Starting phenix.real_space_refine on Fri Oct 11 10:57:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7d_36038/10_2024/8j7d_36038_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7d_36038/10_2024/8j7d_36038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7d_36038/10_2024/8j7d_36038.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7d_36038/10_2024/8j7d_36038.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7d_36038/10_2024/8j7d_36038_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7d_36038/10_2024/8j7d_36038_neut_trim.cif" } resolution = 2.7 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= -0.000 sd= 0.060 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 314 5.16 5 C 35008 2.51 5 N 9744 2.21 5 O 10456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 259 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 55522 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5208 Classifications: {'peptide': 671} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 642} Chain: "B" Number of atoms: 4154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4154 Classifications: {'peptide': 541} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "C" Number of atoms: 4070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4070 Classifications: {'peptide': 529} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 506} Chain breaks: 1 Chain: "D" Number of atoms: 5065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5065 Classifications: {'peptide': 651} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 622} Chain breaks: 2 Chain: "E" Number of atoms: 4070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4070 Classifications: {'peptide': 529} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 506} Chain breaks: 1 Chain: "F" Number of atoms: 5065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5065 Classifications: {'peptide': 651} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 622} Chain breaks: 2 Chain: "G" Number of atoms: 4154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4154 Classifications: {'peptide': 541} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "H" Number of atoms: 5208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5208 Classifications: {'peptide': 671} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 642} Chain: "I" Number of atoms: 5065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5065 Classifications: {'peptide': 651} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 622} Chain breaks: 2 Chain: "J" Number of atoms: 4154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4154 Classifications: {'peptide': 541} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "K" Number of atoms: 4154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4154 Classifications: {'peptide': 541} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "L" Number of atoms: 5065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5065 Classifications: {'peptide': 651} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 622} Chain breaks: 2 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 23.83, per 1000 atoms: 0.43 Number of scatterers: 55522 At special positions: 0 Unit cell: (238.244, 249.223, 154.804, 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 314 16.00 O 10456 8.00 N 9744 7.00 C 35008 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 - 3.00 Amino acid : True - 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.27 Conformation dependent library (CDL) restraints added in 5.6 seconds 14248 Ramachandran restraints generated. 7124 Oldfield, 0 Emsley, 7124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13136 Finding SS restraints... Secondary structure from input PDB file: 279 helices and 78 sheets defined 42.7% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.97 Creating SS restraints... Processing helix chain 'A' and resid 57 through 71 removed outlier: 3.571A pdb=" N ALA A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.506A pdb=" N ARG A 84 " --> pdb=" O GLU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 102 through 106 Processing helix chain 'A' and resid 109 through 120 Processing helix chain 'A' and resid 135 through 145 Processing helix chain 'A' and resid 153 through 162 removed outlier: 3.902A pdb=" N ILE A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 173 Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 223 through 240 Processing helix chain 'A' and resid 295 through 313 Processing helix chain 'A' and resid 343 through 352 removed outlier: 4.175A pdb=" N THR A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 443 through 458 Processing helix chain 'A' and resid 466 through 475 Processing helix chain 'A' and resid 476 through 482 Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 492 through 497 Processing helix chain 'A' and resid 504 through 529 removed outlier: 3.964A pdb=" N GLN A 529 " --> pdb=" O THR A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 539 Processing helix chain 'B' and resid 39 through 65 removed outlier: 3.636A pdb=" N LEU B 65 " --> pdb=" O GLU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 78 Processing helix chain 'B' and resid 82 through 91 Processing helix chain 'B' and resid 114 through 117 Processing helix chain 'B' and resid 140 through 144 Processing helix chain 'B' and resid 146 through 164 Processing helix chain 'B' and resid 177 through 184 removed outlier: 5.810A pdb=" N ALA B 182 " --> pdb=" O PRO B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 204 removed outlier: 4.291A pdb=" N PHE B 195 " --> pdb=" O PHE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 227 removed outlier: 3.522A pdb=" N ALA B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA B 227 " --> pdb=" O VAL B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 252 Processing helix chain 'B' and resid 256 through 261 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 316 through 322 Processing helix chain 'B' and resid 330 through 337 removed outlier: 3.926A pdb=" N VAL B 334 " --> pdb=" O ASP B 330 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 6.672A pdb=" N GLY B 341 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 395 Processing helix chain 'B' and resid 415 through 432 removed outlier: 3.729A pdb=" N ALA B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET B 425 " --> pdb=" O ASP B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 452 removed outlier: 4.110A pdb=" N TYR B 450 " --> pdb=" O GLY B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 458 Processing helix chain 'B' and resid 474 through 494 removed outlier: 3.622A pdb=" N LYS B 487 " --> pdb=" O ALA B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 517 Proline residue: B 508 - end of helix Processing helix chain 'B' and resid 518 through 525 removed outlier: 3.656A pdb=" N ARG B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 535 No H-bonds generated for 'chain 'B' and resid 533 through 535' Processing helix chain 'B' and resid 536 through 549 Processing helix chain 'C' and resid 39 through 65 removed outlier: 3.638A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 78 Processing helix chain 'C' and resid 82 through 91 Processing helix chain 'C' and resid 114 through 117 Processing helix chain 'C' and resid 140 through 144 Processing helix chain 'C' and resid 146 through 164 Processing helix chain 'C' and resid 177 through 184 removed outlier: 5.813A pdb=" N ALA C 182 " --> pdb=" O PRO C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 204 removed outlier: 4.290A pdb=" N PHE C 195 " --> pdb=" O PHE C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 227 removed outlier: 3.579A pdb=" N ALA C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 261 Processing helix chain 'C' and resid 261 through 269 removed outlier: 4.146A pdb=" N LEU C 265 " --> pdb=" O GLY C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 293 Processing helix chain 'C' and resid 316 through 322 Processing helix chain 'C' and resid 330 through 337 removed outlier: 3.924A pdb=" N VAL C 334 " --> pdb=" O ASP C 330 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG C 337 " --> pdb=" O GLU C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 removed outlier: 6.673A pdb=" N GLY C 341 " --> pdb=" O ILE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 395 Processing helix chain 'C' and resid 410 through 416 Processing helix chain 'C' and resid 417 through 432 removed outlier: 3.569A pdb=" N MET C 425 " --> pdb=" O ASP C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 452 removed outlier: 4.109A pdb=" N TYR C 450 " --> pdb=" O GLY C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 458 Processing helix chain 'C' and resid 474 through 494 removed outlier: 3.622A pdb=" N LYS C 487 " --> pdb=" O ALA C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 517 Proline residue: C 508 - end of helix Processing helix chain 'C' and resid 518 through 525 removed outlier: 3.656A pdb=" N ARG C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 535 No H-bonds generated for 'chain 'C' and resid 533 through 535' Processing helix chain 'C' and resid 536 through 549 Processing helix chain 'D' and resid 57 through 72 removed outlier: 3.523A pdb=" N ALA D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 4.486A pdb=" N ASN D 85 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 92 Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'D' and resid 109 through 120 Processing helix chain 'D' and resid 135 through 145 Processing helix chain 'D' and resid 153 through 162 Processing helix chain 'D' and resid 162 through 174 Processing helix chain 'D' and resid 187 through 199 Processing helix chain 'D' and resid 223 through 233 Processing helix chain 'D' and resid 295 through 313 Processing helix chain 'D' and resid 343 through 352 removed outlier: 4.493A pdb=" N THR D 347 " --> pdb=" O GLU D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 365 Processing helix chain 'D' and resid 443 through 457 Processing helix chain 'D' and resid 466 through 476 Processing helix chain 'D' and resid 476 through 482 Processing helix chain 'D' and resid 487 through 492 Processing helix chain 'D' and resid 492 through 497 Processing helix chain 'D' and resid 504 through 530 removed outlier: 3.624A pdb=" N GLN D 529 " --> pdb=" O THR D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 539 Processing helix chain 'D' and resid 634 through 639 Processing helix chain 'D' and resid 639 through 646 removed outlier: 3.889A pdb=" N GLN D 643 " --> pdb=" O SER D 639 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN D 646 " --> pdb=" O SER D 642 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 65 removed outlier: 3.639A pdb=" N LEU E 65 " --> pdb=" O GLU E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 78 Processing helix chain 'E' and resid 82 through 91 Processing helix chain 'E' and resid 114 through 117 Processing helix chain 'E' and resid 140 through 144 Processing helix chain 'E' and resid 146 through 164 Processing helix chain 'E' and resid 177 through 184 removed outlier: 5.813A pdb=" N ALA E 182 " --> pdb=" O PRO E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 204 removed outlier: 4.290A pdb=" N PHE E 195 " --> pdb=" O PHE E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 227 removed outlier: 3.580A pdb=" N ALA E 225 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 261 Processing helix chain 'E' and resid 261 through 269 removed outlier: 4.147A pdb=" N LEU E 265 " --> pdb=" O GLY E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 293 Processing helix chain 'E' and resid 316 through 322 Processing helix chain 'E' and resid 330 through 337 removed outlier: 3.925A pdb=" N VAL E 334 " --> pdb=" O ASP E 330 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG E 337 " --> pdb=" O GLU E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 removed outlier: 6.673A pdb=" N GLY E 341 " --> pdb=" O ILE E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 395 Processing helix chain 'E' and resid 410 through 416 Processing helix chain 'E' and resid 417 through 432 removed outlier: 3.569A pdb=" N MET E 425 " --> pdb=" O ASP E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 452 removed outlier: 4.108A pdb=" N TYR E 450 " --> pdb=" O GLY E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 458 Processing helix chain 'E' and resid 474 through 494 removed outlier: 3.623A pdb=" N LYS E 487 " --> pdb=" O ALA E 483 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 517 Proline residue: E 508 - end of helix Processing helix chain 'E' and resid 518 through 525 removed outlier: 3.656A pdb=" N ARG E 525 " --> pdb=" O TYR E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 535 No H-bonds generated for 'chain 'E' and resid 533 through 535' Processing helix chain 'E' and resid 536 through 549 Processing helix chain 'F' and resid 57 through 72 removed outlier: 3.523A pdb=" N ALA F 61 " --> pdb=" O ARG F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 85 removed outlier: 4.487A pdb=" N ASN F 85 " --> pdb=" O ALA F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 92 Processing helix chain 'F' and resid 102 through 106 Processing helix chain 'F' and resid 109 through 120 Processing helix chain 'F' and resid 135 through 145 Processing helix chain 'F' and resid 153 through 162 Processing helix chain 'F' and resid 162 through 174 Processing helix chain 'F' and resid 187 through 199 Processing helix chain 'F' and resid 223 through 233 Processing helix chain 'F' and resid 295 through 313 Processing helix chain 'F' and resid 343 through 352 removed outlier: 4.493A pdb=" N THR F 347 " --> pdb=" O GLU F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 365 Processing helix chain 'F' and resid 443 through 457 Processing helix chain 'F' and resid 466 through 476 Processing helix chain 'F' and resid 476 through 482 Processing helix chain 'F' and resid 487 through 492 Processing helix chain 'F' and resid 492 through 497 Processing helix chain 'F' and resid 504 through 530 removed outlier: 3.623A pdb=" N GLN F 529 " --> pdb=" O THR F 525 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 539 Processing helix chain 'F' and resid 634 through 639 Processing helix chain 'F' and resid 639 through 646 removed outlier: 3.890A pdb=" N GLN F 643 " --> pdb=" O SER F 639 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN F 646 " --> pdb=" O SER F 642 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 65 removed outlier: 3.638A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 78 Processing helix chain 'G' and resid 82 through 91 Processing helix chain 'G' and resid 114 through 117 Processing helix chain 'G' and resid 140 through 144 Processing helix chain 'G' and resid 146 through 164 Processing helix chain 'G' and resid 177 through 184 removed outlier: 5.812A pdb=" N ALA G 182 " --> pdb=" O PRO G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 204 removed outlier: 4.290A pdb=" N PHE G 195 " --> pdb=" O PHE G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 227 removed outlier: 3.580A pdb=" N ALA G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 252 Processing helix chain 'G' and resid 256 through 261 Processing helix chain 'G' and resid 261 through 269 removed outlier: 4.146A pdb=" N LEU G 265 " --> pdb=" O GLY G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 293 Processing helix chain 'G' and resid 316 through 322 Processing helix chain 'G' and resid 330 through 337 removed outlier: 3.925A pdb=" N VAL G 334 " --> pdb=" O ASP G 330 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG G 337 " --> pdb=" O GLU G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 343 removed outlier: 6.672A pdb=" N GLY G 341 " --> pdb=" O ILE G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 377 through 395 Processing helix chain 'G' and resid 410 through 416 Processing helix chain 'G' and resid 417 through 432 removed outlier: 3.569A pdb=" N MET G 425 " --> pdb=" O ASP G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 446 through 452 removed outlier: 4.108A pdb=" N TYR G 450 " --> pdb=" O GLY G 446 " (cutoff:3.500A) Processing helix chain 'G' and resid 454 through 458 Processing helix chain 'G' and resid 474 through 494 removed outlier: 3.623A pdb=" N LYS G 487 " --> pdb=" O ALA G 483 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 517 Proline residue: G 508 - end of helix Processing helix chain 'G' and resid 518 through 525 removed outlier: 3.656A pdb=" N ARG G 525 " --> pdb=" O TYR G 521 " (cutoff:3.500A) Processing helix chain 'G' and resid 533 through 535 No H-bonds generated for 'chain 'G' and resid 533 through 535' Processing helix chain 'G' and resid 536 through 549 Processing helix chain 'H' and resid 57 through 71 removed outlier: 3.571A pdb=" N ALA H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR H 67 " --> pdb=" O ARG H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 84 removed outlier: 3.506A pdb=" N ARG H 84 " --> pdb=" O GLU H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 92 Processing helix chain 'H' and resid 102 through 106 Processing helix chain 'H' and resid 109 through 120 Processing helix chain 'H' and resid 135 through 145 Processing helix chain 'H' and resid 153 through 162 removed outlier: 3.909A pdb=" N ILE H 162 " --> pdb=" O ARG H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 173 Processing helix chain 'H' and resid 187 through 199 Processing helix chain 'H' and resid 223 through 240 Processing helix chain 'H' and resid 295 through 313 Processing helix chain 'H' and resid 343 through 352 removed outlier: 4.174A pdb=" N THR H 347 " --> pdb=" O GLU H 343 " (cutoff:3.500A) Processing helix chain 'H' and resid 354 through 364 Processing helix chain 'H' and resid 443 through 458 Processing helix chain 'H' and resid 466 through 475 Processing helix chain 'H' and resid 476 through 482 Processing helix chain 'H' and resid 487 through 497 removed outlier: 5.559A pdb=" N LYS H 494 " --> pdb=" O PRO H 490 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN H 495 " --> pdb=" O GLN H 491 " (cutoff:3.500A) Processing helix chain 'H' and resid 504 through 529 removed outlier: 3.964A pdb=" N GLN H 529 " --> pdb=" O THR H 525 " (cutoff:3.500A) Processing helix chain 'H' and resid 535 through 539 Processing helix chain 'I' and resid 57 through 72 removed outlier: 3.524A pdb=" N ALA I 61 " --> pdb=" O ARG I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 85 removed outlier: 4.487A pdb=" N ASN I 85 " --> pdb=" O ALA I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 91 Processing helix chain 'I' and resid 102 through 106 Processing helix chain 'I' and resid 109 through 120 Processing helix chain 'I' and resid 135 through 145 Processing helix chain 'I' and resid 153 through 162 Processing helix chain 'I' and resid 162 through 174 Processing helix chain 'I' and resid 187 through 199 Processing helix chain 'I' and resid 223 through 233 Processing helix chain 'I' and resid 295 through 313 Processing helix chain 'I' and resid 343 through 352 removed outlier: 4.494A pdb=" N THR I 347 " --> pdb=" O GLU I 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 365 Processing helix chain 'I' and resid 443 through 457 Processing helix chain 'I' and resid 466 through 476 Processing helix chain 'I' and resid 476 through 482 Processing helix chain 'I' and resid 487 through 492 Processing helix chain 'I' and resid 492 through 497 Processing helix chain 'I' and resid 504 through 530 removed outlier: 3.623A pdb=" N GLN I 529 " --> pdb=" O THR I 525 " (cutoff:3.500A) Processing helix chain 'I' and resid 535 through 539 Processing helix chain 'I' and resid 634 through 639 Processing helix chain 'I' and resid 639 through 646 removed outlier: 3.890A pdb=" N GLN I 643 " --> pdb=" O SER I 639 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN I 646 " --> pdb=" O SER I 642 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 65 removed outlier: 3.638A pdb=" N LEU J 65 " --> pdb=" O GLU J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 78 Processing helix chain 'J' and resid 82 through 91 Processing helix chain 'J' and resid 114 through 117 Processing helix chain 'J' and resid 140 through 144 Processing helix chain 'J' and resid 146 through 164 Processing helix chain 'J' and resid 177 through 184 removed outlier: 5.813A pdb=" N ALA J 182 " --> pdb=" O PRO J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 204 removed outlier: 4.290A pdb=" N PHE J 195 " --> pdb=" O PHE J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 227 removed outlier: 3.580A pdb=" N ALA J 225 " --> pdb=" O ALA J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 243 through 252 Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 261 through 269 removed outlier: 4.146A pdb=" N LEU J 265 " --> pdb=" O GLY J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 293 Processing helix chain 'J' and resid 316 through 322 Processing helix chain 'J' and resid 330 through 337 removed outlier: 3.925A pdb=" N VAL J 334 " --> pdb=" O ASP J 330 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG J 337 " --> pdb=" O GLU J 333 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 343 removed outlier: 6.673A pdb=" N GLY J 341 " --> pdb=" O ILE J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 395 Processing helix chain 'J' and resid 410 through 416 Processing helix chain 'J' and resid 417 through 432 removed outlier: 3.569A pdb=" N MET J 425 " --> pdb=" O ASP J 421 " (cutoff:3.500A) Processing helix chain 'J' and resid 446 through 452 removed outlier: 4.108A pdb=" N TYR J 450 " --> pdb=" O GLY J 446 " (cutoff:3.500A) Processing helix chain 'J' and resid 454 through 458 Processing helix chain 'J' and resid 474 through 494 removed outlier: 3.623A pdb=" N LYS J 487 " --> pdb=" O ALA J 483 " (cutoff:3.500A) Processing helix chain 'J' and resid 498 through 517 Proline residue: J 508 - end of helix Processing helix chain 'J' and resid 518 through 525 removed outlier: 3.656A pdb=" N ARG J 525 " --> pdb=" O TYR J 521 " (cutoff:3.500A) Processing helix chain 'J' and resid 533 through 535 No H-bonds generated for 'chain 'J' and resid 533 through 535' Processing helix chain 'J' and resid 536 through 549 Processing helix chain 'K' and resid 39 through 65 removed outlier: 3.636A pdb=" N LEU K 65 " --> pdb=" O GLU K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 78 Processing helix chain 'K' and resid 82 through 91 Processing helix chain 'K' and resid 114 through 117 Processing helix chain 'K' and resid 140 through 144 Processing helix chain 'K' and resid 146 through 164 Processing helix chain 'K' and resid 177 through 184 removed outlier: 5.809A pdb=" N ALA K 182 " --> pdb=" O PRO K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 204 removed outlier: 4.292A pdb=" N PHE K 195 " --> pdb=" O PHE K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 227 removed outlier: 3.522A pdb=" N ALA K 225 " --> pdb=" O ALA K 221 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA K 227 " --> pdb=" O VAL K 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 252 Processing helix chain 'K' and resid 256 through 261 Processing helix chain 'K' and resid 263 through 268 Processing helix chain 'K' and resid 279 through 293 Processing helix chain 'K' and resid 316 through 322 Processing helix chain 'K' and resid 330 through 337 removed outlier: 3.926A pdb=" N VAL K 334 " --> pdb=" O ASP K 330 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG K 337 " --> pdb=" O GLU K 333 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 343 removed outlier: 6.672A pdb=" N GLY K 341 " --> pdb=" O ILE K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 377 through 395 Processing helix chain 'K' and resid 415 through 432 removed outlier: 3.692A pdb=" N ALA K 423 " --> pdb=" O ALA K 419 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LYS K 424 " --> pdb=" O LYS K 420 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET K 425 " --> pdb=" O ASP K 421 " (cutoff:3.500A) Processing helix chain 'K' and resid 446 through 452 removed outlier: 4.110A pdb=" N TYR K 450 " --> pdb=" O GLY K 446 " (cutoff:3.500A) Processing helix chain 'K' and resid 454 through 458 Processing helix chain 'K' and resid 474 through 494 removed outlier: 3.622A pdb=" N LYS K 487 " --> pdb=" O ALA K 483 " (cutoff:3.500A) Processing helix chain 'K' and resid 498 through 517 Proline residue: K 508 - end of helix Processing helix chain 'K' and resid 518 through 525 removed outlier: 3.656A pdb=" N ARG K 525 " --> pdb=" O TYR K 521 " (cutoff:3.500A) Processing helix chain 'K' and resid 533 through 535 No H-bonds generated for 'chain 'K' and resid 533 through 535' Processing helix chain 'K' and resid 536 through 549 Processing helix chain 'L' and resid 57 through 72 removed outlier: 3.523A pdb=" N ALA L 61 " --> pdb=" O ARG L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 4.486A pdb=" N ASN L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 92 Processing helix chain 'L' and resid 102 through 106 Processing helix chain 'L' and resid 109 through 120 Processing helix chain 'L' and resid 135 through 145 Processing helix chain 'L' and resid 153 through 162 Processing helix chain 'L' and resid 162 through 174 Processing helix chain 'L' and resid 187 through 199 Processing helix chain 'L' and resid 223 through 233 Processing helix chain 'L' and resid 295 through 313 Processing helix chain 'L' and resid 343 through 352 removed outlier: 4.493A pdb=" N THR L 347 " --> pdb=" O GLU L 343 " (cutoff:3.500A) Processing helix chain 'L' and resid 354 through 365 Processing helix chain 'L' and resid 443 through 457 Processing helix chain 'L' and resid 466 through 476 Processing helix chain 'L' and resid 476 through 482 Processing helix chain 'L' and resid 487 through 492 Processing helix chain 'L' and resid 492 through 497 Processing helix chain 'L' and resid 504 through 530 removed outlier: 3.623A pdb=" N GLN L 529 " --> pdb=" O THR L 525 " (cutoff:3.500A) Processing helix chain 'L' and resid 535 through 539 Processing helix chain 'L' and resid 634 through 639 Processing helix chain 'L' and resid 639 through 646 removed outlier: 3.889A pdb=" N GLN L 643 " --> pdb=" O SER L 639 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLN L 646 " --> pdb=" O SER L 642 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 97 removed outlier: 3.905A pdb=" N GLU A 94 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL A 78 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS A 51 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N HIS A 126 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU A 53 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 216 through 218 removed outlier: 3.540A pdb=" N LYS A 205 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 268 through 270 removed outlier: 5.671A pdb=" N ILE A 324 " --> pdb=" O PHE A 333 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N PHE A 333 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 268 through 270 removed outlier: 5.999A pdb=" N HIS A 255 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS A 276 " --> pdb=" O HIS A 255 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SER A 277 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ILE A 286 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLN A 279 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS A 284 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 13.317A pdb=" N GLN A 283 " --> pdb=" O TYR A 387 " (cutoff:3.500A) removed outlier: 10.754A pdb=" N TYR A 387 " --> pdb=" O GLN A 283 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE A 285 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N HIS A 380 " --> pdb=" O TRP A 440 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TRP A 440 " --> pdb=" O HIS A 380 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE A 382 " --> pdb=" O VAL A 438 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL A 438 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA A 384 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LYS A 436 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 386 " --> pdb=" O ILE A 434 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 389 through 390 removed outlier: 3.540A pdb=" N MET A 396 " --> pdb=" O ASP A 390 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 400 through 401 removed outlier: 3.787A pdb=" N GLY A 400 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 404 through 406 Processing sheet with id=AA8, first strand: chain 'D' and resid 148 through 149 removed outlier: 6.938A pdb=" N LYS D 51 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N HIS D 126 " --> pdb=" O LYS D 51 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU D 53 " --> pdb=" O HIS D 126 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL D 78 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 95 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N THR A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 683 through 687 removed outlier: 3.661A pdb=" N MET A 675 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU A 674 " --> pdb=" O VAL A 660 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL A 660 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL A 676 " --> pdb=" O GLU A 658 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 694 through 697 Processing sheet with id=AB2, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.729A pdb=" N THR B 121 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS B 167 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL B 211 " --> pdb=" O CYS B 167 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TYR B 169 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN B 230 " --> pdb=" O HIS B 275 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA B 277 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE B 232 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 215 through 216 Processing sheet with id=AB4, first strand: chain 'B' and resid 345 through 346 removed outlier: 7.656A pdb=" N LEU B 399 " --> pdb=" O PRO B 366 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY B 368 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU B 401 " --> pdb=" O GLY B 368 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL B 370 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE B 461 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 443 through 445 removed outlier: 6.113A pdb=" N SER B 444 " --> pdb=" O SER B 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.730A pdb=" N THR C 121 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS C 167 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL C 211 " --> pdb=" O CYS C 167 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N TYR C 169 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN C 230 " --> pdb=" O HIS C 275 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ALA C 277 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE C 232 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 215 through 217 removed outlier: 3.654A pdb=" N PHE C 240 " --> pdb=" O CYS C 216 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 345 through 346 removed outlier: 7.656A pdb=" N LEU C 399 " --> pdb=" O PRO C 366 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLY C 368 " --> pdb=" O LEU C 399 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU C 401 " --> pdb=" O GLY C 368 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL C 370 " --> pdb=" O LEU C 401 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE C 461 " --> pdb=" O LYS C 436 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 443 through 445 removed outlier: 6.111A pdb=" N SER C 444 " --> pdb=" O SER C 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 268 through 275 removed outlier: 3.959A pdb=" N GLN D 259 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU D 273 " --> pdb=" O GLU D 257 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU D 257 " --> pdb=" O GLU D 273 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ASP D 275 " --> pdb=" O HIS D 255 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N HIS D 255 " --> pdb=" O ASP D 275 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG D 254 " --> pdb=" O MET D 325 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU D 335 " --> pdb=" O GLU D 322 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE D 324 " --> pdb=" O PHE D 333 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N PHE D 333 " --> pdb=" O ILE D 324 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 279 through 280 Processing sheet with id=AC3, first strand: chain 'D' and resid 286 through 289 Processing sheet with id=AC4, first strand: chain 'D' and resid 404 through 406 Processing sheet with id=AC5, first strand: chain 'D' and resid 543 through 544 removed outlier: 3.924A pdb=" N ARG D 544 " --> pdb=" O ILE D 547 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE D 547 " --> pdb=" O ARG D 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 550 through 557 removed outlier: 4.714A pdb=" N THR D 596 " --> pdb=" O LEU D 611 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 683 through 687 removed outlier: 3.580A pdb=" N MET D 675 " --> pdb=" O ILE D 686 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU D 674 " --> pdb=" O VAL D 660 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL D 660 " --> pdb=" O LEU D 674 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL D 676 " --> pdb=" O GLU D 658 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 694 through 697 Processing sheet with id=AC9, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.729A pdb=" N THR E 121 " --> pdb=" O LEU E 100 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS E 167 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL E 211 " --> pdb=" O CYS E 167 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR E 169 " --> pdb=" O VAL E 211 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN E 230 " --> pdb=" O HIS E 275 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ALA E 277 " --> pdb=" O ASN E 230 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE E 232 " --> pdb=" O ALA E 277 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 215 through 217 removed outlier: 3.654A pdb=" N PHE E 240 " --> pdb=" O CYS E 216 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 345 through 346 removed outlier: 7.656A pdb=" N LEU E 399 " --> pdb=" O PRO E 366 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLY E 368 " --> pdb=" O LEU E 399 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU E 401 " --> pdb=" O GLY E 368 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL E 370 " --> pdb=" O LEU E 401 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE E 461 " --> pdb=" O LYS E 436 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 443 through 445 removed outlier: 6.111A pdb=" N SER E 444 " --> pdb=" O SER E 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 94 through 97 removed outlier: 3.930A pdb=" N VAL F 78 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS F 51 " --> pdb=" O ALA F 124 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N HIS F 126 " --> pdb=" O LYS F 51 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU F 53 " --> pdb=" O HIS F 126 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 268 through 275 removed outlier: 3.959A pdb=" N GLN F 259 " --> pdb=" O LEU F 271 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU F 273 " --> pdb=" O GLU F 257 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU F 257 " --> pdb=" O GLU F 273 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ASP F 275 " --> pdb=" O HIS F 255 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N HIS F 255 " --> pdb=" O ASP F 275 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG F 254 " --> pdb=" O MET F 325 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU F 335 " --> pdb=" O GLU F 322 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ILE F 324 " --> pdb=" O PHE F 333 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N PHE F 333 " --> pdb=" O ILE F 324 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 279 through 280 Processing sheet with id=AD7, first strand: chain 'F' and resid 286 through 289 Processing sheet with id=AD8, first strand: chain 'F' and resid 404 through 406 Processing sheet with id=AD9, first strand: chain 'F' and resid 543 through 544 removed outlier: 3.924A pdb=" N ARG F 544 " --> pdb=" O ILE F 547 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE F 547 " --> pdb=" O ARG F 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'F' and resid 550 through 557 removed outlier: 4.714A pdb=" N THR F 596 " --> pdb=" O LEU F 611 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 683 through 687 removed outlier: 3.580A pdb=" N MET F 675 " --> pdb=" O ILE F 686 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU F 674 " --> pdb=" O VAL F 660 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL F 660 " --> pdb=" O LEU F 674 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL F 676 " --> pdb=" O GLU F 658 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 694 through 697 Processing sheet with id=AE4, first strand: chain 'G' and resid 98 through 100 removed outlier: 4.730A pdb=" N THR G 121 " --> pdb=" O LEU G 100 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N CYS G 167 " --> pdb=" O ILE G 209 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL G 211 " --> pdb=" O CYS G 167 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR G 169 " --> pdb=" O VAL G 211 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN G 230 " --> pdb=" O HIS G 275 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ALA G 277 " --> pdb=" O ASN G 230 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE G 232 " --> pdb=" O ALA G 277 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 215 through 217 removed outlier: 3.654A pdb=" N PHE G 240 " --> pdb=" O CYS G 216 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 345 through 346 removed outlier: 7.656A pdb=" N LEU G 399 " --> pdb=" O PRO G 366 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLY G 368 " --> pdb=" O LEU G 399 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU G 401 " --> pdb=" O GLY G 368 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL G 370 " --> pdb=" O LEU G 401 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE G 461 " --> pdb=" O LYS G 436 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 443 through 445 removed outlier: 6.111A pdb=" N SER G 444 " --> pdb=" O SER G 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'H' and resid 94 through 97 removed outlier: 3.924A pdb=" N GLU H 94 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL H 78 " --> pdb=" O ILE H 54 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS H 51 " --> pdb=" O ALA H 124 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N HIS H 126 " --> pdb=" O LYS H 51 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU H 53 " --> pdb=" O HIS H 126 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 216 through 218 removed outlier: 3.540A pdb=" N LYS H 205 " --> pdb=" O LEU H 245 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 268 through 270 removed outlier: 5.672A pdb=" N ILE H 324 " --> pdb=" O PHE H 333 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE H 333 " --> pdb=" O ILE H 324 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 268 through 270 removed outlier: 5.999A pdb=" N HIS H 255 " --> pdb=" O CYS H 276 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS H 276 " --> pdb=" O HIS H 255 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SER H 277 " --> pdb=" O ILE H 286 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE H 286 " --> pdb=" O SER H 277 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN H 279 " --> pdb=" O LYS H 284 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS H 284 " --> pdb=" O GLN H 279 " (cutoff:3.500A) removed outlier: 13.309A pdb=" N GLN H 283 " --> pdb=" O TYR H 387 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N TYR H 387 " --> pdb=" O GLN H 283 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE H 285 " --> pdb=" O ARG H 385 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N HIS H 380 " --> pdb=" O TRP H 440 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TRP H 440 " --> pdb=" O HIS H 380 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE H 382 " --> pdb=" O VAL H 438 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL H 438 " --> pdb=" O PHE H 382 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA H 384 " --> pdb=" O LYS H 436 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LYS H 436 " --> pdb=" O ALA H 384 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE H 386 " --> pdb=" O ILE H 434 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 389 through 390 removed outlier: 3.540A pdb=" N MET H 396 " --> pdb=" O ASP H 390 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 400 through 401 removed outlier: 3.787A pdb=" N GLY H 400 " --> pdb=" O VAL H 426 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 404 through 406 Processing sheet with id=AF6, first strand: chain 'L' and resid 148 through 149 removed outlier: 6.938A pdb=" N LYS L 51 " --> pdb=" O ALA L 124 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N HIS L 126 " --> pdb=" O LYS L 51 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU L 53 " --> pdb=" O HIS L 126 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL L 78 " --> pdb=" O ILE L 54 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA L 95 " --> pdb=" O ALA H 606 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR H 596 " --> pdb=" O LEU H 611 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 683 through 687 removed outlier: 3.660A pdb=" N MET H 675 " --> pdb=" O ILE H 686 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU H 674 " --> pdb=" O VAL H 660 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL H 660 " --> pdb=" O LEU H 674 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL H 676 " --> pdb=" O GLU H 658 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 694 through 697 Processing sheet with id=AF9, first strand: chain 'I' and resid 94 through 97 removed outlier: 3.930A pdb=" N VAL I 78 " --> pdb=" O ILE I 54 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS I 51 " --> pdb=" O ALA I 124 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N HIS I 126 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU I 53 " --> pdb=" O HIS I 126 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 268 through 275 removed outlier: 3.959A pdb=" N GLN I 259 " --> pdb=" O LEU I 271 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU I 273 " --> pdb=" O GLU I 257 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU I 257 " --> pdb=" O GLU I 273 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASP I 275 " --> pdb=" O HIS I 255 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N HIS I 255 " --> pdb=" O ASP I 275 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG I 254 " --> pdb=" O MET I 325 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU I 335 " --> pdb=" O GLU I 322 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ILE I 324 " --> pdb=" O PHE I 333 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N PHE I 333 " --> pdb=" O ILE I 324 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 279 through 280 Processing sheet with id=AG3, first strand: chain 'I' and resid 286 through 289 Processing sheet with id=AG4, first strand: chain 'I' and resid 404 through 406 Processing sheet with id=AG5, first strand: chain 'I' and resid 543 through 544 removed outlier: 3.923A pdb=" N ARG I 544 " --> pdb=" O ILE I 547 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE I 547 " --> pdb=" O ARG I 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'I' and resid 550 through 557 removed outlier: 4.714A pdb=" N THR I 596 " --> pdb=" O LEU I 611 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 683 through 687 removed outlier: 3.580A pdb=" N MET I 675 " --> pdb=" O ILE I 686 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU I 674 " --> pdb=" O VAL I 660 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL I 660 " --> pdb=" O LEU I 674 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL I 676 " --> pdb=" O GLU I 658 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 694 through 697 Processing sheet with id=AG9, first strand: chain 'J' and resid 98 through 100 removed outlier: 4.730A pdb=" N THR J 121 " --> pdb=" O LEU J 100 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS J 167 " --> pdb=" O ILE J 209 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL J 211 " --> pdb=" O CYS J 167 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N TYR J 169 " --> pdb=" O VAL J 211 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN J 230 " --> pdb=" O HIS J 275 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ALA J 277 " --> pdb=" O ASN J 230 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE J 232 " --> pdb=" O ALA J 277 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 215 through 217 removed outlier: 3.654A pdb=" N PHE J 240 " --> pdb=" O CYS J 216 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 345 through 346 removed outlier: 7.656A pdb=" N LEU J 399 " --> pdb=" O PRO J 366 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLY J 368 " --> pdb=" O LEU J 399 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU J 401 " --> pdb=" O GLY J 368 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL J 370 " --> pdb=" O LEU J 401 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE J 461 " --> pdb=" O LYS J 436 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 443 through 445 removed outlier: 6.111A pdb=" N SER J 444 " --> pdb=" O SER J 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'K' and resid 98 through 100 removed outlier: 4.730A pdb=" N THR K 121 " --> pdb=" O LEU K 100 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS K 167 " --> pdb=" O ILE K 209 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL K 211 " --> pdb=" O CYS K 167 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N TYR K 169 " --> pdb=" O VAL K 211 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 215 through 216 Processing sheet with id=AH6, first strand: chain 'K' and resid 345 through 346 removed outlier: 7.656A pdb=" N LEU K 399 " --> pdb=" O PRO K 366 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY K 368 " --> pdb=" O LEU K 399 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU K 401 " --> pdb=" O GLY K 368 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL K 370 " --> pdb=" O LEU K 401 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE K 461 " --> pdb=" O LYS K 436 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 443 through 445 removed outlier: 6.113A pdb=" N SER K 444 " --> pdb=" O SER K 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'L' and resid 268 through 275 removed outlier: 3.959A pdb=" N GLN L 259 " --> pdb=" O LEU L 271 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU L 273 " --> pdb=" O GLU L 257 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU L 257 " --> pdb=" O GLU L 273 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ASP L 275 " --> pdb=" O HIS L 255 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N HIS L 255 " --> pdb=" O ASP L 275 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG L 254 " --> pdb=" O MET L 325 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU L 335 " --> pdb=" O GLU L 322 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ILE L 324 " --> pdb=" O PHE L 333 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N PHE L 333 " --> pdb=" O ILE L 324 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 279 through 280 Processing sheet with id=AI1, first strand: chain 'L' and resid 286 through 289 Processing sheet with id=AI2, first strand: chain 'L' and resid 404 through 406 Processing sheet with id=AI3, first strand: chain 'L' and resid 543 through 544 removed outlier: 3.924A pdb=" N ARG L 544 " --> pdb=" O ILE L 547 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE L 547 " --> pdb=" O ARG L 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'L' and resid 550 through 557 removed outlier: 4.715A pdb=" N THR L 596 " --> pdb=" O LEU L 611 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'L' and resid 683 through 687 removed outlier: 3.580A pdb=" N MET L 675 " --> pdb=" O ILE L 686 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU L 674 " --> pdb=" O VAL L 660 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL L 660 " --> pdb=" O LEU L 674 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL L 676 " --> pdb=" O GLU L 658 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'L' and resid 694 through 697 2713 hydrogen bonds defined for protein. 7512 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: 28.77 Time building geometry restraints manager: 12.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 9527 1.31 - 1.44: 14240 1.44 - 1.57: 32301 1.57 - 1.70: 2 1.70 - 1.82: 526 Bond restraints: 56596 Sorted by residual: bond pdb=" C LYS G 424 " pdb=" N MET G 425 " ideal model delta sigma weight residual 1.335 1.232 0.103 1.36e-02 5.41e+03 5.75e+01 bond pdb=" C LYS J 424 " pdb=" N MET J 425 " ideal model delta sigma weight residual 1.335 1.232 0.103 1.36e-02 5.41e+03 5.75e+01 bond pdb=" C LYS C 424 " pdb=" N MET C 425 " ideal model delta sigma weight residual 1.335 1.232 0.103 1.36e-02 5.41e+03 5.73e+01 bond pdb=" C LYS E 424 " pdb=" N MET E 425 " ideal model delta sigma weight residual 1.335 1.232 0.103 1.36e-02 5.41e+03 5.73e+01 bond pdb=" CA ALA I 92 " pdb=" C ALA I 92 " ideal model delta sigma weight residual 1.524 1.456 0.068 1.26e-02 6.30e+03 2.90e+01 ... (remaining 56591 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 70628 2.49 - 4.99: 5529 4.99 - 7.48: 213 7.48 - 9.97: 53 9.97 - 12.47: 11 Bond angle restraints: 76434 Sorted by residual: angle pdb=" N ASP K 264 " pdb=" CA ASP K 264 " pdb=" C ASP K 264 " ideal model delta sigma weight residual 112.38 99.91 12.47 1.22e+00 6.72e-01 1.04e+02 angle pdb=" N ASP B 264 " pdb=" CA ASP B 264 " pdb=" C ASP B 264 " ideal model delta sigma weight residual 112.38 99.91 12.47 1.22e+00 6.72e-01 1.04e+02 angle pdb=" N LYS K 487 " pdb=" CA LYS K 487 " pdb=" C LYS K 487 " ideal model delta sigma weight residual 111.36 103.09 8.27 1.09e+00 8.42e-01 5.76e+01 angle pdb=" N LYS B 487 " pdb=" CA LYS B 487 " pdb=" C LYS B 487 " ideal model delta sigma weight residual 111.36 103.10 8.26 1.09e+00 8.42e-01 5.75e+01 angle pdb=" N LYS J 487 " pdb=" CA LYS J 487 " pdb=" C LYS J 487 " ideal model delta sigma weight residual 111.36 103.12 8.24 1.09e+00 8.42e-01 5.71e+01 ... (remaining 76429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 31775 17.84 - 35.68: 1938 35.68 - 53.52: 489 53.52 - 71.36: 114 71.36 - 89.20: 32 Dihedral angle restraints: 34348 sinusoidal: 13820 harmonic: 20528 Sorted by residual: dihedral pdb=" C THR D 486 " pdb=" N THR D 486 " pdb=" CA THR D 486 " pdb=" CB THR D 486 " ideal model delta harmonic sigma weight residual -122.00 -140.60 18.60 0 2.50e+00 1.60e-01 5.53e+01 dihedral pdb=" C THR F 486 " pdb=" N THR F 486 " pdb=" CA THR F 486 " pdb=" CB THR F 486 " ideal model delta harmonic sigma weight residual -122.00 -140.57 18.57 0 2.50e+00 1.60e-01 5.51e+01 dihedral pdb=" C THR L 486 " pdb=" N THR L 486 " pdb=" CA THR L 486 " pdb=" CB THR L 486 " ideal model delta harmonic sigma weight residual -122.00 -140.56 18.56 0 2.50e+00 1.60e-01 5.51e+01 ... (remaining 34345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 7138 0.127 - 0.254: 1213 0.254 - 0.381: 81 0.381 - 0.508: 2 0.508 - 0.635: 6 Chirality restraints: 8440 Sorted by residual: chirality pdb=" CA THR D 486 " pdb=" N THR D 486 " pdb=" C THR D 486 " pdb=" CB THR D 486 " both_signs ideal model delta sigma weight residual False 2.53 1.89 0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CA THR F 486 " pdb=" N THR F 486 " pdb=" C THR F 486 " pdb=" CB THR F 486 " both_signs ideal model delta sigma weight residual False 2.53 1.89 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CA THR L 486 " pdb=" N THR L 486 " pdb=" C THR L 486 " pdb=" CB THR L 486 " both_signs ideal model delta sigma weight residual False 2.53 1.89 0.63 2.00e-01 2.50e+01 1.00e+01 ... (remaining 8437 not shown) Planarity restraints: 10018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 145 " 0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" CD GLU A 145 " -0.067 2.00e-02 2.50e+03 pdb=" OE1 GLU A 145 " 0.024 2.00e-02 2.50e+03 pdb=" OE2 GLU A 145 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 145 " -0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" CD GLU H 145 " 0.067 2.00e-02 2.50e+03 pdb=" OE1 GLU H 145 " -0.024 2.00e-02 2.50e+03 pdb=" OE2 GLU H 145 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 395 " 0.047 2.00e-02 2.50e+03 2.86e-02 1.43e+01 pdb=" CG PHE H 395 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE H 395 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE H 395 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE H 395 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE H 395 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE H 395 " 0.027 2.00e-02 2.50e+03 ... (remaining 10015 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 14482 2.82 - 3.34: 51127 3.34 - 3.86: 91958 3.86 - 4.38: 112490 4.38 - 4.90: 184495 Nonbonded interactions: 454552 Sorted by model distance: nonbonded pdb=" CE MET B 563 " pdb=" CE MET K 563 " model vdw 2.294 3.880 nonbonded pdb=" CD1 LEU I 340 " pdb=" OE1 GLN I 359 " model vdw 2.299 3.460 nonbonded pdb=" CD1 LEU L 340 " pdb=" OE1 GLN L 359 " model vdw 2.299 3.460 nonbonded pdb=" CD1 LEU D 340 " pdb=" OE1 GLN D 359 " model vdw 2.299 3.460 nonbonded pdb=" CD1 LEU F 340 " pdb=" OE1 GLN F 359 " model vdw 2.299 3.460 ... (remaining 454547 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 47 through 204 or resid 216 through 233 or resid 244 throu \ gh 717 or resid 801)) selection = (chain 'D' and (resid 47 through 717 or resid 800)) selection = (chain 'F' and (resid 47 through 717 or resid 800)) selection = (chain 'H' and (resid 47 through 204 or resid 216 through 233 or resid 244 throu \ gh 717 or resid 801)) selection = (chain 'I' and (resid 47 through 717 or resid 800)) selection = (chain 'L' and (resid 47 through 717 or resid 800)) } ncs_group { reference = (chain 'B' and (resid 23 through 243 or resid 256 through 563)) selection = chain 'C' selection = chain 'E' selection = (chain 'G' and (resid 23 through 243 or resid 256 through 563)) selection = (chain 'J' and (resid 23 through 243 or resid 256 through 563)) selection = (chain 'K' and (resid 23 through 243 or resid 256 through 563)) } 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 individual isotropic 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: 1.230 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: 0.070 Extract box with map and model: 1.580 Check model and map are aligned: 0.310 Set scattering table: 0.410 Process input model: 105.120 Find NCS groups from input model: 2.430 Set up NCS constraints: 0.250 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: 0.020 Load rotamer database and sin/cos tables:10.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 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 : 0.009 0.103 56596 Z= 0.619 Angle : 1.287 12.468 76434 Z= 0.937 Chirality : 0.090 0.635 8440 Planarity : 0.006 0.090 10018 Dihedral : 12.919 89.195 21212 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.08 % Favored : 97.82 % Rotamer: Outliers : 1.09 % Allowed : 8.31 % Favored : 90.61 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 3.90 % 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: 1.29 (0.10), residues: 7124 helix: 1.79 (0.10), residues: 2670 sheet: 1.26 (0.14), residues: 1270 loop : -0.07 (0.11), residues: 3184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 440 HIS 0.013 0.002 HIS I 380 PHE 0.047 0.003 PHE H 395 TYR 0.033 0.003 TYR D 200 ARG 0.010 0.001 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14248 Ramachandran restraints generated. 7124 Oldfield, 0 Emsley, 7124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14248 Ramachandran restraints generated. 7124 Oldfield, 0 Emsley, 7124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 758 time to evaluate : 4.648 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: A 70 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7555 (ttpp) REVERT: A 453 TYR cc_start: 0.5230 (t80) cc_final: 0.4745 (t80) REVERT: B 452 MET cc_start: 0.9398 (mmm) cc_final: 0.8972 (mmt) REVERT: D 110 MET cc_start: 0.6359 (mtm) cc_final: 0.6148 (mtp) REVERT: D 203 MET cc_start: 0.2291 (tpp) cc_final: 0.1748 (ttm) REVERT: D 261 PHE cc_start: 0.6860 (OUTLIER) cc_final: 0.6315 (t80) REVERT: D 270 TYR cc_start: 0.7295 (p90) cc_final: 0.6984 (p90) REVERT: D 396 MET cc_start: 0.4141 (ttp) cc_final: 0.3936 (ttt) REVERT: D 454 SER cc_start: 0.9288 (m) cc_final: 0.8925 (p) REVERT: D 681 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.6798 (ptpp) REVERT: F 160 MET cc_start: 0.2800 (mmt) cc_final: 0.2495 (mpp) REVERT: F 261 PHE cc_start: 0.6411 (OUTLIER) cc_final: 0.6202 (t80) REVERT: F 681 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7708 (ptmt) REVERT: G 482 LEU cc_start: 0.9211 (mt) cc_final: 0.8970 (pp) REVERT: H 453 TYR cc_start: 0.5357 (t80) cc_final: 0.4847 (t80) REVERT: I 160 MET cc_start: 0.2787 (mmt) cc_final: 0.2485 (mpp) REVERT: I 681 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7709 (ptmt) REVERT: J 482 LEU cc_start: 0.9205 (mt) cc_final: 0.8968 (pp) REVERT: K 452 MET cc_start: 0.9401 (mmm) cc_final: 0.9093 (mmt) REVERT: L 203 MET cc_start: 0.2382 (tpp) cc_final: 0.1903 (ttm) REVERT: L 261 PHE cc_start: 0.6861 (OUTLIER) cc_final: 0.6318 (t80) REVERT: L 270 TYR cc_start: 0.7297 (p90) cc_final: 0.6984 (p90) REVERT: L 396 MET cc_start: 0.4135 (ttp) cc_final: 0.3934 (ttt) REVERT: L 454 SER cc_start: 0.9285 (m) cc_final: 0.8920 (p) REVERT: L 681 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.6796 (ptpp) outliers start: 64 outliers final: 2 residues processed: 804 average time/residue: 1.6266 time to fit residues: 1596.1181 Evaluate side-chains 434 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 424 time to evaluate : 4.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain D residue 261 PHE Chi-restraints excluded: chain D residue 681 LYS Chi-restraints excluded: chain F residue 261 PHE Chi-restraints excluded: chain F residue 681 LYS Chi-restraints excluded: chain I residue 94 GLU Chi-restraints excluded: chain I residue 681 LYS Chi-restraints excluded: chain L residue 261 PHE Chi-restraints excluded: chain L residue 681 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 602 optimal weight: 2.9990 chunk 541 optimal weight: 1.9990 chunk 300 optimal weight: 40.0000 chunk 184 optimal weight: 1.9990 chunk 365 optimal weight: 6.9990 chunk 289 optimal weight: 2.9990 chunk 559 optimal weight: 6.9990 chunk 216 optimal weight: 0.9980 chunk 340 optimal weight: 5.9990 chunk 416 optimal weight: 6.9990 chunk 648 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 HIS ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 GLN A 283 GLN A 337 ASN A 429 HIS A 457 GLN B 389 GLN B 477 GLN C 477 GLN D 255 HIS D 265 HIS D 279 GLN D 283 GLN D 337 ASN D 341 GLN D 429 HIS D 445 GLN D 457 GLN D 491 GLN ** D 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 708 HIS E 477 GLN F 85 ASN F 88 HIS ** F 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 HIS F 279 GLN F 283 GLN ** F 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 ASN F 429 HIS F 491 GLN G 236 GLN G 389 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 HIS ** H 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 259 GLN H 283 GLN H 337 ASN H 429 HIS I 85 ASN ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS I 279 GLN I 283 GLN ** I 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 337 ASN I 429 HIS I 491 GLN J 236 GLN J 389 GLN K 389 GLN K 477 GLN L 255 HIS L 265 HIS L 279 GLN L 283 GLN L 337 ASN L 341 GLN L 429 HIS L 445 GLN L 457 GLN L 491 GLN ** L 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 708 HIS Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 56596 Z= 0.240 Angle : 0.623 9.037 76434 Z= 0.334 Chirality : 0.046 0.284 8440 Planarity : 0.004 0.047 10018 Dihedral : 5.082 74.120 7929 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.87 % Favored : 98.10 % Rotamer: Outliers : 2.29 % Allowed : 13.25 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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 (0.10), residues: 7124 helix: 1.91 (0.10), residues: 2744 sheet: 0.90 (0.13), residues: 1318 loop : 0.04 (0.11), residues: 3062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 276 HIS 0.010 0.001 HIS A 344 PHE 0.029 0.002 PHE H 333 TYR 0.020 0.001 TYR G 457 ARG 0.010 0.001 ARG I 308 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14248 Ramachandran restraints generated. 7124 Oldfield, 0 Emsley, 7124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14248 Ramachandran restraints generated. 7124 Oldfield, 0 Emsley, 7124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 451 time to evaluate : 4.681 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: A 197 ARG cc_start: 0.1270 (OUTLIER) cc_final: 0.0241 (ppt170) REVERT: A 677 MET cc_start: -0.0239 (ptm) cc_final: -0.0491 (ptp) REVERT: B 269 LYS cc_start: 0.8322 (mmpt) cc_final: 0.7851 (mtmt) REVERT: C 110 ASP cc_start: 0.8399 (p0) cc_final: 0.8029 (p0) REVERT: D 136 MET cc_start: 0.7109 (mpp) cc_final: 0.6468 (mpp) REVERT: D 203 MET cc_start: 0.2091 (tpp) cc_final: 0.1577 (ttm) REVERT: D 261 PHE cc_start: 0.7206 (OUTLIER) cc_final: 0.6627 (m-80) REVERT: D 357 GLU cc_start: 0.6791 (tm-30) cc_final: 0.6501 (tm-30) REVERT: D 454 SER cc_start: 0.9121 (m) cc_final: 0.8768 (p) REVERT: E 110 ASP cc_start: 0.8405 (p0) cc_final: 0.8039 (p0) REVERT: F 110 MET cc_start: 0.6814 (mtm) cc_final: 0.6397 (mmm) REVERT: F 160 MET cc_start: 0.2868 (mmt) cc_final: 0.2602 (mpp) REVERT: F 334 MET cc_start: 0.3592 (tmm) cc_final: 0.2165 (ptm) REVERT: F 348 GLU cc_start: 0.8332 (tt0) cc_final: 0.8081 (tt0) REVERT: F 465 THR cc_start: 0.8150 (p) cc_final: 0.7860 (t) REVERT: F 658 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8101 (mm-30) REVERT: G 110 ASP cc_start: 0.8021 (p0) cc_final: 0.7706 (p0) REVERT: G 482 LEU cc_start: 0.9311 (mt) cc_final: 0.8975 (pp) REVERT: H 197 ARG cc_start: 0.1007 (OUTLIER) cc_final: 0.0091 (ppt170) REVERT: H 203 MET cc_start: 0.4255 (tpp) cc_final: 0.3156 (tpp) REVERT: I 110 MET cc_start: 0.6808 (mtm) cc_final: 0.6393 (mmm) REVERT: I 160 MET cc_start: 0.2852 (mmt) cc_final: 0.2595 (mpp) REVERT: I 261 PHE cc_start: 0.6087 (OUTLIER) cc_final: 0.5452 (t80) REVERT: I 348 GLU cc_start: 0.8327 (tt0) cc_final: 0.8075 (tt0) REVERT: I 465 THR cc_start: 0.8160 (p) cc_final: 0.7868 (t) REVERT: I 658 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8040 (mm-30) REVERT: I 661 PHE cc_start: 0.7917 (m-80) cc_final: 0.7660 (m-80) REVERT: J 110 ASP cc_start: 0.8043 (p0) cc_final: 0.7711 (p0) REVERT: J 482 LEU cc_start: 0.9309 (mt) cc_final: 0.8975 (pp) REVERT: K 269 LYS cc_start: 0.8311 (mmpt) cc_final: 0.7840 (mttt) REVERT: L 203 MET cc_start: 0.2237 (tpp) cc_final: 0.1888 (ttm) REVERT: L 261 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.6628 (m-80) REVERT: L 357 GLU cc_start: 0.6775 (tm-30) cc_final: 0.6487 (tm-30) REVERT: L 454 SER cc_start: 0.9101 (m) cc_final: 0.8753 (p) outliers start: 135 outliers final: 25 residues processed: 534 average time/residue: 1.5135 time to fit residues: 1004.8455 Evaluate side-chains 411 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 379 time to evaluate : 4.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain D residue 261 PHE Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 653 MET Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 361 ARG Chi-restraints excluded: chain F residue 658 GLU Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 197 ARG Chi-restraints excluded: chain H residue 286 ILE Chi-restraints excluded: chain H residue 333 PHE Chi-restraints excluded: chain H residue 498 LEU Chi-restraints excluded: chain I residue 94 GLU Chi-restraints excluded: chain I residue 261 PHE Chi-restraints excluded: chain I residue 361 ARG Chi-restraints excluded: chain I residue 658 GLU Chi-restraints excluded: chain K residue 78 ARG Chi-restraints excluded: chain K residue 482 LEU Chi-restraints excluded: chain L residue 261 PHE Chi-restraints excluded: chain L residue 307 VAL Chi-restraints excluded: chain L residue 467 ILE Chi-restraints excluded: chain L residue 653 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 360 optimal weight: 6.9990 chunk 201 optimal weight: 20.0000 chunk 539 optimal weight: 0.7980 chunk 441 optimal weight: 30.0000 chunk 178 optimal weight: 7.9990 chunk 649 optimal weight: 5.9990 chunk 701 optimal weight: 8.9990 chunk 578 optimal weight: 1.9990 chunk 644 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 521 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN A 684 HIS B 389 GLN ** D 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 ASN F 88 HIS F 194 HIS ** F 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 HIS F 344 HIS G 236 GLN G 389 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 330 ASN H 445 GLN H 684 HIS I 85 ASN I 194 HIS ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 329 HIS I 344 HIS J 236 GLN J 389 GLN K 389 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 56596 Z= 0.321 Angle : 0.608 12.800 76434 Z= 0.325 Chirality : 0.046 0.258 8440 Planarity : 0.004 0.059 10018 Dihedral : 4.861 61.444 7907 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.26 % Favored : 97.71 % Rotamer: Outliers : 2.68 % Allowed : 12.81 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: 1.24 (0.10), residues: 7124 helix: 1.84 (0.10), residues: 2704 sheet: 1.09 (0.14), residues: 1158 loop : -0.09 (0.10), residues: 3262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 276 HIS 0.010 0.001 HIS H 344 PHE 0.028 0.002 PHE C 497 TYR 0.025 0.002 TYR G 457 ARG 0.010 0.001 ARG D 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14248 Ramachandran restraints generated. 7124 Oldfield, 0 Emsley, 7124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14248 Ramachandran restraints generated. 7124 Oldfield, 0 Emsley, 7124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 424 time to evaluate : 4.910 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: A 197 ARG cc_start: 0.1134 (OUTLIER) cc_final: 0.0393 (ptm-80) REVERT: A 467 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7355 (pt) REVERT: A 677 MET cc_start: -0.0172 (ptm) cc_final: -0.0475 (ptp) REVERT: B 130 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.9050 (mt-10) REVERT: B 269 LYS cc_start: 0.8605 (mmpt) cc_final: 0.8273 (mtmt) REVERT: C 110 ASP cc_start: 0.8497 (p0) cc_final: 0.8119 (p0) REVERT: D 170 MET cc_start: 0.5779 (OUTLIER) cc_final: 0.5290 (mpp) REVERT: D 203 MET cc_start: 0.1778 (tpp) cc_final: 0.1499 (ttm) REVERT: D 261 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.7001 (t80) REVERT: D 672 ASP cc_start: 0.6054 (m-30) cc_final: 0.5633 (m-30) REVERT: E 110 ASP cc_start: 0.8486 (p0) cc_final: 0.8100 (p0) REVERT: F 261 PHE cc_start: 0.7070 (OUTLIER) cc_final: 0.6862 (t80) REVERT: F 348 GLU cc_start: 0.8326 (tt0) cc_final: 0.8104 (tt0) REVERT: F 658 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8145 (mm-30) REVERT: G 110 ASP cc_start: 0.8117 (p0) cc_final: 0.7772 (p0) REVERT: G 482 LEU cc_start: 0.9308 (mt) cc_final: 0.8972 (pp) REVERT: H 197 ARG cc_start: 0.1069 (OUTLIER) cc_final: 0.0382 (ptm-80) REVERT: H 675 MET cc_start: 0.1596 (tmm) cc_final: 0.1059 (tmm) REVERT: I 244 MET cc_start: -0.0843 (mtp) cc_final: -0.1275 (mmp) REVERT: I 348 GLU cc_start: 0.8324 (tt0) cc_final: 0.8103 (tt0) REVERT: I 658 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8018 (mm-30) REVERT: J 110 ASP cc_start: 0.8138 (p0) cc_final: 0.7795 (p0) REVERT: J 482 LEU cc_start: 0.9306 (mt) cc_final: 0.8971 (pp) REVERT: K 269 LYS cc_start: 0.8615 (mmpt) cc_final: 0.8275 (mtmt) REVERT: L 170 MET cc_start: 0.5782 (OUTLIER) cc_final: 0.5296 (mpp) REVERT: L 203 MET cc_start: 0.2122 (tpp) cc_final: 0.1885 (ttm) REVERT: L 261 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.6921 (t80) REVERT: L 672 ASP cc_start: 0.6051 (m-30) cc_final: 0.5629 (m-30) outliers start: 158 outliers final: 35 residues processed: 512 average time/residue: 1.4941 time to fit residues: 956.2615 Evaluate side-chains 425 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 379 time to evaluate : 4.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 261 PHE Chi-restraints excluded: chain D residue 458 TYR Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 653 MET Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain F residue 261 PHE Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 658 GLU Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain H residue 197 ARG Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain H residue 464 HIS Chi-restraints excluded: chain H residue 467 ILE Chi-restraints excluded: chain H residue 638 SER Chi-restraints excluded: chain I residue 94 GLU Chi-restraints excluded: chain I residue 288 GLU Chi-restraints excluded: chain I residue 407 THR Chi-restraints excluded: chain I residue 658 GLU Chi-restraints excluded: chain K residue 473 MET Chi-restraints excluded: chain K residue 482 LEU Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 170 MET Chi-restraints excluded: chain L residue 261 PHE Chi-restraints excluded: chain L residue 467 ILE Chi-restraints excluded: chain L residue 498 LEU Chi-restraints excluded: chain L residue 653 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 641 optimal weight: 5.9990 chunk 488 optimal weight: 10.0000 chunk 337 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 309 optimal weight: 40.0000 chunk 436 optimal weight: 40.0000 chunk 651 optimal weight: 8.9990 chunk 690 optimal weight: 7.9990 chunk 340 optimal weight: 3.9990 chunk 617 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 GLN A 182 HIS A 445 GLN ** D 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 HIS G 236 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 329 HIS J 236 GLN L 194 HIS ** L 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 56596 Z= 0.403 Angle : 0.609 8.877 76434 Z= 0.325 Chirality : 0.047 0.209 8440 Planarity : 0.004 0.046 10018 Dihedral : 4.856 58.447 7905 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.40 % Favored : 97.57 % Rotamer: Outliers : 2.53 % Allowed : 13.59 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: 1.05 (0.10), residues: 7124 helix: 1.74 (0.10), residues: 2706 sheet: 0.93 (0.14), residues: 1178 loop : -0.24 (0.10), residues: 3240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 276 HIS 0.012 0.001 HIS H 344 PHE 0.023 0.002 PHE B 497 TYR 0.029 0.002 TYR J 457 ARG 0.012 0.001 ARG D 254 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14248 Ramachandran restraints generated. 7124 Oldfield, 0 Emsley, 7124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14248 Ramachandran restraints generated. 7124 Oldfield, 0 Emsley, 7124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 402 time to evaluate : 4.742 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: A 90 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7765 (m-30) REVERT: A 197 ARG cc_start: 0.1194 (OUTLIER) cc_final: 0.0404 (ptm-80) REVERT: A 467 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7487 (pt) REVERT: A 501 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7614 (pmmt) REVERT: A 677 MET cc_start: 0.0375 (ptm) cc_final: 0.0076 (ptp) REVERT: B 78 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.8857 (mtt-85) REVERT: B 130 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.9064 (mt-10) REVERT: B 269 LYS cc_start: 0.8716 (mmpt) cc_final: 0.8448 (mtmt) REVERT: D 71 LEU cc_start: 0.7925 (mt) cc_final: 0.7605 (tt) REVERT: D 170 MET cc_start: 0.5597 (OUTLIER) cc_final: 0.5017 (mpp) REVERT: D 203 MET cc_start: 0.1840 (tpp) cc_final: 0.1614 (ttm) REVERT: D 244 MET cc_start: 0.0428 (tpp) cc_final: -0.1658 (mmm) REVERT: D 261 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.7030 (t80) REVERT: D 357 GLU cc_start: 0.7001 (tm-30) cc_final: 0.6735 (tm-30) REVERT: D 452 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7887 (mtt-85) REVERT: D 672 ASP cc_start: 0.6127 (m-30) cc_final: 0.5775 (m-30) REVERT: F 244 MET cc_start: -0.0558 (mtp) cc_final: -0.1193 (mmp) REVERT: F 261 PHE cc_start: 0.6942 (OUTLIER) cc_final: 0.6428 (t80) REVERT: F 658 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8147 (mm-30) REVERT: G 110 ASP cc_start: 0.8169 (p0) cc_final: 0.7822 (p0) REVERT: G 161 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8816 (tpp) REVERT: G 482 LEU cc_start: 0.9353 (mt) cc_final: 0.9054 (pp) REVERT: H 197 ARG cc_start: 0.1073 (OUTLIER) cc_final: 0.0315 (ptm-80) REVERT: H 467 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7675 (pt) REVERT: H 501 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7588 (pmmt) REVERT: I 244 MET cc_start: -0.0674 (mtp) cc_final: -0.0998 (mmp) REVERT: I 658 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8122 (mm-30) REVERT: I 661 PHE cc_start: 0.8346 (m-80) cc_final: 0.7834 (m-80) REVERT: J 110 ASP cc_start: 0.8149 (p0) cc_final: 0.7830 (p0) REVERT: J 482 LEU cc_start: 0.9351 (mt) cc_final: 0.9053 (pp) REVERT: K 269 LYS cc_start: 0.8701 (mmpt) cc_final: 0.8429 (mtmt) REVERT: L 71 LEU cc_start: 0.7847 (mt) cc_final: 0.7529 (tt) REVERT: L 170 MET cc_start: 0.5602 (OUTLIER) cc_final: 0.5025 (mpp) REVERT: L 261 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.6901 (t80) REVERT: L 295 LYS cc_start: 0.8342 (mmtp) cc_final: 0.8065 (tppp) REVERT: L 357 GLU cc_start: 0.6982 (tm-30) cc_final: 0.6726 (tm-30) REVERT: L 672 ASP cc_start: 0.6040 (m-30) cc_final: 0.5708 (m-30) outliers start: 149 outliers final: 41 residues processed: 495 average time/residue: 1.4682 time to fit residues: 908.1066 Evaluate side-chains 429 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 370 time to evaluate : 4.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 261 PHE Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 481 VAL Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain F residue 261 PHE Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 658 GLU Chi-restraints excluded: chain F residue 694 VAL Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain H residue 197 ARG Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain H residue 464 HIS Chi-restraints excluded: chain H residue 467 ILE Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 501 LYS Chi-restraints excluded: chain H residue 638 SER Chi-restraints excluded: chain I residue 94 GLU Chi-restraints excluded: chain I residue 288 GLU Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 658 GLU Chi-restraints excluded: chain I residue 694 VAL Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain K residue 490 ARG Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 170 MET Chi-restraints excluded: chain L residue 261 PHE Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 467 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 574 optimal weight: 2.9990 chunk 391 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 513 optimal weight: 7.9990 chunk 284 optimal weight: 7.9990 chunk 588 optimal weight: 7.9990 chunk 477 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 352 optimal weight: 9.9990 chunk 619 optimal weight: 6.9990 chunk 174 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 HIS ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 HIS D 329 HIS ** D 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 457 GLN ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 236 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 341 GLN J 236 GLN ** K 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 56596 Z= 0.399 Angle : 0.602 10.523 76434 Z= 0.320 Chirality : 0.046 0.210 8440 Planarity : 0.004 0.046 10018 Dihedral : 4.861 58.979 7905 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.71 % Favored : 97.26 % Rotamer: Outliers : 2.60 % Allowed : 14.03 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: 0.92 (0.10), residues: 7124 helix: 1.72 (0.10), residues: 2730 sheet: 0.89 (0.14), residues: 1168 loop : -0.43 (0.10), residues: 3226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 276 HIS 0.011 0.001 HIS H 344 PHE 0.016 0.002 PHE K 407 TYR 0.029 0.002 TYR G 457 ARG 0.011 0.000 ARG F 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14248 Ramachandran restraints generated. 7124 Oldfield, 0 Emsley, 7124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14248 Ramachandran restraints generated. 7124 Oldfield, 0 Emsley, 7124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 396 time to evaluate : 5.060 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: A 91 MET cc_start: 0.8270 (ptm) cc_final: 0.8066 (ppp) REVERT: A 197 ARG cc_start: 0.1423 (OUTLIER) cc_final: 0.0997 (ptm-80) REVERT: A 467 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7729 (pt) REVERT: A 501 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7770 (pmmt) REVERT: A 677 MET cc_start: 0.0406 (ptm) cc_final: 0.0108 (ptp) REVERT: A 680 MET cc_start: -0.0654 (mmm) cc_final: -0.1064 (mmt) REVERT: B 78 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8902 (mtt-85) REVERT: B 269 LYS cc_start: 0.8757 (mmpt) cc_final: 0.8515 (mtmt) REVERT: D 71 LEU cc_start: 0.7912 (mt) cc_final: 0.7519 (tt) REVERT: D 170 MET cc_start: 0.5629 (OUTLIER) cc_final: 0.5377 (mpp) REVERT: D 203 MET cc_start: 0.1894 (tpp) cc_final: 0.1608 (ttm) REVERT: D 244 MET cc_start: 0.0527 (tpp) cc_final: -0.1846 (mmm) REVERT: D 261 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.6878 (t80) REVERT: D 452 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7879 (mtt-85) REVERT: D 672 ASP cc_start: 0.5911 (m-30) cc_final: 0.5582 (m-30) REVERT: F 244 MET cc_start: -0.0541 (mtp) cc_final: -0.1046 (mmp) REVERT: F 658 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8159 (mm-30) REVERT: F 661 PHE cc_start: 0.7983 (m-80) cc_final: 0.7694 (m-80) REVERT: F 675 MET cc_start: 0.7107 (ttm) cc_final: 0.6765 (ttm) REVERT: G 110 ASP cc_start: 0.8186 (p0) cc_final: 0.7863 (p0) REVERT: G 161 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8808 (tpp) REVERT: G 482 LEU cc_start: 0.9333 (mt) cc_final: 0.9030 (pp) REVERT: H 197 ARG cc_start: 0.1163 (OUTLIER) cc_final: 0.0255 (ptm-80) REVERT: H 467 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7708 (pt) REVERT: H 501 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7817 (pmmt) REVERT: I 65 MET cc_start: 0.7689 (ttm) cc_final: 0.7414 (ttp) REVERT: I 334 MET cc_start: 0.4043 (tmt) cc_final: 0.2340 (ptm) REVERT: I 658 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8110 (mm-30) REVERT: I 661 PHE cc_start: 0.8356 (m-80) cc_final: 0.7846 (m-80) REVERT: J 110 ASP cc_start: 0.8181 (p0) cc_final: 0.7858 (p0) REVERT: J 482 LEU cc_start: 0.9332 (mt) cc_final: 0.9030 (pp) REVERT: K 269 LYS cc_start: 0.8755 (mmpt) cc_final: 0.8522 (mtmt) REVERT: K 497 PHE cc_start: 0.7072 (OUTLIER) cc_final: 0.6586 (m-10) REVERT: L 71 LEU cc_start: 0.7927 (mt) cc_final: 0.7593 (tt) REVERT: L 110 MET cc_start: 0.6929 (OUTLIER) cc_final: 0.6594 (mtp) REVERT: L 170 MET cc_start: 0.5631 (OUTLIER) cc_final: 0.5006 (mpp) REVERT: L 261 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6933 (t80) REVERT: L 295 LYS cc_start: 0.8323 (mmtp) cc_final: 0.8048 (tppp) REVERT: L 357 GLU cc_start: 0.6729 (tm-30) cc_final: 0.6392 (tm-30) REVERT: L 672 ASP cc_start: 0.5918 (m-30) cc_final: 0.5590 (m-30) outliers start: 153 outliers final: 52 residues processed: 474 average time/residue: 1.4254 time to fit residues: 849.4998 Evaluate side-chains 441 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 372 time to evaluate : 4.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 464 HIS Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 501 LYS Chi-restraints excluded: chain A residue 638 SER Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 261 PHE Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 481 VAL Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 484 THR Chi-restraints excluded: chain F residue 288 GLU Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 658 GLU Chi-restraints excluded: chain F residue 677 MET Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain H residue 197 ARG Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain H residue 464 HIS Chi-restraints excluded: chain H residue 467 ILE Chi-restraints excluded: chain H residue 473 LEU Chi-restraints excluded: chain H residue 501 LYS Chi-restraints excluded: chain H residue 623 LYS Chi-restraints excluded: chain H residue 638 SER Chi-restraints excluded: chain I residue 94 GLU Chi-restraints excluded: chain I residue 288 GLU Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain I residue 407 THR Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 658 GLU Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain K residue 473 MET Chi-restraints excluded: chain K residue 497 PHE Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 110 MET Chi-restraints excluded: chain L residue 170 MET Chi-restraints excluded: chain L residue 261 PHE Chi-restraints excluded: chain L residue 286 ILE Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 342 VAL Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 467 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 232 optimal weight: 30.0000 chunk 621 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 405 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 690 optimal weight: 6.9990 chunk 573 optimal weight: 0.9990 chunk 319 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 228 optimal weight: 4.9990 chunk 362 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 182 HIS ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 236 GLN H 105 GLN ** I 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 236 GLN K 266 HIS ** L 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 56596 Z= 0.213 Angle : 0.550 9.961 76434 Z= 0.289 Chirality : 0.044 0.189 8440 Planarity : 0.004 0.046 10018 Dihedral : 4.706 58.135 7905 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.34 % Favored : 97.63 % Rotamer: Outliers : 2.09 % Allowed : 14.67 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: 1.07 (0.10), residues: 7124 helix: 1.90 (0.10), residues: 2736 sheet: 1.00 (0.14), residues: 1168 loop : -0.42 (0.10), residues: 3220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 276 HIS 0.009 0.001 HIS H 344 PHE 0.025 0.001 PHE I 272 TYR 0.023 0.001 TYR A 458 ARG 0.014 0.000 ARG K 490 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14248 Ramachandran restraints generated. 7124 Oldfield, 0 Emsley, 7124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14248 Ramachandran restraints generated. 7124 Oldfield, 0 Emsley, 7124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 398 time to evaluate : 4.834 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: A 197 ARG cc_start: 0.1187 (OUTLIER) cc_final: 0.0838 (ptm-80) REVERT: A 334 MET cc_start: 0.2985 (OUTLIER) cc_final: 0.2204 (ppp) REVERT: A 433 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.8004 (tpp) REVERT: A 467 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7775 (pt) REVERT: A 677 MET cc_start: 0.0559 (ptm) cc_final: 0.0267 (ptp) REVERT: A 680 MET cc_start: -0.0747 (mmm) cc_final: -0.1097 (mmt) REVERT: B 269 LYS cc_start: 0.8789 (mmpt) cc_final: 0.8571 (mttt) REVERT: D 71 LEU cc_start: 0.7874 (mt) cc_final: 0.7606 (tt) REVERT: D 170 MET cc_start: 0.5608 (OUTLIER) cc_final: 0.5366 (mpp) REVERT: D 203 MET cc_start: 0.1727 (tpp) cc_final: 0.1401 (ttm) REVERT: D 244 MET cc_start: 0.0373 (tpp) cc_final: -0.1918 (mmm) REVERT: D 261 PHE cc_start: 0.7236 (OUTLIER) cc_final: 0.6930 (t80) REVERT: D 357 GLU cc_start: 0.6864 (tm-30) cc_final: 0.6527 (tm-30) REVERT: D 452 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7867 (mtt-85) REVERT: D 672 ASP cc_start: 0.5921 (m-30) cc_final: 0.5639 (m-30) REVERT: F 244 MET cc_start: -0.0708 (mtp) cc_final: -0.1009 (mmp) REVERT: F 658 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8115 (mm-30) REVERT: F 661 PHE cc_start: 0.8015 (m-80) cc_final: 0.7682 (m-80) REVERT: G 110 ASP cc_start: 0.8096 (p0) cc_final: 0.7812 (p0) REVERT: G 482 LEU cc_start: 0.9342 (mt) cc_final: 0.9035 (pp) REVERT: H 197 ARG cc_start: 0.1047 (OUTLIER) cc_final: 0.0719 (ptm-80) REVERT: H 334 MET cc_start: 0.3014 (OUTLIER) cc_final: 0.1978 (ppp) REVERT: H 361 ARG cc_start: 0.7393 (tpp80) cc_final: 0.7117 (tpp80) REVERT: H 467 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7743 (pt) REVERT: H 680 MET cc_start: -0.0792 (mmm) cc_final: -0.1089 (mmt) REVERT: I 658 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8075 (mm-30) REVERT: I 661 PHE cc_start: 0.8250 (m-80) cc_final: 0.7723 (m-80) REVERT: J 110 ASP cc_start: 0.8093 (p0) cc_final: 0.7810 (p0) REVERT: J 482 LEU cc_start: 0.9341 (mt) cc_final: 0.9035 (pp) REVERT: K 269 LYS cc_start: 0.8778 (mmpt) cc_final: 0.8576 (mtmt) REVERT: L 71 LEU cc_start: 0.7942 (mt) cc_final: 0.7695 (tt) REVERT: L 170 MET cc_start: 0.5609 (OUTLIER) cc_final: 0.5373 (mpp) REVERT: L 261 PHE cc_start: 0.7239 (OUTLIER) cc_final: 0.6942 (t80) REVERT: L 295 LYS cc_start: 0.8363 (mmtp) cc_final: 0.7982 (tppp) REVERT: L 357 GLU cc_start: 0.6896 (tm-30) cc_final: 0.6567 (tm-30) REVERT: L 672 ASP cc_start: 0.5928 (m-30) cc_final: 0.5645 (m-30) outliers start: 123 outliers final: 49 residues processed: 462 average time/residue: 1.4398 time to fit residues: 836.8267 Evaluate side-chains 439 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 376 time to evaluate : 4.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 261 PHE Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 458 TYR Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 414 THR Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 653 MET Chi-restraints excluded: chain F residue 658 GLU Chi-restraints excluded: chain F residue 694 VAL Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 197 ARG Chi-restraints excluded: chain H residue 334 MET Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain H residue 467 ILE Chi-restraints excluded: chain H residue 623 LYS Chi-restraints excluded: chain I residue 94 GLU Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 407 THR Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 438 VAL Chi-restraints excluded: chain I residue 658 GLU Chi-restraints excluded: chain I residue 694 VAL Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain K residue 482 LEU Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 170 MET Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain L residue 261 PHE Chi-restraints excluded: chain L residue 286 ILE Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 342 VAL Chi-restraints excluded: chain L residue 458 TYR Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 467 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 666 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 393 optimal weight: 10.0000 chunk 504 optimal weight: 2.9990 chunk 390 optimal weight: 0.9990 chunk 581 optimal weight: 5.9990 chunk 385 optimal weight: 4.9990 chunk 688 optimal weight: 0.0270 chunk 430 optimal weight: 30.0000 chunk 419 optimal weight: 0.1980 chunk 317 optimal weight: 30.0000 overall best weight: 1.6444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 HIS A 283 GLN ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 ASN E 153 GLN ** F 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 341 GLN G 236 GLN H 283 GLN ** I 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 394 ASN J 236 GLN ** L 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 546 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 56596 Z= 0.189 Angle : 0.535 10.695 76434 Z= 0.279 Chirality : 0.044 0.190 8440 Planarity : 0.004 0.048 10018 Dihedral : 4.559 57.808 7905 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.48 % Favored : 97.49 % Rotamer: Outliers : 1.89 % Allowed : 15.37 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: 1.17 (0.10), residues: 7124 helix: 2.01 (0.10), residues: 2738 sheet: 1.07 (0.14), residues: 1166 loop : -0.40 (0.10), residues: 3220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 276 HIS 0.009 0.001 HIS H 344 PHE 0.019 0.001 PHE F 272 TYR 0.021 0.001 TYR K 413 ARG 0.013 0.000 ARG D 361 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14248 Ramachandran restraints generated. 7124 Oldfield, 0 Emsley, 7124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14248 Ramachandran restraints generated. 7124 Oldfield, 0 Emsley, 7124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 396 time to evaluate : 4.736 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: A 197 ARG cc_start: 0.0889 (OUTLIER) cc_final: 0.0643 (ptm-80) REVERT: A 334 MET cc_start: 0.2953 (ptt) cc_final: 0.2253 (ppp) REVERT: A 433 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.8025 (tpp) REVERT: A 467 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7789 (pt) REVERT: A 677 MET cc_start: 0.0554 (ptm) cc_final: 0.0316 (ptp) REVERT: A 680 MET cc_start: -0.0812 (mmm) cc_final: -0.1104 (mmt) REVERT: B 269 LYS cc_start: 0.8815 (mmpt) cc_final: 0.8602 (mttt) REVERT: D 170 MET cc_start: 0.5752 (OUTLIER) cc_final: 0.5044 (mpp) REVERT: D 203 MET cc_start: 0.1615 (tpp) cc_final: 0.1223 (ttm) REVERT: D 244 MET cc_start: 0.0569 (tpp) cc_final: -0.1664 (mmm) REVERT: D 261 PHE cc_start: 0.7195 (OUTLIER) cc_final: 0.6917 (t80) REVERT: D 334 MET cc_start: 0.5554 (ttt) cc_final: 0.5120 (tmm) REVERT: D 452 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7870 (mtt-85) REVERT: D 672 ASP cc_start: 0.5880 (m-30) cc_final: 0.5620 (m-30) REVERT: F 284 LYS cc_start: 0.5674 (OUTLIER) cc_final: 0.5361 (tppt) REVERT: F 334 MET cc_start: 0.3573 (tmt) cc_final: 0.1966 (ptm) REVERT: F 658 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8104 (mm-30) REVERT: F 661 PHE cc_start: 0.7912 (m-80) cc_final: 0.7627 (m-80) REVERT: G 110 ASP cc_start: 0.8061 (p0) cc_final: 0.7779 (p0) REVERT: G 482 LEU cc_start: 0.9339 (mt) cc_final: 0.9033 (pp) REVERT: H 197 ARG cc_start: 0.0756 (OUTLIER) cc_final: 0.0544 (ptm-80) REVERT: H 334 MET cc_start: 0.3235 (ptt) cc_final: 0.2900 (ptt) REVERT: H 361 ARG cc_start: 0.7468 (tpp80) cc_final: 0.7224 (tpp80) REVERT: H 467 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7759 (pt) REVERT: H 680 MET cc_start: -0.1084 (mmm) cc_final: -0.1342 (mmt) REVERT: I 91 MET cc_start: 0.8405 (ppp) cc_final: 0.8118 (pp-130) REVERT: I 658 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8034 (mm-30) REVERT: I 661 PHE cc_start: 0.8236 (m-80) cc_final: 0.7701 (m-80) REVERT: J 110 ASP cc_start: 0.8057 (p0) cc_final: 0.7775 (p0) REVERT: J 482 LEU cc_start: 0.9338 (mt) cc_final: 0.9033 (pp) REVERT: K 269 LYS cc_start: 0.8785 (mmpt) cc_final: 0.8580 (mtmt) REVERT: L 71 LEU cc_start: 0.7893 (mt) cc_final: 0.7484 (tt) REVERT: L 170 MET cc_start: 0.5629 (OUTLIER) cc_final: 0.4950 (mpp) REVERT: L 261 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.7079 (t80) REVERT: L 672 ASP cc_start: 0.5891 (m-30) cc_final: 0.5630 (m-30) outliers start: 111 outliers final: 47 residues processed: 455 average time/residue: 1.4024 time to fit residues: 805.2485 Evaluate side-chains 431 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 371 time to evaluate : 4.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 197 ARG Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 261 PHE Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 458 TYR Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain F residue 284 LYS Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain F residue 658 GLU Chi-restraints excluded: chain F residue 694 VAL Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain H residue 197 ARG Chi-restraints excluded: chain H residue 349 MET Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain H residue 467 ILE Chi-restraints excluded: chain H residue 623 LYS Chi-restraints excluded: chain I residue 94 GLU Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 407 THR Chi-restraints excluded: chain I residue 438 VAL Chi-restraints excluded: chain I residue 658 GLU Chi-restraints excluded: chain I residue 694 VAL Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain K residue 482 LEU Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 110 MET Chi-restraints excluded: chain L residue 170 MET Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain L residue 261 PHE Chi-restraints excluded: chain L residue 286 ILE Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 458 TYR Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 467 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 425 optimal weight: 0.5980 chunk 274 optimal weight: 0.9980 chunk 411 optimal weight: 8.9990 chunk 207 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 437 optimal weight: 10.0000 chunk 468 optimal weight: 1.9990 chunk 340 optimal weight: 4.9990 chunk 64 optimal weight: 20.0000 chunk 540 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 HIS A 329 HIS ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 236 GLN H 182 HIS H 337 ASN ** I 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 236 GLN ** L 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 56596 Z= 0.168 Angle : 0.534 10.805 76434 Z= 0.276 Chirality : 0.044 0.196 8440 Planarity : 0.004 0.047 10018 Dihedral : 4.458 59.575 7905 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.30 % Favored : 97.67 % Rotamer: Outliers : 1.63 % Allowed : 15.68 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: 1.28 (0.10), residues: 7124 helix: 2.11 (0.10), residues: 2742 sheet: 1.09 (0.14), residues: 1200 loop : -0.36 (0.10), residues: 3182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 276 HIS 0.011 0.001 HIS H 344 PHE 0.019 0.001 PHE K 497 TYR 0.023 0.001 TYR D 270 ARG 0.010 0.000 ARG D 409 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14248 Ramachandran restraints generated. 7124 Oldfield, 0 Emsley, 7124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14248 Ramachandran restraints generated. 7124 Oldfield, 0 Emsley, 7124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 398 time to evaluate : 4.753 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: A 334 MET cc_start: 0.2950 (OUTLIER) cc_final: 0.2113 (ppp) REVERT: A 361 ARG cc_start: 0.7450 (tpp80) cc_final: 0.7246 (tpp80) REVERT: A 467 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7795 (pt) REVERT: A 677 MET cc_start: 0.0558 (ptm) cc_final: 0.0315 (ptp) REVERT: A 680 MET cc_start: -0.1067 (mmm) cc_final: -0.1351 (mmt) REVERT: B 269 LYS cc_start: 0.8812 (mmpt) cc_final: 0.8597 (mttt) REVERT: D 170 MET cc_start: 0.5741 (OUTLIER) cc_final: 0.4971 (mpp) REVERT: D 203 MET cc_start: 0.1741 (tpp) cc_final: 0.1327 (ttm) REVERT: D 244 MET cc_start: 0.0547 (tpp) cc_final: -0.1673 (mmm) REVERT: D 261 PHE cc_start: 0.7180 (OUTLIER) cc_final: 0.6941 (t80) REVERT: D 321 VAL cc_start: 0.4835 (OUTLIER) cc_final: 0.4615 (p) REVERT: D 334 MET cc_start: 0.5527 (ttt) cc_final: 0.5103 (tmm) REVERT: D 357 GLU cc_start: 0.6703 (tm-30) cc_final: 0.6365 (tm-30) REVERT: D 452 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7876 (mtt-85) REVERT: D 672 ASP cc_start: 0.5896 (m-30) cc_final: 0.5651 (m-30) REVERT: F 334 MET cc_start: 0.3618 (tmt) cc_final: 0.2078 (ptm) REVERT: F 658 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8062 (mm-30) REVERT: F 661 PHE cc_start: 0.7871 (m-80) cc_final: 0.7547 (m-80) REVERT: G 110 ASP cc_start: 0.8017 (p0) cc_final: 0.7745 (p0) REVERT: G 482 LEU cc_start: 0.9364 (mt) cc_final: 0.9035 (pp) REVERT: G 505 LEU cc_start: 0.9054 (mt) cc_final: 0.8807 (pp) REVERT: H 334 MET cc_start: 0.2976 (ptt) cc_final: 0.1773 (ppp) REVERT: H 361 ARG cc_start: 0.7404 (tpp80) cc_final: 0.7182 (tpp80) REVERT: H 467 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7801 (pt) REVERT: H 680 MET cc_start: -0.1186 (mmm) cc_final: -0.1406 (mmt) REVERT: I 334 MET cc_start: 0.4006 (tmt) cc_final: 0.3517 (tmm) REVERT: I 658 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8037 (mm-30) REVERT: I 661 PHE cc_start: 0.8231 (m-80) cc_final: 0.7679 (m-80) REVERT: J 110 ASP cc_start: 0.8016 (p0) cc_final: 0.7742 (p0) REVERT: J 482 LEU cc_start: 0.9354 (mt) cc_final: 0.9049 (pp) REVERT: K 269 LYS cc_start: 0.8813 (mmpt) cc_final: 0.8595 (mtmt) REVERT: L 71 LEU cc_start: 0.7807 (mt) cc_final: 0.7516 (tt) REVERT: L 170 MET cc_start: 0.5737 (OUTLIER) cc_final: 0.5450 (mpp) REVERT: L 261 PHE cc_start: 0.7331 (OUTLIER) cc_final: 0.7081 (t80) REVERT: L 672 ASP cc_start: 0.5902 (m-30) cc_final: 0.5658 (m-30) outliers start: 96 outliers final: 48 residues processed: 454 average time/residue: 1.3908 time to fit residues: 797.4020 Evaluate side-chains 429 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 370 time to evaluate : 4.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 261 PHE Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 458 TYR Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain F residue 658 GLU Chi-restraints excluded: chain F residue 694 VAL Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain H residue 467 ILE Chi-restraints excluded: chain H residue 468 ASP Chi-restraints excluded: chain H residue 623 LYS Chi-restraints excluded: chain H residue 677 MET Chi-restraints excluded: chain I residue 94 GLU Chi-restraints excluded: chain I residue 110 MET Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 407 THR Chi-restraints excluded: chain I residue 413 SER Chi-restraints excluded: chain I residue 576 MET Chi-restraints excluded: chain I residue 658 GLU Chi-restraints excluded: chain I residue 694 VAL Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain K residue 482 LEU Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 110 MET Chi-restraints excluded: chain L residue 170 MET Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain L residue 261 PHE Chi-restraints excluded: chain L residue 286 ILE Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 342 VAL Chi-restraints excluded: chain L residue 418 THR Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 467 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 626 optimal weight: 7.9990 chunk 659 optimal weight: 9.9990 chunk 601 optimal weight: 4.9990 chunk 641 optimal weight: 8.9990 chunk 385 optimal weight: 10.0000 chunk 279 optimal weight: 5.9990 chunk 503 optimal weight: 0.0970 chunk 196 optimal weight: 5.9990 chunk 579 optimal weight: 2.9990 chunk 606 optimal weight: 0.7980 chunk 639 optimal weight: 1.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 HIS ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN ** F 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 394 ASN G 236 GLN H 182 HIS ** H 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 236 GLN ** L 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 56596 Z= 0.223 Angle : 0.566 11.725 76434 Z= 0.292 Chirality : 0.044 0.187 8440 Planarity : 0.004 0.052 10018 Dihedral : 4.482 57.688 7905 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.60 % Favored : 97.38 % Rotamer: Outliers : 1.41 % Allowed : 16.30 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: 1.23 (0.10), residues: 7124 helix: 2.08 (0.10), residues: 2738 sheet: 1.07 (0.14), residues: 1166 loop : -0.38 (0.10), residues: 3220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 276 HIS 0.009 0.001 HIS H 344 PHE 0.010 0.001 PHE C 497 TYR 0.021 0.001 TYR L 270 ARG 0.012 0.000 ARG L 409 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14248 Ramachandran restraints generated. 7124 Oldfield, 0 Emsley, 7124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14248 Ramachandran restraints generated. 7124 Oldfield, 0 Emsley, 7124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 384 time to evaluate : 4.755 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: A 334 MET cc_start: 0.3205 (OUTLIER) cc_final: 0.2265 (ppp) REVERT: A 361 ARG cc_start: 0.7445 (tpp80) cc_final: 0.7189 (tpp80) REVERT: A 433 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7962 (tpp) REVERT: A 467 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7819 (pt) REVERT: A 677 MET cc_start: 0.0558 (ptm) cc_final: 0.0331 (ptp) REVERT: A 680 MET cc_start: -0.1004 (mmm) cc_final: -0.1292 (mmt) REVERT: B 269 LYS cc_start: 0.8808 (mmpt) cc_final: 0.8582 (mtmt) REVERT: D 87 MET cc_start: 0.6601 (pmm) cc_final: 0.6368 (pmm) REVERT: D 170 MET cc_start: 0.5658 (OUTLIER) cc_final: 0.5360 (mpp) REVERT: D 203 MET cc_start: 0.1783 (tpp) cc_final: 0.1368 (ttm) REVERT: D 244 MET cc_start: 0.0469 (tpp) cc_final: -0.1706 (mmm) REVERT: D 261 PHE cc_start: 0.7186 (OUTLIER) cc_final: 0.6944 (t80) REVERT: D 321 VAL cc_start: 0.4870 (OUTLIER) cc_final: 0.4666 (p) REVERT: D 334 MET cc_start: 0.5521 (ttt) cc_final: 0.5112 (tmm) REVERT: D 452 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7871 (mtt-85) REVERT: F 334 MET cc_start: 0.3835 (tmt) cc_final: 0.2456 (ptm) REVERT: F 658 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8057 (mm-30) REVERT: F 661 PHE cc_start: 0.7865 (m-80) cc_final: 0.7537 (m-80) REVERT: G 110 ASP cc_start: 0.8033 (p0) cc_final: 0.7756 (p0) REVERT: G 482 LEU cc_start: 0.9369 (mt) cc_final: 0.9037 (pp) REVERT: G 488 ASP cc_start: 0.8123 (m-30) cc_final: 0.7448 (p0) REVERT: G 505 LEU cc_start: 0.9102 (mt) cc_final: 0.8866 (pp) REVERT: H 334 MET cc_start: 0.3344 (ptt) cc_final: 0.3074 (tmm) REVERT: H 361 ARG cc_start: 0.7437 (tpp80) cc_final: 0.7225 (tpp80) REVERT: H 467 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7833 (pt) REVERT: H 677 MET cc_start: -0.0775 (OUTLIER) cc_final: -0.1308 (ptt) REVERT: I 334 MET cc_start: 0.3994 (tmt) cc_final: 0.3666 (tmt) REVERT: I 658 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8037 (mm-30) REVERT: I 661 PHE cc_start: 0.8245 (m-80) cc_final: 0.7692 (m-80) REVERT: J 110 ASP cc_start: 0.8029 (p0) cc_final: 0.7752 (p0) REVERT: J 482 LEU cc_start: 0.9367 (mt) cc_final: 0.9062 (pp) REVERT: J 488 ASP cc_start: 0.8124 (m-30) cc_final: 0.7446 (p0) REVERT: K 269 LYS cc_start: 0.8813 (mmpt) cc_final: 0.8591 (mtmt) REVERT: L 71 LEU cc_start: 0.7944 (mt) cc_final: 0.6755 (tt) REVERT: L 170 MET cc_start: 0.5652 (OUTLIER) cc_final: 0.5352 (mpp) REVERT: L 261 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.7093 (t80) REVERT: L 672 ASP cc_start: 0.5736 (m-30) cc_final: 0.5533 (m-30) outliers start: 83 outliers final: 47 residues processed: 433 average time/residue: 1.4200 time to fit residues: 773.5963 Evaluate side-chains 427 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 367 time to evaluate : 4.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 261 PHE Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 458 TYR Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 658 GLU Chi-restraints excluded: chain F residue 694 VAL Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain H residue 349 MET Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain H residue 467 ILE Chi-restraints excluded: chain H residue 468 ASP Chi-restraints excluded: chain H residue 623 LYS Chi-restraints excluded: chain H residue 677 MET Chi-restraints excluded: chain I residue 110 MET Chi-restraints excluded: chain I residue 407 THR Chi-restraints excluded: chain I residue 413 SER Chi-restraints excluded: chain I residue 658 GLU Chi-restraints excluded: chain I residue 694 VAL Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain K residue 482 LEU Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 110 MET Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 170 MET Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain L residue 261 PHE Chi-restraints excluded: chain L residue 286 ILE Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 342 VAL Chi-restraints excluded: chain L residue 418 THR Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 467 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 421 optimal weight: 3.9990 chunk 678 optimal weight: 8.9990 chunk 413 optimal weight: 8.9990 chunk 321 optimal weight: 7.9990 chunk 471 optimal weight: 40.0000 chunk 711 optimal weight: 0.1980 chunk 654 optimal weight: 7.9990 chunk 566 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 chunk 437 optimal weight: 9.9990 chunk 347 optimal weight: 6.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN A 182 HIS ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 ASN G 236 GLN H 182 HIS ** H 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 236 GLN L 74 GLN ** L 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 56596 Z= 0.276 Angle : 0.586 12.912 76434 Z= 0.302 Chirality : 0.045 0.222 8440 Planarity : 0.004 0.086 10018 Dihedral : 4.497 57.803 7902 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.75 % Favored : 97.22 % Rotamer: Outliers : 1.39 % Allowed : 16.39 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: 1.14 (0.10), residues: 7124 helix: 2.03 (0.10), residues: 2734 sheet: 0.81 (0.14), residues: 1296 loop : -0.40 (0.11), residues: 3094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 358 HIS 0.011 0.001 HIS H 344 PHE 0.030 0.001 PHE K 497 TYR 0.023 0.001 TYR G 457 ARG 0.016 0.000 ARG L 158 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14248 Ramachandran restraints generated. 7124 Oldfield, 0 Emsley, 7124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14248 Ramachandran restraints generated. 7124 Oldfield, 0 Emsley, 7124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 386 time to evaluate : 4.865 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: A 203 MET cc_start: 0.4642 (tpp) cc_final: 0.4224 (tpp) REVERT: A 334 MET cc_start: 0.3198 (OUTLIER) cc_final: 0.2136 (ppp) REVERT: A 361 ARG cc_start: 0.7397 (tpp80) cc_final: 0.7150 (tpp80) REVERT: A 433 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7921 (tpp) REVERT: A 467 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7896 (pt) REVERT: A 677 MET cc_start: 0.0548 (ptm) cc_final: 0.0347 (ptp) REVERT: A 680 MET cc_start: -0.1121 (mmm) cc_final: -0.1418 (mmt) REVERT: C 408 MET cc_start: 0.7227 (tpt) cc_final: 0.6229 (tpt) REVERT: D 87 MET cc_start: 0.6729 (pmm) cc_final: 0.6519 (pmm) REVERT: D 170 MET cc_start: 0.5622 (OUTLIER) cc_final: 0.4827 (mpp) REVERT: D 203 MET cc_start: 0.1678 (tpp) cc_final: 0.1287 (ttm) REVERT: D 244 MET cc_start: 0.0590 (tpp) cc_final: -0.1645 (mmm) REVERT: D 261 PHE cc_start: 0.7198 (OUTLIER) cc_final: 0.6946 (t80) REVERT: D 321 VAL cc_start: 0.4940 (OUTLIER) cc_final: 0.4734 (p) REVERT: D 334 MET cc_start: 0.5513 (ttt) cc_final: 0.5106 (tmm) REVERT: D 452 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7882 (mtt-85) REVERT: F 334 MET cc_start: 0.3848 (tmt) cc_final: 0.2501 (ptm) REVERT: F 658 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8066 (mm-30) REVERT: F 661 PHE cc_start: 0.7866 (m-80) cc_final: 0.7588 (m-80) REVERT: G 110 ASP cc_start: 0.8054 (p0) cc_final: 0.7787 (p0) REVERT: G 482 LEU cc_start: 0.9366 (mt) cc_final: 0.9052 (pp) REVERT: G 488 ASP cc_start: 0.8141 (m-30) cc_final: 0.7445 (p0) REVERT: H 65 MET cc_start: 0.8043 (ptp) cc_final: 0.7777 (ptm) REVERT: H 334 MET cc_start: 0.3095 (ptt) cc_final: 0.2832 (tmm) REVERT: H 361 ARG cc_start: 0.7464 (tpp80) cc_final: 0.7258 (tpp80) REVERT: H 467 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7882 (pt) REVERT: H 677 MET cc_start: -0.0639 (OUTLIER) cc_final: -0.1221 (ptp) REVERT: I 334 MET cc_start: 0.3941 (tmt) cc_final: 0.3615 (tmt) REVERT: I 348 GLU cc_start: 0.8363 (tt0) cc_final: 0.8065 (pt0) REVERT: I 658 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8051 (mm-30) REVERT: I 661 PHE cc_start: 0.8238 (m-80) cc_final: 0.7683 (m-80) REVERT: J 110 ASP cc_start: 0.8052 (p0) cc_final: 0.7779 (p0) REVERT: J 482 LEU cc_start: 0.9364 (mt) cc_final: 0.9051 (pp) REVERT: J 488 ASP cc_start: 0.8143 (m-30) cc_final: 0.7446 (p0) REVERT: K 269 LYS cc_start: 0.8777 (mmpt) cc_final: 0.8573 (mtmt) REVERT: L 170 MET cc_start: 0.5568 (OUTLIER) cc_final: 0.4746 (mpp) REVERT: L 261 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.7086 (t80) REVERT: L 396 MET cc_start: 0.5104 (ptt) cc_final: 0.4828 (ptm) outliers start: 82 outliers final: 46 residues processed: 433 average time/residue: 1.4382 time to fit residues: 783.6295 Evaluate side-chains 425 residues out of total 5888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 366 time to evaluate : 4.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 261 PHE Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 452 ARG Chi-restraints excluded: chain D residue 458 TYR Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 407 THR Chi-restraints excluded: chain F residue 413 SER Chi-restraints excluded: chain F residue 658 GLU Chi-restraints excluded: chain F residue 694 VAL Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain H residue 349 MET Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain H residue 467 ILE Chi-restraints excluded: chain H residue 468 ASP Chi-restraints excluded: chain H residue 623 LYS Chi-restraints excluded: chain H residue 677 MET Chi-restraints excluded: chain I residue 110 MET Chi-restraints excluded: chain I residue 407 THR Chi-restraints excluded: chain I residue 411 ASP Chi-restraints excluded: chain I residue 413 SER Chi-restraints excluded: chain I residue 658 GLU Chi-restraints excluded: chain I residue 694 VAL Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 170 MET Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain L residue 261 PHE Chi-restraints excluded: chain L residue 336 MET Chi-restraints excluded: chain L residue 342 VAL Chi-restraints excluded: chain L residue 418 THR Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 467 ILE Chi-restraints excluded: chain L residue 677 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 449 optimal weight: 5.9990 chunk 603 optimal weight: 0.0980 chunk 173 optimal weight: 6.9990 chunk 522 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 567 optimal weight: 0.9990 chunk 237 optimal weight: 0.7980 chunk 582 optimal weight: 0.4980 chunk 71 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 HIS ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 ASN G 236 GLN H 182 HIS ** H 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 330 ASN J 236 GLN ** L 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.140574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.086199 restraints weight = 141943.778| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.89 r_work: 0.2837 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 56596 Z= 0.154 Angle : 0.554 12.398 76434 Z= 0.283 Chirality : 0.043 0.178 8440 Planarity : 0.004 0.067 10018 Dihedral : 4.369 57.761 7902 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.40 % Favored : 97.57 % Rotamer: Outliers : 1.24 % Allowed : 16.76 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.90 % 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: 1.28 (0.10), residues: 7124 helix: 2.14 (0.10), residues: 2740 sheet: 0.85 (0.14), residues: 1316 loop : -0.32 (0.11), residues: 3068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 358 HIS 0.010 0.001 HIS H 344 PHE 0.028 0.001 PHE K 497 TYR 0.020 0.001 TYR D 270 ARG 0.015 0.000 ARG I 409 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17867.13 seconds wall clock time: 310 minutes 3.46 seconds (18603.46 seconds total)