 0.9360 (ttm) cc_final: 0.8803 (tmm) REVERT: E 354 MET cc_start: 0.9225 (ppp) cc_final: 0.8811 (ppp) REVERT: E 411 LEU cc_start: 0.9621 (OUTLIER) cc_final: 0.9138 (mt) REVERT: E 507 MET cc_start: 0.9267 (mmm) cc_final: 0.8924 (mtt) REVERT: F 229 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7303 (mpt) REVERT: F 323 MET cc_start: 0.9355 (ttm) cc_final: 0.8789 (tmm) REVERT: F 354 MET cc_start: 0.9249 (ppp) cc_final: 0.8818 (ppp) REVERT: F 411 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9148 (mt) REVERT: F 507 MET cc_start: 0.9257 (mmm) cc_final: 0.8916 (mtt) REVERT: G 229 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7300 (mpt) REVERT: G 323 MET cc_start: 0.9363 (ttm) cc_final: 0.8798 (tmm) REVERT: G 354 MET cc_start: 0.9246 (ppp) cc_final: 0.8812 (ppp) REVERT: G 411 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9143 (mt) REVERT: G 507 MET cc_start: 0.9253 (mmm) cc_final: 0.8912 (mtt) REVERT: H 229 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7326 (mpt) REVERT: H 323 MET cc_start: 0.9352 (ttm) cc_final: 0.8791 (tmm) REVERT: H 341 LEU cc_start: 0.9874 (OUTLIER) cc_final: 0.9658 (pp) REVERT: H 354 MET cc_start: 0.9255 (ppp) cc_final: 0.8824 (ppp) REVERT: H 411 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9136 (mt) REVERT: H 507 MET cc_start: 0.9276 (mmm) cc_final: 0.8927 (mtt) REVERT: I 229 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7271 (mpt) REVERT: I 323 MET cc_start: 0.9335 (ttm) cc_final: 0.8776 (tmm) REVERT: I 354 MET cc_start: 0.9244 (ppp) cc_final: 0.8792 (ppp) REVERT: I 411 LEU cc_start: 0.9612 (OUTLIER) cc_final: 0.9146 (mt) REVERT: I 507 MET cc_start: 0.9268 (mmm) cc_final: 0.8925 (mtt) REVERT: J 229 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7326 (mpt) REVERT: J 323 MET cc_start: 0.9352 (ttm) cc_final: 0.8791 (tmm) REVERT: J 341 LEU cc_start: 0.9874 (OUTLIER) cc_final: 0.9658 (pp) REVERT: J 354 MET cc_start: 0.9255 (ppp) cc_final: 0.8824 (ppp) REVERT: J 411 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9136 (mt) REVERT: J 507 MET cc_start: 0.9276 (mmm) cc_final: 0.8927 (mtt) REVERT: K 229 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7326 (mpt) REVERT: K 323 MET cc_start: 0.9352 (ttm) cc_final: 0.8791 (tmm) REVERT: K 341 LEU cc_start: 0.9874 (OUTLIER) cc_final: 0.9658 (pp) REVERT: K 354 MET cc_start: 0.9255 (ppp) cc_final: 0.8824 (ppp) REVERT: K 411 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9136 (mt) REVERT: K 507 MET cc_start: 0.9276 (mmm) cc_final: 0.8927 (mtt) REVERT: L 229 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7252 (mpt) REVERT: L 323 MET cc_start: 0.9357 (ttm) cc_final: 0.8799 (tmm) REVERT: L 354 MET cc_start: 0.9250 (ppp) cc_final: 0.8820 (ppp) REVERT: L 411 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9144 (mt) REVERT: L 507 MET cc_start: 0.9260 (mmm) cc_final: 0.8923 (mtt) REVERT: M 229 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7303 (mpt) REVERT: M 323 MET cc_start: 0.9355 (ttm) cc_final: 0.8789 (tmm) REVERT: M 354 MET cc_start: 0.9249 (ppp) cc_final: 0.8818 (ppp) REVERT: M 411 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9148 (mt) REVERT: M 507 MET cc_start: 0.9257 (mmm) cc_final: 0.8916 (mtt) REVERT: N 229 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7300 (mpt) REVERT: N 323 MET cc_start: 0.9363 (ttm) cc_final: 0.8798 (tmm) REVERT: N 354 MET cc_start: 0.9246 (ppp) cc_final: 0.8812 (ppp) REVERT: N 411 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9143 (mt) REVERT: N 507 MET cc_start: 0.9253 (mmm) cc_final: 0.8912 (mtt) REVERT: O 229 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7252 (mpt) REVERT: O 323 MET cc_start: 0.9357 (ttm) cc_final: 0.8799 (tmm) REVERT: O 354 MET cc_start: 0.9250 (ppp) cc_final: 0.8820 (ppp) REVERT: O 411 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9144 (mt) REVERT: O 507 MET cc_start: 0.9260 (mmm) cc_final: 0.8923 (mtt) REVERT: P 229 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7271 (mpt) REVERT: P 323 MET cc_start: 0.9335 (ttm) cc_final: 0.8776 (tmm) REVERT: P 354 MET cc_start: 0.9244 (ppp) cc_final: 0.8792 (ppp) REVERT: P 411 LEU cc_start: 0.9612 (OUTLIER) cc_final: 0.9146 (mt) REVERT: P 507 MET cc_start: 0.9268 (mmm) cc_final: 0.8925 (mtt) REVERT: Q 229 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7262 (mpt) REVERT: Q 323 MET cc_start: 0.9339 (ttm) cc_final: 0.8787 (tmm) REVERT: Q 354 MET cc_start: 0.9209 (ppp) cc_final: 0.8744 (ppp) REVERT: Q 411 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9128 (mt) REVERT: Q 507 MET cc_start: 0.9262 (mmm) cc_final: 0.8927 (mtt) REVERT: R 229 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7302 (mpt) REVERT: R 323 MET cc_start: 0.9359 (ttm) cc_final: 0.8800 (tmm) REVERT: R 354 MET cc_start: 0.9235 (ppp) cc_final: 0.8810 (ppp) REVERT: R 411 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9153 (mt) REVERT: R 507 MET cc_start: 0.9260 (mmm) cc_final: 0.8919 (mtt) REVERT: S 229 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7318 (mpt) REVERT: S 323 MET cc_start: 0.9359 (ttm) cc_final: 0.8803 (tmm) REVERT: S 354 MET cc_start: 0.9225 (ppp) cc_final: 0.8811 (ppp) REVERT: S 411 LEU cc_start: 0.9621 (OUTLIER) cc_final: 0.9137 (mt) REVERT: S 507 MET cc_start: 0.9267 (mmm) cc_final: 0.8924 (mtt) REVERT: T 229 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.7300 (mpt) REVERT: T 323 MET cc_start: 0.9363 (ttm) cc_final: 0.8798 (tmm) REVERT: T 354 MET cc_start: 0.9246 (ppp) cc_final: 0.8812 (ppp) REVERT: T 411 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9143 (mt) REVERT: T 507 MET cc_start: 0.9253 (mmm) cc_final: 0.8912 (mtt) REVERT: V 229 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7303 (mpt) REVERT: V 323 MET cc_start: 0.9355 (ttm) cc_final: 0.8789 (tmm) REVERT: V 354 MET cc_start: 0.9249 (ppp) cc_final: 0.8818 (ppp) REVERT: V 411 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9148 (mt) REVERT: V 507 MET cc_start: 0.9257 (mmm) cc_final: 0.8916 (mtt) REVERT: W 229 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7318 (mpt) REVERT: W 323 MET cc_start: 0.9360 (ttm) cc_final: 0.8803 (tmm) REVERT: W 354 MET cc_start: 0.9225 (ppp) cc_final: 0.8811 (ppp) REVERT: W 411 LEU cc_start: 0.9621 (OUTLIER) cc_final: 0.9137 (mt) REVERT: W 507 MET cc_start: 0.9267 (mmm) cc_final: 0.8924 (mtt) REVERT: X 229 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7262 (mpt) REVERT: X 323 MET cc_start: 0.9339 (ttm) cc_final: 0.8787 (tmm) REVERT: X 354 MET cc_start: 0.9209 (ppp) cc_final: 0.8744 (ppp) REVERT: X 411 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9128 (mt) REVERT: X 507 MET cc_start: 0.9262 (mmm) cc_final: 0.8927 (mtt) REVERT: Y 229 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7302 (mpt) REVERT: Y 323 MET cc_start: 0.9359 (ttm) cc_final: 0.8800 (tmm) REVERT: Y 354 MET cc_start: 0.9235 (ppp) cc_final: 0.8810 (ppp) REVERT: Y 411 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9153 (mt) REVERT: Y 507 MET cc_start: 0.9259 (mmm) cc_final: 0.8919 (mtt) outliers start: 153 outliers final: 72 residues processed: 651 average time/residue: 0.8039 time to fit residues: 947.5627 Evaluate side-chains 675 residues out of total 11496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 552 time to evaluate : 9.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 596 MET Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 596 MET Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 596 MET Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 229 MET Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 596 MET Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 229 MET Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 596 MET Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 229 MET Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 596 MET Chi-restraints excluded: chain G residue 46 MET Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 596 MET Chi-restraints excluded: chain H residue 46 MET Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 341 LEU Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain H residue 596 MET Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 411 LEU Chi-restraints excluded: chain I residue 596 MET Chi-restraints excluded: chain J residue 46 MET Chi-restraints excluded: chain J residue 60 ASN Chi-restraints excluded: chain J residue 229 MET Chi-restraints excluded: chain J residue 341 LEU Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain J residue 596 MET Chi-restraints excluded: chain K residue 46 MET Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain K residue 229 MET Chi-restraints excluded: chain K residue 341 LEU Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain K residue 596 MET Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 229 MET Chi-restraints excluded: chain L residue 411 LEU Chi-restraints excluded: chain L residue 596 MET Chi-restraints excluded: chain M residue 46 MET Chi-restraints excluded: chain M residue 60 ASN Chi-restraints excluded: chain M residue 229 MET Chi-restraints excluded: chain M residue 411 LEU Chi-restraints excluded: chain M residue 596 MET Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 229 MET Chi-restraints excluded: chain N residue 411 LEU Chi-restraints excluded: chain N residue 596 MET Chi-restraints excluded: chain O residue 46 MET Chi-restraints excluded: chain O residue 60 ASN Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain O residue 411 LEU Chi-restraints excluded: chain O residue 596 MET Chi-restraints excluded: chain P residue 46 MET Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain P residue 229 MET Chi-restraints excluded: chain P residue 411 LEU Chi-restraints excluded: chain P residue 596 MET Chi-restraints excluded: chain Q residue 46 MET Chi-restraints excluded: chain Q residue 60 ASN Chi-restraints excluded: chain Q residue 229 MET Chi-restraints excluded: chain Q residue 411 LEU Chi-restraints excluded: chain Q residue 596 MET Chi-restraints excluded: chain R residue 46 MET Chi-restraints excluded: chain R residue 60 ASN Chi-restraints excluded: chain R residue 229 MET Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 596 MET Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 60 ASN Chi-restraints excluded: chain S residue 229 MET Chi-restraints excluded: chain S residue 411 LEU Chi-restraints excluded: chain S residue 596 MET Chi-restraints excluded: chain T residue 46 MET Chi-restraints excluded: chain T residue 60 ASN Chi-restraints excluded: chain T residue 229 MET Chi-restraints excluded: chain T residue 411 LEU Chi-restraints excluded: chain T residue 596 MET Chi-restraints excluded: chain V residue 46 MET Chi-restraints excluded: chain V residue 60 ASN Chi-restraints excluded: chain V residue 229 MET Chi-restraints excluded: chain V residue 411 LEU Chi-restraints excluded: chain V residue 596 MET Chi-restraints excluded: chain W residue 46 MET Chi-restraints excluded: chain W residue 60 ASN Chi-restraints excluded: chain W residue 229 MET Chi-restraints excluded: chain W residue 411 LEU Chi-restraints excluded: chain W residue 596 MET Chi-restraints excluded: chain X residue 46 MET Chi-restraints excluded: chain X residue 60 ASN Chi-restraints excluded: chain X residue 229 MET Chi-restraints excluded: chain X residue 411 LEU Chi-restraints excluded: chain X residue 596 MET Chi-restraints excluded: chain Y residue 46 MET Chi-restraints excluded: chain Y residue 60 ASN Chi-restraints excluded: chain Y residue 229 MET Chi-restraints excluded: chain Y residue 411 LEU Chi-restraints excluded: chain Y residue 596 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 1276 optimal weight: 0.4980 chunk 149 optimal weight: 10.0000 chunk 754 optimal weight: 0.4980 chunk 966 optimal weight: 40.0000 chunk 748 optimal weight: 20.0000 chunk 1114 optimal weight: 5.9990 chunk 739 optimal weight: 30.0000 chunk 1318 optimal weight: 6.9990 chunk 825 optimal weight: 40.0000 chunk 803 optimal weight: 20.0000 chunk 608 optimal weight: 2.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 393 GLN ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 393 GLN ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 GLN ** G 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 GLN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 393 GLN ** I 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 393 GLN ** J 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 393 GLN ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 393 GLN ** L 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 393 GLN ** M 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 393 GLN ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 393 GLN ** O 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 393 GLN ** P 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 393 GLN ** Q 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 393 GLN ** R 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 393 GLN ** X 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 393 GLN ** Y 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 393 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 109440 Z= 0.150 Angle : 0.573 13.083 148968 Z= 0.284 Chirality : 0.041 0.163 16680 Planarity : 0.003 0.038 19632 Dihedral : 4.045 38.172 15264 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.12 % Allowed : 17.07 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.07), residues: 13608 helix: 1.78 (0.08), residues: 4704 sheet: 1.09 (0.09), residues: 3240 loop : 1.01 (0.09), residues: 5664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP X 554 HIS 0.002 0.000 HIS X 538 PHE 0.017 0.001 PHE L 225 TYR 0.009 0.001 TYR C 309 ARG 0.003 0.000 ARG L 533 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27216 Ramachandran restraints generated. 13608 Oldfield, 0 Emsley, 13608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27216 Ramachandran restraints generated. 13608 Oldfield, 0 Emsley, 13608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 11496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 552 time to evaluate : 9.393 Fit side-chains REVERT: A 46 MET cc_start: 0.9339 (OUTLIER) cc_final: 0.9074 (pmm) REVERT: A 323 MET cc_start: 0.9344 (ttm) cc_final: 0.8738 (tmm) REVERT: A 354 MET cc_start: 0.9255 (ppp) cc_final: 0.8925 (ppp) REVERT: A 411 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.9145 (mt) REVERT: A 507 MET cc_start: 0.9234 (mmm) cc_final: 0.8811 (mtm) REVERT: B 46 MET cc_start: 0.9353 (OUTLIER) cc_final: 0.9081 (pmm) REVERT: B 323 MET cc_start: 0.9325 (ttm) cc_final: 0.8724 (tmm) REVERT: B 354 MET cc_start: 0.9220 (ppp) cc_final: 0.8863 (ppp) REVERT: B 411 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9129 (mt) REVERT: B 507 MET cc_start: 0.9235 (mmm) cc_final: 0.8817 (mtm) REVERT: C 46 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.9085 (pmm) REVERT: C 323 MET cc_start: 0.9321 (ttm) cc_final: 0.8712 (tmm) REVERT: C 354 MET cc_start: 0.9256 (ppp) cc_final: 0.8908 (ppp) REVERT: C 411 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9147 (mt) REVERT: C 507 MET cc_start: 0.9242 (mmm) cc_final: 0.8814 (mtm) REVERT: D 46 MET cc_start: 0.9328 (OUTLIER) cc_final: 0.9071 (pmm) REVERT: D 323 MET cc_start: 0.9347 (ttm) cc_final: 0.8740 (tmm) REVERT: D 354 MET cc_start: 0.9240 (ppp) cc_final: 0.8914 (ppp) REVERT: D 411 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9154 (mt) REVERT: D 507 MET cc_start: 0.9233 (mmm) cc_final: 0.8808 (mtm) REVERT: E 46 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.9076 (pmm) REVERT: E 323 MET cc_start: 0.9344 (ttm) cc_final: 0.8742 (tmm) REVERT: E 354 MET cc_start: 0.9231 (ppp) cc_final: 0.8915 (ppp) REVERT: E 411 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9138 (mt) REVERT: E 507 MET cc_start: 0.9240 (mmm) cc_final: 0.8813 (mtm) REVERT: F 46 MET cc_start: 0.9319 (OUTLIER) cc_final: 0.9078 (pmm) REVERT: F 323 MET cc_start: 0.9340 (ttm) cc_final: 0.8727 (tmm) REVERT: F 354 MET cc_start: 0.9257 (ppp) cc_final: 0.8927 (ppp) REVERT: F 411 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9149 (mt) REVERT: F 507 MET cc_start: 0.9231 (mmm) cc_final: 0.8805 (mtm) REVERT: G 46 MET cc_start: 0.9307 (OUTLIER) cc_final: 0.9083 (pmm) REVERT: G 323 MET cc_start: 0.9350 (ttm) cc_final: 0.8738 (tmm) REVERT: G 354 MET cc_start: 0.9253 (ppp) cc_final: 0.8921 (ppp) REVERT: G 411 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9143 (mt) REVERT: G 507 MET cc_start: 0.9226 (mmm) cc_final: 0.8803 (mtm) REVERT: H 46 MET cc_start: 0.9337 (OUTLIER) cc_final: 0.9070 (pmm) REVERT: H 323 MET cc_start: 0.9341 (ttm) cc_final: 0.8731 (tmm) REVERT: H 341 LEU cc_start: 0.9864 (OUTLIER) cc_final: 0.9660 (pp) REVERT: H 354 MET cc_start: 0.9264 (ppp) cc_final: 0.8932 (ppp) REVERT: H 411 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9138 (mt) REVERT: H 507 MET cc_start: 0.9247 (mmm) cc_final: 0.8816 (mtm) REVERT: I 46 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.9084 (pmm) REVERT: I 323 MET cc_start: 0.9321 (ttm) cc_final: 0.8712 (tmm) REVERT: I 354 MET cc_start: 0.9256 (ppp) cc_final: 0.8908 (ppp) REVERT: I 411 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9147 (mt) REVERT: I 507 MET cc_start: 0.9242 (mmm) cc_final: 0.8814 (mtm) REVERT: J 46 MET cc_start: 0.9337 (OUTLIER) cc_final: 0.9070 (pmm) REVERT: J 323 MET cc_start: 0.9341 (ttm) cc_final: 0.8731 (tmm) REVERT: J 341 LEU cc_start: 0.9864 (OUTLIER) cc_final: 0.9660 (pp) REVERT: J 354 MET cc_start: 0.9264 (ppp) cc_final: 0.8932 (ppp) REVERT: J 411 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9138 (mt) REVERT: J 507 MET cc_start: 0.9247 (mmm) cc_final: 0.8816 (mtm) REVERT: K 46 MET cc_start: 0.9337 (OUTLIER) cc_final: 0.9070 (pmm) REVERT: K 323 MET cc_start: 0.9341 (ttm) cc_final: 0.8731 (tmm) REVERT: K 341 LEU cc_start: 0.9864 (OUTLIER) cc_final: 0.9660 (pp) REVERT: K 354 MET cc_start: 0.9264 (ppp) cc_final: 0.8932 (ppp) REVERT: K 411 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9138 (mt) REVERT: K 507 MET cc_start: 0.9247 (mmm) cc_final: 0.8816 (mtm) REVERT: L 46 MET cc_start: 0.9339 (OUTLIER) cc_final: 0.9074 (pmm) REVERT: L 323 MET cc_start: 0.9344 (ttm) cc_final: 0.8738 (tmm) REVERT: L 354 MET cc_start: 0.9255 (ppp) cc_final: 0.8925 (ppp) REVERT: L 411 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9145 (mt) REVERT: L 507 MET cc_start: 0.9234 (mmm) cc_final: 0.8811 (mtm) REVERT: M 46 MET cc_start: 0.9319 (OUTLIER) cc_final: 0.9078 (pmm) REVERT: M 323 MET cc_start: 0.9340 (ttm) cc_final: 0.8727 (tmm) REVERT: M 354 MET cc_start: 0.9257 (ppp) cc_final: 0.8927 (ppp) REVERT: M 411 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9149 (mt) REVERT: M 507 MET cc_start: 0.9231 (mmm) cc_final: 0.8805 (mtm) REVERT: N 46 MET cc_start: 0.9307 (OUTLIER) cc_final: 0.9083 (pmm) REVERT: N 323 MET cc_start: 0.9350 (ttm) cc_final: 0.8738 (tmm) REVERT: N 354 MET cc_start: 0.9253 (ppp) cc_final: 0.8921 (ppp) REVERT: N 411 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9143 (mt) REVERT: N 507 MET cc_start: 0.9226 (mmm) cc_final: 0.8803 (mtm) REVERT: O 46 MET cc_start: 0.9339 (OUTLIER) cc_final: 0.9074 (pmm) REVERT: O 323 MET cc_start: 0.9344 (ttm) cc_final: 0.8738 (tmm) REVERT: O 354 MET cc_start: 0.9255 (ppp) cc_final: 0.8925 (ppp) REVERT: O 411 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9145 (mt) REVERT: O 507 MET cc_start: 0.9234 (mmm) cc_final: 0.8811 (mtm) REVERT: P 46 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.9084 (pmm) REVERT: P 323 MET cc_start: 0.9321 (ttm) cc_final: 0.8712 (tmm) REVERT: P 354 MET cc_start: 0.9256 (ppp) cc_final: 0.8908 (ppp) REVERT: P 411 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9147 (mt) REVERT: P 507 MET cc_start: 0.9242 (mmm) cc_final: 0.8814 (mtm) REVERT: Q 46 MET cc_start: 0.9353 (OUTLIER) cc_final: 0.9081 (pmm) REVERT: Q 323 MET cc_start: 0.9325 (ttm) cc_final: 0.8724 (tmm) REVERT: Q 354 MET cc_start: 0.9220 (ppp) cc_final: 0.8863 (ppp) REVERT: Q 411 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9129 (mt) REVERT: Q 507 MET cc_start: 0.9235 (mmm) cc_final: 0.8817 (mtm) REVERT: R 46 MET cc_start: 0.9328 (OUTLIER) cc_final: 0.9071 (pmm) REVERT: R 323 MET cc_start: 0.9347 (ttm) cc_final: 0.8740 (tmm) REVERT: R 354 MET cc_start: 0.9240 (ppp) cc_final: 0.8914 (ppp) REVERT: R 411 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9154 (mt) REVERT: R 507 MET cc_start: 0.9233 (mmm) cc_final: 0.8808 (mtm) REVERT: S 46 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.9076 (pmm) REVERT: S 323 MET cc_start: 0.9344 (ttm) cc_final: 0.8742 (tmm) REVERT: S 354 MET cc_start: 0.9231 (ppp) cc_final: 0.8915 (ppp) REVERT: S 411 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9138 (mt) REVERT: S 507 MET cc_start: 0.9240 (mmm) cc_final: 0.8813 (mtm) REVERT: T 46 MET cc_start: 0.9307 (OUTLIER) cc_final: 0.9083 (pmm) REVERT: T 323 MET cc_start: 0.9350 (ttm) cc_final: 0.8738 (tmm) REVERT: T 354 MET cc_start: 0.9253 (ppp) cc_final: 0.8921 (ppp) REVERT: T 411 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9143 (mt) REVERT: T 507 MET cc_start: 0.9226 (mmm) cc_final: 0.8803 (mtm) REVERT: V 46 MET cc_start: 0.9319 (OUTLIER) cc_final: 0.9078 (pmm) REVERT: V 323 MET cc_start: 0.9340 (ttm) cc_final: 0.8727 (tmm) REVERT: V 354 MET cc_start: 0.9257 (ppp) cc_final: 0.8927 (ppp) REVERT: V 411 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9149 (mt) REVERT: V 507 MET cc_start: 0.9231 (mmm) cc_final: 0.8805 (mtm) REVERT: W 46 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.9076 (pmm) REVERT: W 323 MET cc_start: 0.9344 (ttm) cc_final: 0.8742 (tmm) REVERT: W 354 MET cc_start: 0.9231 (ppp) cc_final: 0.8915 (ppp) REVERT: W 411 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9138 (mt) REVERT: W 507 MET cc_start: 0.9240 (mmm) cc_final: 0.8813 (mtm) REVERT: X 46 MET cc_start: 0.9353 (OUTLIER) cc_final: 0.9081 (pmm) REVERT: X 323 MET cc_start: 0.9325 (ttm) cc_final: 0.8724 (tmm) REVERT: X 354 MET cc_start: 0.9220 (ppp) cc_final: 0.8864 (ppp) REVERT: X 411 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9129 (mt) REVERT: X 507 MET cc_start: 0.9235 (mmm) cc_final: 0.8817 (mtm) REVERT: Y 46 MET cc_start: 0.9328 (OUTLIER) cc_final: 0.9071 (pmm) REVERT: Y 323 MET cc_start: 0.9347 (ttm) cc_final: 0.8740 (tmm) REVERT: Y 354 MET cc_start: 0.9240 (ppp) cc_final: 0.8914 (ppp) REVERT: Y 411 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9154 (mt) REVERT: Y 507 MET cc_start: 0.9233 (mmm) cc_final: 0.8808 (mtm) outliers start: 129 outliers final: 24 residues processed: 627 average time/residue: 0.8171 time to fit residues: 930.2591 Evaluate side-chains 603 residues out of total 11496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 528 time to evaluate : 8.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain G residue 46 MET Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain H residue 46 MET Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 341 LEU Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain I residue 411 LEU Chi-restraints excluded: chain J residue 46 MET Chi-restraints excluded: chain J residue 60 ASN Chi-restraints excluded: chain J residue 341 LEU Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain K residue 46 MET Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain K residue 341 LEU Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 411 LEU Chi-restraints excluded: chain M residue 46 MET Chi-restraints excluded: chain M residue 60 ASN Chi-restraints excluded: chain M residue 411 LEU Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 411 LEU Chi-restraints excluded: chain O residue 46 MET Chi-restraints excluded: chain O residue 60 ASN Chi-restraints excluded: chain O residue 411 LEU Chi-restraints excluded: chain P residue 46 MET Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain P residue 411 LEU Chi-restraints excluded: chain Q residue 46 MET Chi-restraints excluded: chain Q residue 60 ASN Chi-restraints excluded: chain Q residue 411 LEU Chi-restraints excluded: chain R residue 46 MET Chi-restraints excluded: chain R residue 60 ASN Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 60 ASN Chi-restraints excluded: chain S residue 411 LEU Chi-restraints excluded: chain T residue 46 MET Chi-restraints excluded: chain T residue 60 ASN Chi-restraints excluded: chain T residue 411 LEU Chi-restraints excluded: chain V residue 46 MET Chi-restraints excluded: chain V residue 60 ASN Chi-restraints excluded: chain V residue 411 LEU Chi-restraints excluded: chain W residue 46 MET Chi-restraints excluded: chain W residue 60 ASN Chi-restraints excluded: chain W residue 411 LEU Chi-restraints excluded: chain X residue 46 MET Chi-restraints excluded: chain X residue 60 ASN Chi-restraints excluded: chain X residue 411 LEU Chi-restraints excluded: chain Y residue 46 MET Chi-restraints excluded: chain Y residue 60 ASN Chi-restraints excluded: chain Y residue 411 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 815 optimal weight: 0.6980 chunk 526 optimal weight: 40.0000 chunk 787 optimal weight: 6.9990 chunk 397 optimal weight: 9.9990 chunk 259 optimal weight: 0.8980 chunk 255 optimal weight: 30.0000 chunk 838 optimal weight: 5.9990 chunk 898 optimal weight: 20.0000 chunk 651 optimal weight: 30.0000 chunk 122 optimal weight: 0.0060 chunk 1036 optimal weight: 3.9990 overall best weight: 2.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 GLN ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 393 GLN ** S 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 393 GLN ** T 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 393 GLN ** V 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 393 GLN ** W 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 109440 Z= 0.139 Angle : 0.594 12.463 148968 Z= 0.295 Chirality : 0.042 0.155 16680 Planarity : 0.004 0.037 19632 Dihedral : 3.997 37.206 15264 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.65 % Allowed : 17.54 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.07), residues: 13608 helix: 1.53 (0.08), residues: 4848 sheet: 1.13 (0.09), residues: 3264 loop : 0.98 (0.09), residues: 5496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 554 HIS 0.002 0.000 HIS N 538 PHE 0.014 0.001 PHE W 225 TYR 0.008 0.001 TYR P 309 ARG 0.002 0.000 ARG I 366 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27216 Ramachandran restraints generated. 13608 Oldfield, 0 Emsley, 13608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27216 Ramachandran restraints generated. 13608 Oldfield, 0 Emsley, 13608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 11496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 552 time to evaluate : 8.975 Fit side-chains REVERT: A 46 MET cc_start: 0.9378 (OUTLIER) cc_final: 0.9087 (pmm) REVERT: A 230 MET cc_start: 0.7718 (ppp) cc_final: 0.7161 (ppp) REVERT: A 323 MET cc_start: 0.9318 (ttm) cc_final: 0.8709 (tmm) REVERT: A 354 MET cc_start: 0.9251 (ppp) cc_final: 0.8933 (ppp) REVERT: A 411 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9139 (mt) REVERT: A 507 MET cc_start: 0.9180 (mmm) cc_final: 0.8855 (mtm) REVERT: B 46 MET cc_start: 0.9393 (OUTLIER) cc_final: 0.9087 (pmm) REVERT: B 230 MET cc_start: 0.7678 (ppp) cc_final: 0.7108 (ppp) REVERT: B 323 MET cc_start: 0.9300 (ttm) cc_final: 0.8696 (tmm) REVERT: B 354 MET cc_start: 0.9216 (ppp) cc_final: 0.8872 (ppp) REVERT: B 411 LEU cc_start: 0.9590 (OUTLIER) cc_final: 0.9124 (mt) REVERT: B 507 MET cc_start: 0.9188 (mmm) cc_final: 0.8820 (mtt) REVERT: C 46 MET cc_start: 0.9380 (OUTLIER) cc_final: 0.9090 (pmm) REVERT: C 230 MET cc_start: 0.7715 (ppp) cc_final: 0.7132 (ppp) REVERT: C 323 MET cc_start: 0.9295 (ttm) cc_final: 0.8683 (tmm) REVERT: C 354 MET cc_start: 0.9251 (ppp) cc_final: 0.8917 (ppp) REVERT: C 411 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9142 (mt) REVERT: C 507 MET cc_start: 0.9186 (mmm) cc_final: 0.8865 (mtm) REVERT: D 46 MET cc_start: 0.9370 (OUTLIER) cc_final: 0.9076 (pmm) REVERT: D 230 MET cc_start: 0.7740 (ppp) cc_final: 0.7183 (ppp) REVERT: D 323 MET cc_start: 0.9320 (ttm) cc_final: 0.8709 (tmm) REVERT: D 354 MET cc_start: 0.9236 (ppp) cc_final: 0.8923 (ppp) REVERT: D 411 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9148 (mt) REVERT: D 507 MET cc_start: 0.9180 (mmm) cc_final: 0.8853 (mtm) REVERT: E 46 MET cc_start: 0.9365 (OUTLIER) cc_final: 0.9084 (pmm) REVERT: E 230 MET cc_start: 0.7775 (ppp) cc_final: 0.7227 (ppp) REVERT: E 323 MET cc_start: 0.9319 (ttm) cc_final: 0.8714 (tmm) REVERT: E 354 MET cc_start: 0.9225 (ppp) cc_final: 0.8922 (ppp) REVERT: E 411 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9132 (mt) REVERT: E 507 MET cc_start: 0.9185 (mmm) cc_final: 0.8861 (mtm) REVERT: F 46 MET cc_start: 0.9360 (OUTLIER) cc_final: 0.9085 (pmm) REVERT: F 230 MET cc_start: 0.7770 (ppp) cc_final: 0.7202 (ppp) REVERT: F 323 MET cc_start: 0.9315 (ttm) cc_final: 0.8698 (tmm) REVERT: F 354 MET cc_start: 0.9252 (ppp) cc_final: 0.8934 (ppp) REVERT: F 411 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9143 (mt) REVERT: F 507 MET cc_start: 0.9177 (mmm) cc_final: 0.8852 (mtm) REVERT: G 46 MET cc_start: 0.9346 (OUTLIER) cc_final: 0.9093 (pmm) REVERT: G 230 MET cc_start: 0.7730 (ppp) cc_final: 0.7161 (ppp) REVERT: G 323 MET cc_start: 0.9325 (ttm) cc_final: 0.8709 (tmm) REVERT: G 354 MET cc_start: 0.9249 (ppp) cc_final: 0.8929 (ppp) REVERT: G 411 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9137 (mt) REVERT: G 507 MET cc_start: 0.9172 (mmm) cc_final: 0.8852 (mtm) REVERT: H 46 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.9077 (pmm) REVERT: H 230 MET cc_start: 0.7728 (ppp) cc_final: 0.7187 (ppp) REVERT: H 323 MET cc_start: 0.9316 (ttm) cc_final: 0.8701 (tmm) REVERT: H 341 LEU cc_start: 0.9866 (OUTLIER) cc_final: 0.9661 (pp) REVERT: H 354 MET cc_start: 0.9260 (ppp) cc_final: 0.8941 (ppp) REVERT: H 411 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9131 (mt) REVERT: H 507 MET cc_start: 0.9202 (mmm) cc_final: 0.8820 (mtt) REVERT: I 46 MET cc_start: 0.9380 (OUTLIER) cc_final: 0.9090 (pmm) REVERT: I 230 MET cc_start: 0.7715 (ppp) cc_final: 0.7132 (ppp) REVERT: I 323 MET cc_start: 0.9295 (ttm) cc_final: 0.8684 (tmm) REVERT: I 354 MET cc_start: 0.9251 (ppp) cc_final: 0.8917 (ppp) REVERT: I 411 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9142 (mt) REVERT: I 507 MET cc_start: 0.9186 (mmm) cc_final: 0.8865 (mtm) REVERT: J 46 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.9077 (pmm) REVERT: J 230 MET cc_start: 0.7728 (ppp) cc_final: 0.7187 (ppp) REVERT: J 323 MET cc_start: 0.9316 (ttm) cc_final: 0.8701 (tmm) REVERT: J 341 LEU cc_start: 0.9866 (OUTLIER) cc_final: 0.9661 (pp) REVERT: J 354 MET cc_start: 0.9260 (ppp) cc_final: 0.8941 (ppp) REVERT: J 411 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9131 (mt) REVERT: J 507 MET cc_start: 0.9202 (mmm) cc_final: 0.8820 (mtt) REVERT: K 46 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.9077 (pmm) REVERT: K 230 MET cc_start: 0.7728 (ppp) cc_final: 0.7187 (ppp) REVERT: K 323 MET cc_start: 0.9316 (ttm) cc_final: 0.8701 (tmm) REVERT: K 341 LEU cc_start: 0.9866 (OUTLIER) cc_final: 0.9661 (pp) REVERT: K 354 MET cc_start: 0.9260 (ppp) cc_final: 0.8941 (ppp) REVERT: K 411 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9131 (mt) REVERT: K 507 MET cc_start: 0.9202 (mmm) cc_final: 0.8820 (mtt) REVERT: L 46 MET cc_start: 0.9378 (OUTLIER) cc_final: 0.9087 (pmm) REVERT: L 230 MET cc_start: 0.7718 (ppp) cc_final: 0.7161 (ppp) REVERT: L 323 MET cc_start: 0.9318 (ttm) cc_final: 0.8709 (tmm) REVERT: L 354 MET cc_start: 0.9251 (ppp) cc_final: 0.8933 (ppp) REVERT: L 411 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9139 (mt) REVERT: L 507 MET cc_start: 0.9180 (mmm) cc_final: 0.8854 (mtm) REVERT: M 46 MET cc_start: 0.9360 (OUTLIER) cc_final: 0.9085 (pmm) REVERT: M 230 MET cc_start: 0.7770 (ppp) cc_final: 0.7202 (ppp) REVERT: M 323 MET cc_start: 0.9314 (ttm) cc_final: 0.8698 (tmm) REVERT: M 354 MET cc_start: 0.9252 (ppp) cc_final: 0.8934 (ppp) REVERT: M 411 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9143 (mt) REVERT: M 507 MET cc_start: 0.9177 (mmm) cc_final: 0.8852 (mtm) REVERT: N 46 MET cc_start: 0.9346 (OUTLIER) cc_final: 0.9093 (pmm) REVERT: N 230 MET cc_start: 0.7730 (ppp) cc_final: 0.7161 (ppp) REVERT: N 323 MET cc_start: 0.9325 (ttm) cc_final: 0.8709 (tmm) REVERT: N 354 MET cc_start: 0.9249 (ppp) cc_final: 0.8929 (ppp) REVERT: N 411 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9137 (mt) REVERT: N 507 MET cc_start: 0.9172 (mmm) cc_final: 0.8852 (mtm) REVERT: O 46 MET cc_start: 0.9378 (OUTLIER) cc_final: 0.9087 (pmm) REVERT: O 230 MET cc_start: 0.7719 (ppp) cc_final: 0.7161 (ppp) REVERT: O 323 MET cc_start: 0.9318 (ttm) cc_final: 0.8709 (tmm) REVERT: O 354 MET cc_start: 0.9251 (ppp) cc_final: 0.8933 (ppp) REVERT: O 411 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9139 (mt) REVERT: O 507 MET cc_start: 0.9180 (mmm) cc_final: 0.8855 (mtm) REVERT: P 46 MET cc_start: 0.9380 (OUTLIER) cc_final: 0.9090 (pmm) REVERT: P 230 MET cc_start: 0.7715 (ppp) cc_final: 0.7132 (ppp) REVERT: P 323 MET cc_start: 0.9295 (ttm) cc_final: 0.8684 (tmm) REVERT: P 354 MET cc_start: 0.9251 (ppp) cc_final: 0.8917 (ppp) REVERT: P 411 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9142 (mt) REVERT: P 507 MET cc_start: 0.9186 (mmm) cc_final: 0.8865 (mtm) REVERT: Q 46 MET cc_start: 0.9393 (OUTLIER) cc_final: 0.9087 (pmm) REVERT: Q 230 MET cc_start: 0.7678 (ppp) cc_final: 0.7108 (ppp) REVERT: Q 323 MET cc_start: 0.9300 (ttm) cc_final: 0.8696 (tmm) REVERT: Q 354 MET cc_start: 0.9216 (ppp) cc_final: 0.8872 (ppp) REVERT: Q 411 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9123 (mt) REVERT: Q 507 MET cc_start: 0.9188 (mmm) cc_final: 0.8820 (mtt) REVERT: R 46 MET cc_start: 0.9370 (OUTLIER) cc_final: 0.9076 (pmm) REVERT: R 230 MET cc_start: 0.7740 (ppp) cc_final: 0.7183 (ppp) REVERT: R 323 MET cc_start: 0.9320 (ttm) cc_final: 0.8709 (tmm) REVERT: R 354 MET cc_start: 0.9236 (ppp) cc_final: 0.8923 (ppp) REVERT: R 411 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9148 (mt) REVERT: R 507 MET cc_start: 0.9180 (mmm) cc_final: 0.8853 (mtm) REVERT: S 46 MET cc_start: 0.9365 (OUTLIER) cc_final: 0.9084 (pmm) REVERT: S 230 MET cc_start: 0.7775 (ppp) cc_final: 0.7227 (ppp) REVERT: S 323 MET cc_start: 0.9319 (ttm) cc_final: 0.8714 (tmm) REVERT: S 354 MET cc_start: 0.9225 (ppp) cc_final: 0.8922 (ppp) REVERT: S 411 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9132 (mt) REVERT: S 507 MET cc_start: 0.9185 (mmm) cc_final: 0.8861 (mtm) REVERT: T 46 MET cc_start: 0.9347 (OUTLIER) cc_final: 0.9093 (pmm) REVERT: T 230 MET cc_start: 0.7730 (ppp) cc_final: 0.7161 (ppp) REVERT: T 323 MET cc_start: 0.9325 (ttm) cc_final: 0.8709 (tmm) REVERT: T 354 MET cc_start: 0.9249 (ppp) cc_final: 0.8929 (ppp) REVERT: T 411 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9137 (mt) REVERT: T 507 MET cc_start: 0.9172 (mmm) cc_final: 0.8852 (mtm) REVERT: V 46 MET cc_start: 0.9360 (OUTLIER) cc_final: 0.9085 (pmm) REVERT: V 230 MET cc_start: 0.7769 (ppp) cc_final: 0.7202 (ppp) REVERT: V 323 MET cc_start: 0.9315 (ttm) cc_final: 0.8698 (tmm) REVERT: V 354 MET cc_start: 0.9252 (ppp) cc_final: 0.8934 (ppp) REVERT: V 411 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9143 (mt) REVERT: V 507 MET cc_start: 0.9177 (mmm) cc_final: 0.8852 (mtm) REVERT: W 46 MET cc_start: 0.9365 (OUTLIER) cc_final: 0.9084 (pmm) REVERT: W 230 MET cc_start: 0.7775 (ppp) cc_final: 0.7227 (ppp) REVERT: W 323 MET cc_start: 0.9319 (ttm) cc_final: 0.8714 (tmm) REVERT: W 354 MET cc_start: 0.9225 (ppp) cc_final: 0.8922 (ppp) REVERT: W 411 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9132 (mt) REVERT: W 507 MET cc_start: 0.9185 (mmm) cc_final: 0.8861 (mtm) REVERT: X 46 MET cc_start: 0.9393 (OUTLIER) cc_final: 0.9087 (pmm) REVERT: X 230 MET cc_start: 0.7678 (ppp) cc_final: 0.7108 (ppp) REVERT: X 323 MET cc_start: 0.9300 (ttm) cc_final: 0.8696 (tmm) REVERT: X 354 MET cc_start: 0.9217 (ppp) cc_final: 0.8872 (ppp) REVERT: X 411 LEU cc_start: 0.9590 (OUTLIER) cc_final: 0.9124 (mt) REVERT: X 507 MET cc_start: 0.9188 (mmm) cc_final: 0.8820 (mtt) REVERT: Y 46 MET cc_start: 0.9370 (OUTLIER) cc_final: 0.9076 (pmm) REVERT: Y 230 MET cc_start: 0.7740 (ppp) cc_final: 0.7183 (ppp) REVERT: Y 323 MET cc_start: 0.9320 (ttm) cc_final: 0.8709 (tmm) REVERT: Y 354 MET cc_start: 0.9235 (ppp) cc_final: 0.8923 (ppp) REVERT: Y 411 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9148 (mt) REVERT: Y 507 MET cc_start: 0.9180 (mmm) cc_final: 0.8853 (mtm) outliers start: 75 outliers final: 24 residues processed: 603 average time/residue: 0.8287 time to fit residues: 901.6040 Evaluate side-chains 603 residues out of total 11496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 528 time to evaluate : 9.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain G residue 46 MET Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain H residue 46 MET Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 341 LEU Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 411 LEU Chi-restraints excluded: chain J residue 46 MET Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 341 LEU Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain K residue 46 MET Chi-restraints excluded: chain K residue 216 LEU Chi-restraints excluded: chain K residue 341 LEU Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 411 LEU Chi-restraints excluded: chain M residue 46 MET Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain M residue 411 LEU Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 216 LEU Chi-restraints excluded: chain N residue 411 LEU Chi-restraints excluded: chain O residue 46 MET Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain O residue 411 LEU Chi-restraints excluded: chain P residue 46 MET Chi-restraints excluded: chain P residue 216 LEU Chi-restraints excluded: chain P residue 411 LEU Chi-restraints excluded: chain Q residue 46 MET Chi-restraints excluded: chain Q residue 216 LEU Chi-restraints excluded: chain Q residue 411 LEU Chi-restraints excluded: chain R residue 46 MET Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 411 LEU Chi-restraints excluded: chain T residue 46 MET Chi-restraints excluded: chain T residue 216 LEU Chi-restraints excluded: chain T residue 411 LEU Chi-restraints excluded: chain V residue 46 MET Chi-restraints excluded: chain V residue 216 LEU Chi-restraints excluded: chain V residue 411 LEU Chi-restraints excluded: chain W residue 46 MET Chi-restraints excluded: chain W residue 216 LEU Chi-restraints excluded: chain W residue 411 LEU Chi-restraints excluded: chain X residue 46 MET Chi-restraints excluded: chain X residue 216 LEU Chi-restraints excluded: chain X residue 411 LEU Chi-restraints excluded: chain Y residue 46 MET Chi-restraints excluded: chain Y residue 216 LEU Chi-restraints excluded: chain Y residue 411 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 1199 optimal weight: 10.0000 chunk 1263 optimal weight: 40.0000 chunk 1152 optimal weight: 8.9990 chunk 1228 optimal weight: 0.9990 chunk 1262 optimal weight: 5.9990 chunk 739 optimal weight: 20.0000 chunk 535 optimal weight: 3.9990 chunk 964 optimal weight: 30.0000 chunk 377 optimal weight: 20.0000 chunk 1110 optimal weight: 30.0000 chunk 1162 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 109440 Z= 0.175 Angle : 0.608 11.406 148968 Z= 0.297 Chirality : 0.041 0.191 16680 Planarity : 0.004 0.038 19632 Dihedral : 3.891 35.643 15216 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.65 % Allowed : 17.17 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.08), residues: 13608 helix: 1.62 (0.08), residues: 4848 sheet: 1.11 (0.09), residues: 3240 loop : 1.05 (0.09), residues: 5520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP X 554 HIS 0.002 0.001 HIS T 116 PHE 0.017 0.001 PHE X 225 TYR 0.007 0.001 TYR J 309 ARG 0.003 0.000 ARG C 366 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27216 Ramachandran restraints generated. 13608 Oldfield, 0 Emsley, 13608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27216 Ramachandran restraints generated. 13608 Oldfield, 0 Emsley, 13608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 11496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 528 time to evaluate : 9.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7316 (mpp) cc_final: 0.7110 (mpp) REVERT: A 230 MET cc_start: 0.7825 (ppp) cc_final: 0.7583 (ppp) REVERT: A 323 MET cc_start: 0.9377 (ttm) cc_final: 0.8755 (tmm) REVERT: A 354 MET cc_start: 0.9225 (ppp) cc_final: 0.8898 (ppp) REVERT: A 378 MET cc_start: 0.8569 (mpp) cc_final: 0.8294 (mpp) REVERT: A 411 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.8993 (mt) REVERT: B 229 MET cc_start: 0.7324 (mpp) cc_final: 0.7118 (mpp) REVERT: B 230 MET cc_start: 0.7784 (ppp) cc_final: 0.7536 (ppp) REVERT: B 323 MET cc_start: 0.9354 (ttm) cc_final: 0.8741 (tmm) REVERT: B 354 MET cc_start: 0.9208 (ppp) cc_final: 0.8854 (ppp) REVERT: B 378 MET cc_start: 0.8606 (mpp) cc_final: 0.8335 (mpp) REVERT: B 411 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.8966 (mt) REVERT: C 229 MET cc_start: 0.7326 (mpp) cc_final: 0.7120 (mpp) REVERT: C 230 MET cc_start: 0.7824 (ppp) cc_final: 0.7562 (ppp) REVERT: C 323 MET cc_start: 0.9351 (ttm) cc_final: 0.8729 (tmm) REVERT: C 354 MET cc_start: 0.9238 (ppp) cc_final: 0.8893 (ppp) REVERT: C 378 MET cc_start: 0.8579 (mpp) cc_final: 0.8307 (mpp) REVERT: C 411 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.8988 (mt) REVERT: D 229 MET cc_start: 0.7327 (mpp) cc_final: 0.7121 (mpp) REVERT: D 230 MET cc_start: 0.7846 (ppp) cc_final: 0.7595 (ppp) REVERT: D 323 MET cc_start: 0.9381 (ttm) cc_final: 0.8756 (tmm) REVERT: D 354 MET cc_start: 0.9210 (ppp) cc_final: 0.8888 (ppp) REVERT: D 378 MET cc_start: 0.8591 (mpp) cc_final: 0.8298 (mpp) REVERT: D 411 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9008 (mt) REVERT: E 229 MET cc_start: 0.7348 (mpp) cc_final: 0.7137 (mpp) REVERT: E 230 MET cc_start: 0.7881 (ppp) cc_final: 0.7629 (ppp) REVERT: E 323 MET cc_start: 0.9379 (ttm) cc_final: 0.8759 (tmm) REVERT: E 354 MET cc_start: 0.9198 (ppp) cc_final: 0.8884 (ppp) REVERT: E 378 MET cc_start: 0.8588 (mpp) cc_final: 0.8300 (mpp) REVERT: E 411 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.8984 (mt) REVERT: F 229 MET cc_start: 0.7363 (mpp) cc_final: 0.7155 (mpp) REVERT: F 230 MET cc_start: 0.7882 (ppp) cc_final: 0.7622 (ppp) REVERT: F 323 MET cc_start: 0.9373 (ttm) cc_final: 0.8744 (tmm) REVERT: F 354 MET cc_start: 0.9230 (ppp) cc_final: 0.8903 (ppp) REVERT: F 378 MET cc_start: 0.8615 (mpp) cc_final: 0.8327 (mpp) REVERT: F 411 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.8998 (mt) REVERT: G 229 MET cc_start: 0.7353 (mpp) cc_final: 0.7144 (mpp) REVERT: G 230 MET cc_start: 0.7834 (ppp) cc_final: 0.7579 (ppp) REVERT: G 323 MET cc_start: 0.9383 (ttm) cc_final: 0.8754 (tmm) REVERT: G 354 MET cc_start: 0.9225 (ppp) cc_final: 0.8895 (ppp) REVERT: G 378 MET cc_start: 0.8584 (mpp) cc_final: 0.8306 (mpp) REVERT: G 411 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.8991 (mt) REVERT: H 230 MET cc_start: 0.7846 (ppp) cc_final: 0.7642 (ppp) REVERT: H 323 MET cc_start: 0.9375 (ttm) cc_final: 0.8747 (tmm) REVERT: H 354 MET cc_start: 0.9238 (ppp) cc_final: 0.8908 (ppp) REVERT: H 378 MET cc_start: 0.8604 (mpp) cc_final: 0.8330 (mpp) REVERT: H 411 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.8980 (mt) REVERT: I 229 MET cc_start: 0.7326 (mpp) cc_final: 0.7120 (mpp) REVERT: I 230 MET cc_start: 0.7823 (ppp) cc_final: 0.7562 (ppp) REVERT: I 323 MET cc_start: 0.9351 (ttm) cc_final: 0.8730 (tmm) REVERT: I 354 MET cc_start: 0.9238 (ppp) cc_final: 0.8893 (ppp) REVERT: I 378 MET cc_start: 0.8579 (mpp) cc_final: 0.8307 (mpp) REVERT: I 411 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.8988 (mt) REVERT: J 230 MET cc_start: 0.7846 (ppp) cc_final: 0.7642 (ppp) REVERT: J 323 MET cc_start: 0.9375 (ttm) cc_final: 0.8747 (tmm) REVERT: J 354 MET cc_start: 0.9238 (ppp) cc_final: 0.8908 (ppp) REVERT: J 378 MET cc_start: 0.8604 (mpp) cc_final: 0.8330 (mpp) REVERT: J 411 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.8980 (mt) REVERT: K 230 MET cc_start: 0.7846 (ppp) cc_final: 0.7641 (ppp) REVERT: K 323 MET cc_start: 0.9375 (ttm) cc_final: 0.8747 (tmm) REVERT: K 354 MET cc_start: 0.9238 (ppp) cc_final: 0.8908 (ppp) REVERT: K 378 MET cc_start: 0.8604 (mpp) cc_final: 0.8330 (mpp) REVERT: K 411 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.8980 (mt) REVERT: L 229 MET cc_start: 0.7316 (mpp) cc_final: 0.7110 (mpp) REVERT: L 230 MET cc_start: 0.7825 (ppp) cc_final: 0.7583 (ppp) REVERT: L 323 MET cc_start: 0.9377 (ttm) cc_final: 0.8755 (tmm) REVERT: L 354 MET cc_start: 0.9225 (ppp) cc_final: 0.8898 (ppp) REVERT: L 378 MET cc_start: 0.8569 (mpp) cc_final: 0.8294 (mpp) REVERT: L 411 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.8993 (mt) REVERT: M 229 MET cc_start: 0.7363 (mpp) cc_final: 0.7155 (mpp) REVERT: M 230 MET cc_start: 0.7882 (ppp) cc_final: 0.7622 (ppp) REVERT: M 323 MET cc_start: 0.9373 (ttm) cc_final: 0.8744 (tmm) REVERT: M 354 MET cc_start: 0.9230 (ppp) cc_final: 0.8903 (ppp) REVERT: M 378 MET cc_start: 0.8615 (mpp) cc_final: 0.8327 (mpp) REVERT: M 411 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.8998 (mt) REVERT: N 229 MET cc_start: 0.7353 (mpp) cc_final: 0.7144 (mpp) REVERT: N 230 MET cc_start: 0.7834 (ppp) cc_final: 0.7579 (ppp) REVERT: N 323 MET cc_start: 0.9383 (ttm) cc_final: 0.8754 (tmm) REVERT: N 354 MET cc_start: 0.9225 (ppp) cc_final: 0.8895 (ppp) REVERT: N 378 MET cc_start: 0.8584 (mpp) cc_final: 0.8306 (mpp) REVERT: N 411 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.8991 (mt) REVERT: O 229 MET cc_start: 0.7316 (mpp) cc_final: 0.7110 (mpp) REVERT: O 230 MET cc_start: 0.7825 (ppp) cc_final: 0.7583 (ppp) REVERT: O 323 MET cc_start: 0.9377 (ttm) cc_final: 0.8755 (tmm) REVERT: O 354 MET cc_start: 0.9225 (ppp) cc_final: 0.8898 (ppp) REVERT: O 378 MET cc_start: 0.8569 (mpp) cc_final: 0.8294 (mpp) REVERT: O 411 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.8993 (mt) REVERT: P 229 MET cc_start: 0.7326 (mpp) cc_final: 0.7120 (mpp) REVERT: P 230 MET cc_start: 0.7823 (ppp) cc_final: 0.7562 (ppp) REVERT: P 323 MET cc_start: 0.9351 (ttm) cc_final: 0.8730 (tmm) REVERT: P 354 MET cc_start: 0.9238 (ppp) cc_final: 0.8893 (ppp) REVERT: P 378 MET cc_start: 0.8579 (mpp) cc_final: 0.8307 (mpp) REVERT: P 411 LEU cc_start: 0.9541 (OUTLIER) cc_final: 0.8988 (mt) REVERT: Q 229 MET cc_start: 0.7324 (mpp) cc_final: 0.7118 (mpp) REVERT: Q 230 MET cc_start: 0.7784 (ppp) cc_final: 0.7536 (ppp) REVERT: Q 323 MET cc_start: 0.9354 (ttm) cc_final: 0.8741 (tmm) REVERT: Q 354 MET cc_start: 0.9208 (ppp) cc_final: 0.8854 (ppp) REVERT: Q 378 MET cc_start: 0.8606 (mpp) cc_final: 0.8335 (mpp) REVERT: Q 411 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.8966 (mt) REVERT: R 229 MET cc_start: 0.7327 (mpp) cc_final: 0.7121 (mpp) REVERT: R 230 MET cc_start: 0.7846 (ppp) cc_final: 0.7596 (ppp) REVERT: R 323 MET cc_start: 0.9381 (ttm) cc_final: 0.8756 (tmm) REVERT: R 354 MET cc_start: 0.9210 (ppp) cc_final: 0.8888 (ppp) REVERT: R 378 MET cc_start: 0.8591 (mpp) cc_final: 0.8298 (mpp) REVERT: R 411 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9008 (mt) REVERT: S 229 MET cc_start: 0.7348 (mpp) cc_final: 0.7137 (mpp) REVERT: S 230 MET cc_start: 0.7881 (ppp) cc_final: 0.7629 (ppp) REVERT: S 323 MET cc_start: 0.9379 (ttm) cc_final: 0.8759 (tmm) REVERT: S 354 MET cc_start: 0.9198 (ppp) cc_final: 0.8884 (ppp) REVERT: S 378 MET cc_start: 0.8587 (mpp) cc_final: 0.8300 (mpp) REVERT: S 411 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.8984 (mt) REVERT: T 229 MET cc_start: 0.7353 (mpp) cc_final: 0.7144 (mpp) REVERT: T 230 MET cc_start: 0.7834 (ppp) cc_final: 0.7579 (ppp) REVERT: T 323 MET cc_start: 0.9383 (ttm) cc_final: 0.8754 (tmm) REVERT: T 354 MET cc_start: 0.9225 (ppp) cc_final: 0.8895 (ppp) REVERT: T 378 MET cc_start: 0.8584 (mpp) cc_final: 0.8306 (mpp) REVERT: T 411 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.8991 (mt) REVERT: V 229 MET cc_start: 0.7363 (mpp) cc_final: 0.7155 (mpp) REVERT: V 230 MET cc_start: 0.7882 (ppp) cc_final: 0.7622 (ppp) REVERT: V 323 MET cc_start: 0.9373 (ttm) cc_final: 0.8744 (tmm) REVERT: V 354 MET cc_start: 0.9230 (ppp) cc_final: 0.8903 (ppp) REVERT: V 378 MET cc_start: 0.8615 (mpp) cc_final: 0.8328 (mpp) REVERT: V 411 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.8998 (mt) REVERT: W 229 MET cc_start: 0.7348 (mpp) cc_final: 0.7137 (mpp) REVERT: W 230 MET cc_start: 0.7881 (ppp) cc_final: 0.7629 (ppp) REVERT: W 323 MET cc_start: 0.9379 (ttm) cc_final: 0.8759 (tmm) REVERT: W 354 MET cc_start: 0.9198 (ppp) cc_final: 0.8884 (ppp) REVERT: W 378 MET cc_start: 0.8587 (mpp) cc_final: 0.8300 (mpp) REVERT: W 411 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.8984 (mt) REVERT: X 229 MET cc_start: 0.7324 (mpp) cc_final: 0.7118 (mpp) REVERT: X 230 MET cc_start: 0.7784 (ppp) cc_final: 0.7536 (ppp) REVERT: X 323 MET cc_start: 0.9354 (ttm) cc_final: 0.8741 (tmm) REVERT: X 354 MET cc_start: 0.9208 (ppp) cc_final: 0.8854 (ppp) REVERT: X 378 MET cc_start: 0.8606 (mpp) cc_final: 0.8335 (mpp) REVERT: X 411 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.8966 (mt) REVERT: Y 229 MET cc_start: 0.7327 (mpp) cc_final: 0.7121 (mpp) REVERT: Y 230 MET cc_start: 0.7846 (ppp) cc_final: 0.7595 (ppp) REVERT: Y 323 MET cc_start: 0.9381 (ttm) cc_final: 0.8756 (tmm) REVERT: Y 354 MET cc_start: 0.9210 (ppp) cc_final: 0.8888 (ppp) REVERT: Y 378 MET cc_start: 0.8591 (mpp) cc_final: 0.8298 (mpp) REVERT: Y 411 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9008 (mt) outliers start: 75 outliers final: 48 residues processed: 579 average time/residue: 0.8690 time to fit residues: 906.9469 Evaluate side-chains 600 residues out of total 11496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 528 time to evaluate : 8.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain G residue 46 MET Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain H residue 46 MET Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain I residue 411 LEU Chi-restraints excluded: chain J residue 46 MET Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain K residue 46 MET Chi-restraints excluded: chain K residue 216 LEU Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain L residue 411 LEU Chi-restraints excluded: chain M residue 46 MET Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain M residue 411 LEU Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 216 LEU Chi-restraints excluded: chain N residue 411 LEU Chi-restraints excluded: chain O residue 46 MET Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain O residue 411 LEU Chi-restraints excluded: chain P residue 46 MET Chi-restraints excluded: chain P residue 216 LEU Chi-restraints excluded: chain P residue 411 LEU Chi-restraints excluded: chain Q residue 46 MET Chi-restraints excluded: chain Q residue 216 LEU Chi-restraints excluded: chain Q residue 411 LEU Chi-restraints excluded: chain R residue 46 MET Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain S residue 411 LEU Chi-restraints excluded: chain T residue 46 MET Chi-restraints excluded: chain T residue 216 LEU Chi-restraints excluded: chain T residue 411 LEU Chi-restraints excluded: chain V residue 46 MET Chi-restraints excluded: chain V residue 216 LEU Chi-restraints excluded: chain V residue 411 LEU Chi-restraints excluded: chain W residue 46 MET Chi-restraints excluded: chain W residue 216 LEU Chi-restraints excluded: chain W residue 411 LEU Chi-restraints excluded: chain X residue 46 MET Chi-restraints excluded: chain X residue 216 LEU Chi-restraints excluded: chain X residue 411 LEU Chi-restraints excluded: chain Y residue 46 MET Chi-restraints excluded: chain Y residue 216 LEU Chi-restraints excluded: chain Y residue 411 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 1224 optimal weight: 20.0000 chunk 806 optimal weight: 8.9990 chunk 1299 optimal weight: 0.5980 chunk 793 optimal weight: 30.0000 chunk 616 optimal weight: 7.9990 chunk 903 optimal weight: 20.0000 chunk 1362 optimal weight: 30.0000 chunk 1254 optimal weight: 50.0000 chunk 1085 optimal weight: 0.0010 chunk 112 optimal weight: 40.0000 chunk 838 optimal weight: 30.0000 overall best weight: 7.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 GLN ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 109440 Z= 0.221 Angle : 0.640 17.719 148968 Z= 0.315 Chirality : 0.042 0.223 16680 Planarity : 0.004 0.037 19632 Dihedral : 3.999 35.230 15216 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.84 % Allowed : 16.79 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.08), residues: 13608 helix: 1.50 (0.08), residues: 4848 sheet: 1.09 (0.10), residues: 3072 loop : 0.96 (0.09), residues: 5688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Q 554 HIS 0.002 0.001 HIS H 195 PHE 0.023 0.001 PHE K 225 TYR 0.007 0.001 TYR X 309 ARG 0.003 0.000 ARG I 366 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27216 Ramachandran restraints generated. 13608 Oldfield, 0 Emsley, 13608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27216 Ramachandran restraints generated. 13608 Oldfield, 0 Emsley, 13608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 11496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 528 time to evaluate : 9.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7287 (mpp) cc_final: 0.7081 (mpp) REVERT: A 323 MET cc_start: 0.9408 (ttm) cc_final: 0.8796 (tmm) REVERT: A 354 MET cc_start: 0.9244 (ppp) cc_final: 0.8948 (ppp) REVERT: A 378 MET cc_start: 0.8740 (mpp) cc_final: 0.8496 (mpp) REVERT: B 229 MET cc_start: 0.7294 (mpp) cc_final: 0.7089 (mpp) REVERT: B 323 MET cc_start: 0.9386 (ttm) cc_final: 0.8781 (tmm) REVERT: B 354 MET cc_start: 0.9234 (ppp) cc_final: 0.8921 (ppp) REVERT: B 378 MET cc_start: 0.8777 (mpp) cc_final: 0.8542 (mpp) REVERT: C 229 MET cc_start: 0.7294 (mpp) cc_final: 0.7090 (mpp) REVERT: C 323 MET cc_start: 0.9383 (ttm) cc_final: 0.8769 (tmm) REVERT: C 354 MET cc_start: 0.9258 (ppp) cc_final: 0.8950 (ppp) REVERT: C 378 MET cc_start: 0.8753 (mpp) cc_final: 0.8514 (mpp) REVERT: D 229 MET cc_start: 0.7292 (mpp) cc_final: 0.7087 (mpp) REVERT: D 323 MET cc_start: 0.9413 (ttm) cc_final: 0.8797 (tmm) REVERT: D 354 MET cc_start: 0.9228 (ppp) cc_final: 0.8939 (ppp) REVERT: D 378 MET cc_start: 0.8761 (mpp) cc_final: 0.8500 (mpp) REVERT: E 229 MET cc_start: 0.7313 (mpp) cc_final: 0.7103 (mpp) REVERT: E 323 MET cc_start: 0.9410 (ttm) cc_final: 0.8800 (tmm) REVERT: E 354 MET cc_start: 0.9219 (ppp) cc_final: 0.8937 (ppp) REVERT: E 378 MET cc_start: 0.8757 (mpp) cc_final: 0.8504 (mpp) REVERT: F 229 MET cc_start: 0.7329 (mpp) cc_final: 0.7122 (mpp) REVERT: F 323 MET cc_start: 0.9404 (ttm) cc_final: 0.8786 (tmm) REVERT: F 354 MET cc_start: 0.9248 (ppp) cc_final: 0.8953 (ppp) REVERT: F 378 MET cc_start: 0.8782 (mpp) cc_final: 0.8528 (mpp) REVERT: G 229 MET cc_start: 0.7324 (mpp) cc_final: 0.7115 (mpp) REVERT: G 323 MET cc_start: 0.9414 (ttm) cc_final: 0.8795 (tmm) REVERT: G 354 MET cc_start: 0.9243 (ppp) cc_final: 0.8946 (ppp) REVERT: G 378 MET cc_start: 0.8760 (mpp) cc_final: 0.8516 (mpp) REVERT: H 229 MET cc_start: 0.7324 (mpp) cc_final: 0.7093 (mpp) REVERT: H 323 MET cc_start: 0.9403 (ttm) cc_final: 0.8786 (tmm) REVERT: H 354 MET cc_start: 0.9266 (ppp) cc_final: 0.8944 (ppp) REVERT: H 378 MET cc_start: 0.8778 (mpp) cc_final: 0.8538 (mpp) REVERT: I 229 MET cc_start: 0.7294 (mpp) cc_final: 0.7090 (mpp) REVERT: I 323 MET cc_start: 0.9382 (ttm) cc_final: 0.8770 (tmm) REVERT: I 354 MET cc_start: 0.9258 (ppp) cc_final: 0.8950 (ppp) REVERT: I 378 MET cc_start: 0.8753 (mpp) cc_final: 0.8514 (mpp) REVERT: J 229 MET cc_start: 0.7324 (mpp) cc_final: 0.7093 (mpp) REVERT: J 323 MET cc_start: 0.9403 (ttm) cc_final: 0.8786 (tmm) REVERT: J 354 MET cc_start: 0.9266 (ppp) cc_final: 0.8944 (ppp) REVERT: J 378 MET cc_start: 0.8778 (mpp) cc_final: 0.8538 (mpp) REVERT: K 229 MET cc_start: 0.7324 (mpp) cc_final: 0.7093 (mpp) REVERT: K 323 MET cc_start: 0.9403 (ttm) cc_final: 0.8786 (tmm) REVERT: K 354 MET cc_start: 0.9266 (ppp) cc_final: 0.8944 (ppp) REVERT: K 378 MET cc_start: 0.8778 (mpp) cc_final: 0.8538 (mpp) REVERT: L 229 MET cc_start: 0.7287 (mpp) cc_final: 0.7081 (mpp) REVERT: L 323 MET cc_start: 0.9408 (ttm) cc_final: 0.8796 (tmm) REVERT: L 354 MET cc_start: 0.9244 (ppp) cc_final: 0.8948 (ppp) REVERT: L 378 MET cc_start: 0.8740 (mpp) cc_final: 0.8496 (mpp) REVERT: M 229 MET cc_start: 0.7329 (mpp) cc_final: 0.7122 (mpp) REVERT: M 323 MET cc_start: 0.9404 (ttm) cc_final: 0.8786 (tmm) REVERT: M 354 MET cc_start: 0.9248 (ppp) cc_final: 0.8953 (ppp) REVERT: M 378 MET cc_start: 0.8782 (mpp) cc_final: 0.8528 (mpp) REVERT: N 229 MET cc_start: 0.7324 (mpp) cc_final: 0.7115 (mpp) REVERT: N 323 MET cc_start: 0.9414 (ttm) cc_final: 0.8795 (tmm) REVERT: N 354 MET cc_start: 0.9243 (ppp) cc_final: 0.8946 (ppp) REVERT: N 378 MET cc_start: 0.8760 (mpp) cc_final: 0.8516 (mpp) REVERT: O 229 MET cc_start: 0.7287 (mpp) cc_final: 0.7081 (mpp) REVERT: O 323 MET cc_start: 0.9408 (ttm) cc_final: 0.8796 (tmm) REVERT: O 354 MET cc_start: 0.9244 (ppp) cc_final: 0.8948 (ppp) REVERT: O 378 MET cc_start: 0.8740 (mpp) cc_final: 0.8496 (mpp) REVERT: P 229 MET cc_start: 0.7294 (mpp) cc_final: 0.7090 (mpp) REVERT: P 323 MET cc_start: 0.9382 (ttm) cc_final: 0.8770 (tmm) REVERT: P 354 MET cc_start: 0.9258 (ppp) cc_final: 0.8950 (ppp) REVERT: P 378 MET cc_start: 0.8753 (mpp) cc_final: 0.8514 (mpp) REVERT: Q 229 MET cc_start: 0.7294 (mpp) cc_final: 0.7089 (mpp) REVERT: Q 323 MET cc_start: 0.9386 (ttm) cc_final: 0.8781 (tmm) REVERT: Q 354 MET cc_start: 0.9234 (ppp) cc_final: 0.8921 (ppp) REVERT: Q 378 MET cc_start: 0.8777 (mpp) cc_final: 0.8542 (mpp) REVERT: R 229 MET cc_start: 0.7292 (mpp) cc_final: 0.7087 (mpp) REVERT: R 323 MET cc_start: 0.9413 (ttm) cc_final: 0.8797 (tmm) REVERT: R 354 MET cc_start: 0.9228 (ppp) cc_final: 0.8939 (ppp) REVERT: R 378 MET cc_start: 0.8761 (mpp) cc_final: 0.8500 (mpp) REVERT: S 229 MET cc_start: 0.7313 (mpp) cc_final: 0.7103 (mpp) REVERT: S 323 MET cc_start: 0.9410 (ttm) cc_final: 0.8800 (tmm) REVERT: S 354 MET cc_start: 0.9219 (ppp) cc_final: 0.8937 (ppp) REVERT: S 378 MET cc_start: 0.8757 (mpp) cc_final: 0.8503 (mpp) REVERT: T 229 MET cc_start: 0.7324 (mpp) cc_final: 0.7115 (mpp) REVERT: T 323 MET cc_start: 0.9414 (ttm) cc_final: 0.8795 (tmm) REVERT: T 354 MET cc_start: 0.9243 (ppp) cc_final: 0.8947 (ppp) REVERT: T 378 MET cc_start: 0.8760 (mpp) cc_final: 0.8516 (mpp) REVERT: V 229 MET cc_start: 0.7329 (mpp) cc_final: 0.7122 (mpp) REVERT: V 323 MET cc_start: 0.9404 (ttm) cc_final: 0.8786 (tmm) REVERT: V 354 MET cc_start: 0.9248 (ppp) cc_final: 0.8953 (ppp) REVERT: V 378 MET cc_start: 0.8782 (mpp) cc_final: 0.8528 (mpp) REVERT: W 229 MET cc_start: 0.7313 (mpp) cc_final: 0.7103 (mpp) REVERT: W 323 MET cc_start: 0.9410 (ttm) cc_final: 0.8800 (tmm) REVERT: W 354 MET cc_start: 0.9219 (ppp) cc_final: 0.8937 (ppp) REVERT: W 378 MET cc_start: 0.8757 (mpp) cc_final: 0.8503 (mpp) REVERT: X 229 MET cc_start: 0.7294 (mpp) cc_final: 0.7089 (mpp) REVERT: X 323 MET cc_start: 0.9386 (ttm) cc_final: 0.8781 (tmm) REVERT: X 354 MET cc_start: 0.9234 (ppp) cc_final: 0.8921 (ppp) REVERT: X 378 MET cc_start: 0.8776 (mpp) cc_final: 0.8542 (mpp) REVERT: Y 229 MET cc_start: 0.7292 (mpp) cc_final: 0.7087 (mpp) REVERT: Y 323 MET cc_start: 0.9413 (ttm) cc_final: 0.8797 (tmm) REVERT: Y 354 MET cc_start: 0.9228 (ppp) cc_final: 0.8939 (ppp) REVERT: Y 378 MET cc_start: 0.8761 (mpp) cc_final: 0.8500 (mpp) outliers start: 96 outliers final: 72 residues processed: 600 average time/residue: 0.8164 time to fit residues: 885.0512 Evaluate side-chains 600 residues out of total 11496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 528 time to evaluate : 8.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain G residue 46 MET Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain H residue 46 MET Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 216 LEU Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain I residue 216 LEU Chi-restraints excluded: chain J residue 46 MET Chi-restraints excluded: chain J residue 60 ASN Chi-restraints excluded: chain J residue 216 LEU Chi-restraints excluded: chain K residue 46 MET Chi-restraints excluded: chain K residue 60 ASN Chi-restraints excluded: chain K residue 216 LEU Chi-restraints excluded: chain L residue 46 MET Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 216 LEU Chi-restraints excluded: chain M residue 46 MET Chi-restraints excluded: chain M residue 60 ASN Chi-restraints excluded: chain M residue 216 LEU Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 60 ASN Chi-restraints excluded: chain N residue 216 LEU Chi-restraints excluded: chain O residue 46 MET Chi-restraints excluded: chain O residue 60 ASN Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain P residue 46 MET Chi-restraints excluded: chain P residue 60 ASN Chi-restraints excluded: chain P residue 216 LEU Chi-restraints excluded: chain Q residue 46 MET Chi-restraints excluded: chain Q residue 60 ASN Chi-restraints excluded: chain Q residue 216 LEU Chi-restraints excluded: chain R residue 46 MET Chi-restraints excluded: chain R residue 60 ASN Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 60 ASN Chi-restraints excluded: chain S residue 216 LEU Chi-restraints excluded: chain T residue 46 MET Chi-restraints excluded: chain T residue 60 ASN Chi-restraints excluded: chain T residue 216 LEU Chi-restraints excluded: chain V residue 46 MET Chi-restraints excluded: chain V residue 60 ASN Chi-restraints excluded: chain V residue 216 LEU Chi-restraints excluded: chain W residue 46 MET Chi-restraints excluded: chain W residue 60 ASN Chi-restraints excluded: chain W residue 216 LEU Chi-restraints excluded: chain X residue 46 MET Chi-restraints excluded: chain X residue 60 ASN Chi-restraints excluded: chain X residue 216 LEU Chi-restraints excluded: chain Y residue 46 MET Chi-restraints excluded: chain Y residue 60 ASN Chi-restraints excluded: chain Y residue 216 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1368 random chunks: chunk 665 optimal weight: 4.9990 chunk 862 optimal weight: 8.9990 chunk 1156 optimal weight: 30.0000 chunk 332 optimal weight: 10.0000 chunk 1000 optimal weight: 10.0000 chunk 160 optimal weight: 0.3980 chunk 301 optimal weight: 40.0000 chunk 1086 optimal weight: 30.0000 chunk 454 optimal weight: 20.0000 chunk 1116 optimal weight: 40.0000 chunk 137 optimal weight: 20.0000 overall best weight: 6.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 GLN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 GLN ** F 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 GLN ** G 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 295 GLN ** I 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 295 GLN ** N 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 295 GLN ** Q 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 295 GLN ** R 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 295 GLN ** S 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 295 GLN ** V 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 295 GLN ** W 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 295 GLN ** Y 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.031892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.024242 restraints weight = 1603258.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.024633 restraints weight = 1168981.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.024910 restraints weight = 963681.188| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 109440 Z= 0.214 Angle : 0.694 14.516 148968 Z= 0.339 Chirality : 0.043 0.218 16680 Planarity : 0.004 0.037 19632 Dihedral : 4.055 35.962 15216 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.63 % Allowed : 17.72 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.08), residues: 13608 helix: 1.44 (0.08), residues: 4848 sheet: 1.11 (0.10), residues: 3072 loop : 0.97 (0.09), residues: 5688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 519 HIS 0.002 0.001 HIS Q 116 PHE 0.026 0.001 PHE K 225 TYR 0.008 0.001 TYR H 166 ARG 0.005 0.000 ARG X 320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17029.38 seconds wall clock time: 302 minutes 34.49 seconds (18154.49 seconds total)