Starting phenix.real_space_refine on Sun Sep 29 04:46:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2n_0609/09_2024/6o2n_0609.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2n_0609/09_2024/6o2n_0609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2n_0609/09_2024/6o2n_0609.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2n_0609/09_2024/6o2n_0609.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2n_0609/09_2024/6o2n_0609.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2n_0609/09_2024/6o2n_0609.cif" } resolution = 3.7 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= 0.001 sd= 0.008 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 140 5.16 5 C 45474 2.51 5 N 11801 2.21 5 O 15222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 300 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 72637 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5196 Classifications: {'peptide': 659} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 631} Chain: "B" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5196 Classifications: {'peptide': 659} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 631} Chain: "C" Number of atoms: 5182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5182 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 27, 'TRANS': 630} Chain: "D" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5196 Classifications: {'peptide': 659} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 631} Chain: "E" Number of atoms: 5182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5182 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 27, 'TRANS': 630} Chain: "F" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5196 Classifications: {'peptide': 659} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 631} Chain: "G" Number of atoms: 5182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5182 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 27, 'TRANS': 630} Chain: "H" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5196 Classifications: {'peptide': 659} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 631} Chain: "I" Number of atoms: 5182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5182 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 27, 'TRANS': 630} Chain: "J" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5196 Classifications: {'peptide': 659} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 631} Chain: "K" Number of atoms: 5182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5182 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 27, 'TRANS': 630} Chain: "L" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5196 Classifications: {'peptide': 659} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 631} Chain: "M" Number of atoms: 5182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5182 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 27, 'TRANS': 630} Chain: "Z" Number of atoms: 5173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5173 Classifications: {'peptide': 657} Link IDs: {'PTRANS': 27, 'TRANS': 629} Time building chain proxies: 31.55, per 1000 atoms: 0.43 Number of scatterers: 72637 At special positions: 0 Unit cell: (184.15, 181.25, 269.7, 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 140 16.00 O 15222 8.00 N 11801 7.00 C 45474 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=0, symmetry=0 Time building additional restraints: 12.48 Conformation dependent library (CDL) restraints added in 7.0 seconds 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17288 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 156 sheets defined 11.8% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.68 Creating SS restraints... Processing helix chain 'A' and resid 227 through 232 removed outlier: 3.890A pdb=" N ARG A 232 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 removed outlier: 3.757A pdb=" N ALA A 250 " --> pdb=" O ASP A 247 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 278 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 502 through 505 removed outlier: 4.204A pdb=" N ASP A 505 " --> pdb=" O SER A 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 502 through 505' Processing helix chain 'A' and resid 506 through 512 removed outlier: 3.704A pdb=" N SER A 512 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 555 removed outlier: 3.592A pdb=" N GLU A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE A 555 " --> pdb=" O ILE A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 563 removed outlier: 4.036A pdb=" N GLY A 562 " --> pdb=" O LYS A 559 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 563 " --> pdb=" O LYS A 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 559 through 563' Processing helix chain 'A' and resid 581 through 591 Processing helix chain 'A' and resid 599 through 603 removed outlier: 3.566A pdb=" N ASN A 602 " --> pdb=" O LYS A 599 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 603 " --> pdb=" O ILE A 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 599 through 603' Processing helix chain 'A' and resid 661 through 663 No H-bonds generated for 'chain 'A' and resid 661 through 663' Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 829 through 831 No H-bonds generated for 'chain 'A' and resid 829 through 831' Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.808A pdb=" N ARG B 232 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 250 removed outlier: 3.555A pdb=" N PHE B 249 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B 250 " --> pdb=" O ASP B 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 246 through 250' Processing helix chain 'B' and resid 272 through 278 Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.633A pdb=" N ARG B 290 " --> pdb=" O THR B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 472 Processing helix chain 'B' and resid 502 through 505 removed outlier: 4.263A pdb=" N ASP B 505 " --> pdb=" O SER B 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 502 through 505' Processing helix chain 'B' and resid 506 through 511 Processing helix chain 'B' and resid 546 through 555 removed outlier: 3.799A pdb=" N PHE B 555 " --> pdb=" O ILE B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 563 removed outlier: 3.982A pdb=" N GLY B 562 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 589 Processing helix chain 'B' and resid 661 through 663 No H-bonds generated for 'chain 'B' and resid 661 through 663' Processing helix chain 'B' and resid 796 through 800 Processing helix chain 'B' and resid 829 through 831 No H-bonds generated for 'chain 'B' and resid 829 through 831' Processing helix chain 'C' and resid 227 through 233 removed outlier: 3.618A pdb=" N ASN C 233 " --> pdb=" O SER C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 279 removed outlier: 3.541A pdb=" N LYS C 276 " --> pdb=" O THR C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 291 removed outlier: 3.988A pdb=" N ASP C 291 " --> pdb=" O GLU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 337 removed outlier: 3.564A pdb=" N ALA C 337 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 502 through 505 removed outlier: 4.276A pdb=" N ASP C 505 " --> pdb=" O SER C 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 502 through 505' Processing helix chain 'C' and resid 506 through 511 Processing helix chain 'C' and resid 546 through 555 removed outlier: 3.794A pdb=" N GLU C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE C 555 " --> pdb=" O ILE C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 590 removed outlier: 3.753A pdb=" N ALA C 585 " --> pdb=" O ASP C 581 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN C 586 " --> pdb=" O ASP C 582 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C 587 " --> pdb=" O ASN C 583 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP C 590 " --> pdb=" O ASN C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 603 removed outlier: 3.655A pdb=" N ASN C 602 " --> pdb=" O LYS C 599 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL C 603 " --> pdb=" O ILE C 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 599 through 603' Processing helix chain 'C' and resid 760 through 764 removed outlier: 3.839A pdb=" N ASP C 763 " --> pdb=" O GLU C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 831 No H-bonds generated for 'chain 'C' and resid 829 through 831' Processing helix chain 'D' and resid 226 through 230 Processing helix chain 'D' and resid 246 through 250 removed outlier: 3.561A pdb=" N PHE D 249 " --> pdb=" O GLU D 246 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA D 250 " --> pdb=" O ASP D 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 246 through 250' Processing helix chain 'D' and resid 273 through 278 Processing helix chain 'D' and resid 286 through 290 removed outlier: 3.605A pdb=" N ARG D 290 " --> pdb=" O THR D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 472 Processing helix chain 'D' and resid 506 through 511 Processing helix chain 'D' and resid 546 through 555 removed outlier: 3.527A pdb=" N GLU D 552 " --> pdb=" O GLY D 548 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE D 555 " --> pdb=" O ILE D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 563 removed outlier: 3.917A pdb=" N GLY D 562 " --> pdb=" O LYS D 559 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 563 " --> pdb=" O LYS D 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 559 through 563' Processing helix chain 'D' and resid 581 through 589 Processing helix chain 'D' and resid 661 through 663 No H-bonds generated for 'chain 'D' and resid 661 through 663' Processing helix chain 'D' and resid 796 through 800 Processing helix chain 'D' and resid 829 through 831 No H-bonds generated for 'chain 'D' and resid 829 through 831' Processing helix chain 'E' and resid 227 through 233 removed outlier: 3.656A pdb=" N ASN E 233 " --> pdb=" O SER E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 279 removed outlier: 3.537A pdb=" N LYS E 276 " --> pdb=" O THR E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 290 removed outlier: 3.541A pdb=" N ARG E 290 " --> pdb=" O THR E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 Processing helix chain 'E' and resid 463 through 472 Processing helix chain 'E' and resid 502 through 505 removed outlier: 4.202A pdb=" N ASP E 505 " --> pdb=" O SER E 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 502 through 505' Processing helix chain 'E' and resid 506 through 511 Processing helix chain 'E' and resid 546 through 555 removed outlier: 3.817A pdb=" N GLU E 552 " --> pdb=" O GLY E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 590 removed outlier: 3.707A pdb=" N ALA E 585 " --> pdb=" O ASP E 581 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN E 586 " --> pdb=" O ASP E 582 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP E 590 " --> pdb=" O ASN E 586 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 603 removed outlier: 3.600A pdb=" N ASN E 602 " --> pdb=" O LYS E 599 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL E 603 " --> pdb=" O ILE E 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 599 through 603' Processing helix chain 'E' and resid 760 through 764 removed outlier: 3.911A pdb=" N ASP E 763 " --> pdb=" O GLU E 760 " (cutoff:3.500A) Processing helix chain 'E' and resid 829 through 831 No H-bonds generated for 'chain 'E' and resid 829 through 831' Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.675A pdb=" N ARG F 232 " --> pdb=" O ASP F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 250 removed outlier: 3.576A pdb=" N PHE F 249 " --> pdb=" O GLU F 246 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA F 250 " --> pdb=" O ASP F 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 246 through 250' Processing helix chain 'F' and resid 272 through 278 Processing helix chain 'F' and resid 286 through 290 Processing helix chain 'F' and resid 463 through 472 Processing helix chain 'F' and resid 502 through 505 removed outlier: 4.309A pdb=" N ASP F 505 " --> pdb=" O SER F 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 502 through 505' Processing helix chain 'F' and resid 506 through 512 removed outlier: 3.879A pdb=" N SER F 512 " --> pdb=" O SER F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 555 removed outlier: 3.744A pdb=" N GLU F 552 " --> pdb=" O GLY F 548 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE F 555 " --> pdb=" O ILE F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 592 Processing helix chain 'F' and resid 661 through 663 No H-bonds generated for 'chain 'F' and resid 661 through 663' Processing helix chain 'F' and resid 796 through 800 Processing helix chain 'F' and resid 829 through 831 No H-bonds generated for 'chain 'F' and resid 829 through 831' Processing helix chain 'G' and resid 227 through 233 removed outlier: 3.652A pdb=" N ASN G 233 " --> pdb=" O SER G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 279 removed outlier: 3.545A pdb=" N LYS G 276 " --> pdb=" O THR G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 291 removed outlier: 3.616A pdb=" N ARG G 290 " --> pdb=" O THR G 287 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP G 291 " --> pdb=" O GLU G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 375 through 379 removed outlier: 3.629A pdb=" N LEU G 379 " --> pdb=" O ASN G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 Processing helix chain 'G' and resid 463 through 472 Processing helix chain 'G' and resid 506 through 511 Processing helix chain 'G' and resid 547 through 555 removed outlier: 3.602A pdb=" N GLU G 552 " --> pdb=" O GLY G 548 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE G 555 " --> pdb=" O ILE G 551 " (cutoff:3.500A) Processing helix chain 'G' and resid 581 through 590 removed outlier: 3.543A pdb=" N ALA G 585 " --> pdb=" O ASP G 581 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN G 586 " --> pdb=" O ASP G 582 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS G 587 " --> pdb=" O ASN G 583 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP G 590 " --> pdb=" O ASN G 586 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 603 removed outlier: 3.683A pdb=" N ASN G 602 " --> pdb=" O LYS G 599 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL G 603 " --> pdb=" O ILE G 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 599 through 603' Processing helix chain 'G' and resid 829 through 831 No H-bonds generated for 'chain 'G' and resid 829 through 831' Processing helix chain 'H' and resid 227 through 232 removed outlier: 3.935A pdb=" N ARG H 232 " --> pdb=" O ASP H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 250 removed outlier: 3.564A pdb=" N PHE H 249 " --> pdb=" O GLU H 246 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA H 250 " --> pdb=" O ASP H 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 246 through 250' Processing helix chain 'H' and resid 272 through 278 Processing helix chain 'H' and resid 286 through 290 removed outlier: 3.628A pdb=" N ARG H 290 " --> pdb=" O THR H 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 463 through 472 Processing helix chain 'H' and resid 506 through 512 removed outlier: 3.749A pdb=" N SER H 512 " --> pdb=" O SER H 508 " (cutoff:3.500A) Processing helix chain 'H' and resid 546 through 555 removed outlier: 3.774A pdb=" N GLU H 552 " --> pdb=" O GLY H 548 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE H 555 " --> pdb=" O ILE H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 559 through 563 removed outlier: 3.869A pdb=" N GLY H 562 " --> pdb=" O LYS H 559 " (cutoff:3.500A) Processing helix chain 'H' and resid 581 through 591 Processing helix chain 'H' and resid 661 through 663 No H-bonds generated for 'chain 'H' and resid 661 through 663' Processing helix chain 'H' and resid 796 through 800 Processing helix chain 'H' and resid 829 through 831 No H-bonds generated for 'chain 'H' and resid 829 through 831' Processing helix chain 'I' and resid 227 through 233 removed outlier: 3.640A pdb=" N ASN I 233 " --> pdb=" O SER I 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 272 through 279 removed outlier: 3.529A pdb=" N LYS I 276 " --> pdb=" O THR I 272 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 291 removed outlier: 4.058A pdb=" N ASP I 291 " --> pdb=" O GLU I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.625A pdb=" N GLN I 428 " --> pdb=" O GLN I 425 " (cutoff:3.500A) Processing helix chain 'I' and resid 463 through 472 Processing helix chain 'I' and resid 502 through 505 removed outlier: 4.190A pdb=" N ASP I 505 " --> pdb=" O SER I 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 502 through 505' Processing helix chain 'I' and resid 506 through 511 Processing helix chain 'I' and resid 546 through 555 removed outlier: 3.699A pdb=" N GLU I 552 " --> pdb=" O GLY I 548 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE I 555 " --> pdb=" O ILE I 551 " (cutoff:3.500A) Processing helix chain 'I' and resid 581 through 590 removed outlier: 3.603A pdb=" N ALA I 585 " --> pdb=" O ASP I 581 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN I 586 " --> pdb=" O ASP I 582 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS I 587 " --> pdb=" O ASN I 583 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP I 590 " --> pdb=" O ASN I 586 " (cutoff:3.500A) Processing helix chain 'I' and resid 599 through 603 removed outlier: 3.547A pdb=" N ASN I 602 " --> pdb=" O LYS I 599 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL I 603 " --> pdb=" O ILE I 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 599 through 603' Processing helix chain 'I' and resid 760 through 764 removed outlier: 3.894A pdb=" N ASP I 763 " --> pdb=" O GLU I 760 " (cutoff:3.500A) Processing helix chain 'I' and resid 829 through 831 No H-bonds generated for 'chain 'I' and resid 829 through 831' Processing helix chain 'J' and resid 227 through 232 removed outlier: 3.860A pdb=" N ARG J 232 " --> pdb=" O ASP J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 250 removed outlier: 3.737A pdb=" N PHE J 249 " --> pdb=" O GLU J 246 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA J 250 " --> pdb=" O ASP J 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 246 through 250' Processing helix chain 'J' and resid 272 through 278 Processing helix chain 'J' and resid 286 through 290 removed outlier: 3.660A pdb=" N ARG J 290 " --> pdb=" O THR J 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 463 through 472 removed outlier: 3.543A pdb=" N ALA J 472 " --> pdb=" O LYS J 468 " (cutoff:3.500A) Processing helix chain 'J' and resid 502 through 505 removed outlier: 4.253A pdb=" N ASP J 505 " --> pdb=" O SER J 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 502 through 505' Processing helix chain 'J' and resid 506 through 512 removed outlier: 3.775A pdb=" N SER J 512 " --> pdb=" O SER J 508 " (cutoff:3.500A) Processing helix chain 'J' and resid 546 through 555 removed outlier: 3.597A pdb=" N GLU J 552 " --> pdb=" O GLY J 548 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE J 555 " --> pdb=" O ILE J 551 " (cutoff:3.500A) Processing helix chain 'J' and resid 581 through 589 Processing helix chain 'J' and resid 661 through 663 No H-bonds generated for 'chain 'J' and resid 661 through 663' Processing helix chain 'J' and resid 796 through 800 Processing helix chain 'J' and resid 829 through 831 No H-bonds generated for 'chain 'J' and resid 829 through 831' Processing helix chain 'K' and resid 227 through 233 removed outlier: 3.671A pdb=" N ASN K 233 " --> pdb=" O SER K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 279 removed outlier: 3.511A pdb=" N LYS K 276 " --> pdb=" O THR K 272 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 290 removed outlier: 3.502A pdb=" N ARG K 290 " --> pdb=" O THR K 287 " (cutoff:3.500A) Processing helix chain 'K' and resid 333 through 337 removed outlier: 3.542A pdb=" N ALA K 337 " --> pdb=" O SER K 334 " (cutoff:3.500A) Processing helix chain 'K' and resid 425 through 429 removed outlier: 3.516A pdb=" N GLN K 428 " --> pdb=" O GLN K 425 " (cutoff:3.500A) Processing helix chain 'K' and resid 463 through 472 Processing helix chain 'K' and resid 506 through 511 Processing helix chain 'K' and resid 546 through 555 removed outlier: 3.826A pdb=" N GLU K 552 " --> pdb=" O GLY K 548 " (cutoff:3.500A) Processing helix chain 'K' and resid 581 through 589 removed outlier: 3.537A pdb=" N ALA K 585 " --> pdb=" O ASP K 581 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN K 586 " --> pdb=" O ASP K 582 " (cutoff:3.500A) Processing helix chain 'K' and resid 599 through 603 removed outlier: 3.658A pdb=" N ASN K 602 " --> pdb=" O LYS K 599 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL K 603 " --> pdb=" O ILE K 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 599 through 603' Processing helix chain 'K' and resid 760 through 764 removed outlier: 3.951A pdb=" N ASP K 763 " --> pdb=" O GLU K 760 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 232 removed outlier: 3.919A pdb=" N ARG L 232 " --> pdb=" O ASP L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 246 through 250 removed outlier: 3.657A pdb=" N PHE L 249 " --> pdb=" O GLU L 246 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA L 250 " --> pdb=" O ASP L 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 246 through 250' Processing helix chain 'L' and resid 272 through 278 Processing helix chain 'L' and resid 286 through 290 removed outlier: 3.703A pdb=" N ARG L 290 " --> pdb=" O THR L 287 " (cutoff:3.500A) Processing helix chain 'L' and resid 463 through 472 removed outlier: 3.602A pdb=" N ALA L 472 " --> pdb=" O LYS L 468 " (cutoff:3.500A) Processing helix chain 'L' and resid 502 through 505 removed outlier: 4.185A pdb=" N ASP L 505 " --> pdb=" O SER L 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 502 through 505' Processing helix chain 'L' and resid 506 through 512 removed outlier: 3.732A pdb=" N SER L 512 " --> pdb=" O SER L 508 " (cutoff:3.500A) Processing helix chain 'L' and resid 546 through 555 removed outlier: 3.621A pdb=" N GLU L 552 " --> pdb=" O GLY L 548 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE L 555 " --> pdb=" O ILE L 551 " (cutoff:3.500A) Processing helix chain 'L' and resid 581 through 589 Processing helix chain 'L' and resid 661 through 663 No H-bonds generated for 'chain 'L' and resid 661 through 663' Processing helix chain 'L' and resid 796 through 800 Processing helix chain 'L' and resid 829 through 831 No H-bonds generated for 'chain 'L' and resid 829 through 831' Processing helix chain 'M' and resid 227 through 233 removed outlier: 3.611A pdb=" N ASN M 233 " --> pdb=" O SER M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 272 through 279 removed outlier: 3.701A pdb=" N LYS M 276 " --> pdb=" O THR M 272 " (cutoff:3.500A) Processing helix chain 'M' and resid 286 through 291 removed outlier: 4.065A pdb=" N ASP M 291 " --> pdb=" O GLU M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 425 through 429 Processing helix chain 'M' and resid 463 through 472 Processing helix chain 'M' and resid 502 through 505 removed outlier: 4.219A pdb=" N ASP M 505 " --> pdb=" O SER M 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 502 through 505' Processing helix chain 'M' and resid 506 through 511 Processing helix chain 'M' and resid 546 through 555 removed outlier: 3.771A pdb=" N GLU M 552 " --> pdb=" O GLY M 548 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE M 555 " --> pdb=" O ILE M 551 " (cutoff:3.500A) Processing helix chain 'M' and resid 581 through 590 removed outlier: 3.885A pdb=" N ASN M 586 " --> pdb=" O ASP M 582 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS M 587 " --> pdb=" O ASN M 583 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP M 590 " --> pdb=" O ASN M 586 " (cutoff:3.500A) Processing helix chain 'M' and resid 599 through 603 removed outlier: 3.681A pdb=" N ASN M 602 " --> pdb=" O LYS M 599 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL M 603 " --> pdb=" O ILE M 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 599 through 603' Processing helix chain 'M' and resid 760 through 764 removed outlier: 3.942A pdb=" N ASP M 763 " --> pdb=" O GLU M 760 " (cutoff:3.500A) Processing helix chain 'M' and resid 829 through 831 No H-bonds generated for 'chain 'M' and resid 829 through 831' Processing helix chain 'Z' and resid 227 through 233 removed outlier: 3.649A pdb=" N ASN Z 233 " --> pdb=" O SER Z 229 " (cutoff:3.500A) Processing helix chain 'Z' and resid 272 through 279 removed outlier: 3.504A pdb=" N LYS Z 276 " --> pdb=" O THR Z 272 " (cutoff:3.500A) Processing helix chain 'Z' and resid 286 through 291 removed outlier: 3.973A pdb=" N ASP Z 291 " --> pdb=" O GLU Z 288 " (cutoff:3.500A) Processing helix chain 'Z' and resid 333 through 337 removed outlier: 3.562A pdb=" N ALA Z 337 " --> pdb=" O SER Z 334 " (cutoff:3.500A) Processing helix chain 'Z' and resid 425 through 429 removed outlier: 3.648A pdb=" N ILE Z 429 " --> pdb=" O GLU Z 426 " (cutoff:3.500A) Processing helix chain 'Z' and resid 463 through 472 Processing helix chain 'Z' and resid 506 through 511 Processing helix chain 'Z' and resid 546 through 555 removed outlier: 3.716A pdb=" N GLU Z 552 " --> pdb=" O GLY Z 548 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE Z 555 " --> pdb=" O ILE Z 551 " (cutoff:3.500A) Processing helix chain 'Z' and resid 581 through 590 removed outlier: 3.657A pdb=" N ALA Z 585 " --> pdb=" O ASP Z 581 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN Z 586 " --> pdb=" O ASP Z 582 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP Z 590 " --> pdb=" O ASN Z 586 " (cutoff:3.500A) Processing helix chain 'Z' and resid 599 through 603 removed outlier: 3.725A pdb=" N ASN Z 602 " --> pdb=" O LYS Z 599 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL Z 603 " --> pdb=" O ILE Z 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 599 through 603' Processing helix chain 'Z' and resid 760 through 764 removed outlier: 4.012A pdb=" N ASP Z 763 " --> pdb=" O GLU Z 760 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 238 Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 311 removed outlier: 3.615A pdb=" N ILE A 299 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY A 301 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN A 392 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU A 307 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASN A 390 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE A 309 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TYR A 388 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 437 through 439 removed outlier: 3.798A pdb=" N ASP A 437 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR A 439 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 387 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 316 through 345 removed outlier: 3.516A pdb=" N ALA A 351 " --> pdb=" O TYR B 345 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 343 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 341 " --> pdb=" O THR A 355 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR A 357 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 337 " --> pdb=" O HIS A 359 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 361 " --> pdb=" O ASN B 335 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN A 363 " --> pdb=" O GLU B 333 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS B 331 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B 327 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP A 375 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN B 319 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 351 " --> pdb=" O TYR D 345 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL D 341 " --> pdb=" O THR B 355 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR B 357 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA D 337 " --> pdb=" O HIS B 359 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN B 363 " --> pdb=" O GLU D 333 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS D 331 " --> pdb=" O THR B 365 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR D 327 " --> pdb=" O ASP B 369 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP B 375 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS D 321 " --> pdb=" O TRP B 375 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA D 351 " --> pdb=" O TYR F 345 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL F 341 " --> pdb=" O THR D 355 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR D 357 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS D 359 " --> pdb=" O ALA F 337 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA F 337 " --> pdb=" O HIS D 359 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN D 363 " --> pdb=" O GLU F 333 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS F 331 " --> pdb=" O THR D 365 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR F 327 " --> pdb=" O ASP D 369 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP D 375 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS F 321 " --> pdb=" O TRP D 375 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN F 319 " --> pdb=" O THR D 377 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA F 351 " --> pdb=" O TYR H 345 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL H 341 " --> pdb=" O THR F 355 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR F 357 " --> pdb=" O VAL H 339 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN F 363 " --> pdb=" O GLU H 333 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS H 331 " --> pdb=" O THR F 365 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP F 369 " --> pdb=" O THR H 327 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR H 327 " --> pdb=" O ASP F 369 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP F 375 " --> pdb=" O LYS H 321 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS H 321 " --> pdb=" O TRP F 375 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN H 319 " --> pdb=" O THR F 377 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA H 351 " --> pdb=" O TYR J 345 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL J 343 " --> pdb=" O VAL H 353 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL J 341 " --> pdb=" O THR H 355 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR H 357 " --> pdb=" O VAL J 339 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA J 337 " --> pdb=" O HIS H 359 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR H 361 " --> pdb=" O ASN J 335 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN H 363 " --> pdb=" O GLU J 333 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS J 331 " --> pdb=" O THR H 365 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR J 327 " --> pdb=" O ASP H 369 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP H 375 " --> pdb=" O LYS J 321 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN J 319 " --> pdb=" O THR H 377 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA J 351 " --> pdb=" O TYR L 345 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL L 341 " --> pdb=" O THR J 355 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR J 357 " --> pdb=" O VAL L 339 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA L 337 " --> pdb=" O HIS J 359 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN J 363 " --> pdb=" O GLU L 333 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS L 331 " --> pdb=" O THR J 365 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR L 327 " --> pdb=" O ASP J 369 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP J 375 " --> pdb=" O LYS L 321 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS L 321 " --> pdb=" O TRP J 375 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN L 319 " --> pdb=" O THR J 377 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA L 351 " --> pdb=" O TYR A 345 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 343 " --> pdb=" O VAL L 353 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 341 " --> pdb=" O THR L 355 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR L 357 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS L 359 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 337 " --> pdb=" O HIS L 359 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN L 363 " --> pdb=" O GLU A 333 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A 331 " --> pdb=" O THR L 365 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 327 " --> pdb=" O ASP L 369 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 321 " --> pdb=" O TRP L 375 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN A 319 " --> pdb=" O THR L 377 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 420 through 423 removed outlier: 3.760A pdb=" N SER A 420 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS A 405 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLY A 485 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR A 407 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N VAL A 483 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N THR A 409 " --> pdb=" O THR A 481 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 489 through 490 removed outlier: 3.652A pdb=" N THR A 489 " --> pdb=" O VAL A 497 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 525 through 531 Processing sheet with id=AA8, first strand: chain 'A' and resid 564 through 565 removed outlier: 4.143A pdb=" N LEU A 564 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 618 through 619 removed outlier: 3.571A pdb=" N TYR A 618 " --> pdb=" O ILE A 738 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 651 through 659 Processing sheet with id=AB2, first strand: chain 'A' and resid 768 through 775 removed outlier: 6.246A pdb=" N PHE A 769 " --> pdb=" O MET A 786 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N MET A 786 " --> pdb=" O PHE A 769 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASP A 771 " --> pdb=" O ASN A 784 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASN A 780 " --> pdb=" O ASN A 775 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET A 786 " --> pdb=" O VAL A 840 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 816 through 822 removed outlier: 5.445A pdb=" N ASP A 817 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA A 808 " --> pdb=" O ASP A 817 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLY A 819 " --> pdb=" O VAL A 806 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 806 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 804 " --> pdb=" O LYS A 821 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS A 803 " --> pdb=" O TYR A 861 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE A 860 " --> pdb=" O ARG A 868 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ARG A 868 " --> pdb=" O ILE A 860 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 826 through 827 removed outlier: 3.527A pdb=" N ARG A 826 " --> pdb=" O THR A 837 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AB6, first strand: chain 'B' and resid 303 through 311 removed outlier: 6.738A pdb=" N ASN B 392 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU B 307 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASN B 390 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ILE B 309 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TYR B 388 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 303 through 311 removed outlier: 6.738A pdb=" N ASN B 392 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU B 307 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASN B 390 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ILE B 309 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TYR B 388 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 420 through 423 removed outlier: 3.787A pdb=" N SER B 420 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LYS B 405 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY B 485 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR B 407 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL B 483 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N THR B 409 " --> pdb=" O THR B 481 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AC1, first strand: chain 'B' and resid 525 through 531 Processing sheet with id=AC2, first strand: chain 'B' and resid 564 through 565 removed outlier: 4.092A pdb=" N LEU B 564 " --> pdb=" O ILE B 571 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 651 through 659 Processing sheet with id=AC4, first strand: chain 'B' and resid 707 through 712 removed outlier: 3.735A pdb=" N PHE B 711 " --> pdb=" O TYR B 669 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR B 669 " --> pdb=" O PHE B 711 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 768 through 775 removed outlier: 6.149A pdb=" N PHE B 769 " --> pdb=" O MET B 786 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N MET B 786 " --> pdb=" O PHE B 769 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASP B 771 " --> pdb=" O ASN B 784 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASN B 780 " --> pdb=" O ASN B 775 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET B 786 " --> pdb=" O VAL B 840 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 840 " --> pdb=" O MET B 786 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 788 " --> pdb=" O ASN B 838 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN B 838 " --> pdb=" O PHE B 788 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 816 through 822 removed outlier: 5.463A pdb=" N ASP B 817 " --> pdb=" O ALA B 808 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA B 808 " --> pdb=" O ASP B 817 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY B 819 " --> pdb=" O VAL B 806 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B 806 " --> pdb=" O GLY B 819 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS B 821 " --> pdb=" O TYR B 804 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR B 804 " --> pdb=" O LYS B 821 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS B 803 " --> pdb=" O TYR B 861 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU B 858 " --> pdb=" O GLU B 869 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=AC8, first strand: chain 'C' and resid 366 through 367 removed outlier: 5.839A pdb=" N GLU C 305 " --> pdb=" O THR C 327 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N MET C 304 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ARG C 394 " --> pdb=" O MET C 304 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS C 306 " --> pdb=" O ASN C 392 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE C 460 " --> pdb=" O ILE C 389 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 352 through 353 removed outlier: 6.542A pdb=" N SER C 516 " --> pdb=" O ILE C 611 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE C 613 " --> pdb=" O SER C 516 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE C 518 " --> pdb=" O ILE C 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 362 through 364 removed outlier: 3.781A pdb=" N SER C 420 " --> pdb=" O LEU C 412 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 489 through 490 removed outlier: 3.531A pdb=" N THR C 489 " --> pdb=" O VAL C 497 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL C 497 " --> pdb=" O THR C 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 558 through 559 removed outlier: 3.691A pdb=" N LEU C 564 " --> pdb=" O ILE C 571 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 618 through 620 removed outlier: 6.510A pdb=" N ARG C 668 " --> pdb=" O LEU C 741 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 654 through 659 removed outlier: 3.625A pdb=" N SER C 683 " --> pdb=" O THR C 695 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR C 695 " --> pdb=" O SER C 683 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 768 through 771 Processing sheet with id=AD7, first strand: chain 'C' and resid 816 through 822 removed outlier: 4.144A pdb=" N VAL C 806 " --> pdb=" O ILE C 818 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR C 820 " --> pdb=" O TYR C 804 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR C 804 " --> pdb=" O THR C 820 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU C 870 " --> pdb=" O LEU C 858 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE C 860 " --> pdb=" O ARG C 868 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ARG C 868 " --> pdb=" O ILE C 860 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 824 through 827 Processing sheet with id=AD9, first strand: chain 'D' and resid 235 through 238 Processing sheet with id=AE1, first strand: chain 'D' and resid 298 through 311 removed outlier: 3.681A pdb=" N GLY D 301 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG D 394 " --> pdb=" O GLY D 303 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN D 392 " --> pdb=" O GLU D 305 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU D 307 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASN D 390 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE D 309 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYR D 388 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 298 through 311 removed outlier: 3.681A pdb=" N GLY D 301 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG D 394 " --> pdb=" O GLY D 303 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN D 392 " --> pdb=" O GLU D 305 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU D 307 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASN D 390 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE D 309 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYR D 388 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 420 through 423 removed outlier: 3.903A pdb=" N SER D 420 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS D 405 " --> pdb=" O GLY D 485 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY D 485 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR D 407 " --> pdb=" O VAL D 483 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL D 483 " --> pdb=" O THR D 407 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR D 409 " --> pdb=" O THR D 481 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 489 through 490 removed outlier: 3.559A pdb=" N THR D 489 " --> pdb=" O VAL D 497 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 525 through 531 Processing sheet with id=AE6, first strand: chain 'D' and resid 564 through 565 removed outlier: 4.119A pdb=" N LEU D 564 " --> pdb=" O ILE D 571 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 651 through 659 Processing sheet with id=AE8, first strand: chain 'D' and resid 707 through 712 removed outlier: 3.762A pdb=" N PHE D 711 " --> pdb=" O TYR D 669 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR D 669 " --> pdb=" O PHE D 711 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 770 through 775 removed outlier: 6.681A pdb=" N ASP D 771 " --> pdb=" O ASN D 784 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASN D 780 " --> pdb=" O ASN D 775 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET D 786 " --> pdb=" O VAL D 840 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL D 840 " --> pdb=" O MET D 786 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 816 through 822 removed outlier: 5.412A pdb=" N ASP D 817 " --> pdb=" O ALA D 808 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ALA D 808 " --> pdb=" O ASP D 817 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLY D 819 " --> pdb=" O VAL D 806 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL D 806 " --> pdb=" O GLY D 819 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR D 804 " --> pdb=" O LYS D 821 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS D 803 " --> pdb=" O TYR D 861 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU D 858 " --> pdb=" O GLU D 869 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 826 through 827 Processing sheet with id=AF3, first strand: chain 'E' and resid 235 through 238 Processing sheet with id=AF4, first strand: chain 'E' and resid 418 through 421 removed outlier: 3.816A pdb=" N SER E 420 " --> pdb=" O LEU E 412 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE E 476 " --> pdb=" O THR E 365 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER E 364 " --> pdb=" O SER E 330 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER E 330 " --> pdb=" O SER E 364 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N GLU E 305 " --> pdb=" O THR E 327 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ASN E 329 " --> pdb=" O GLY E 303 " (cutoff:3.500A) removed outlier: 9.459A pdb=" N GLY E 303 " --> pdb=" O ASN E 329 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN E 392 " --> pdb=" O GLU E 305 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU E 307 " --> pdb=" O ASN E 390 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASN E 390 " --> pdb=" O LEU E 307 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE E 309 " --> pdb=" O TYR E 388 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TYR E 388 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE E 460 " --> pdb=" O ILE E 389 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 352 through 353 removed outlier: 6.053A pdb=" N ASN E 352 " --> pdb=" O PHE E 580 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER E 516 " --> pdb=" O ILE E 611 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ILE E 613 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE E 518 " --> pdb=" O ILE E 613 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 489 through 490 Processing sheet with id=AF7, first strand: chain 'E' and resid 558 through 559 removed outlier: 3.641A pdb=" N LEU E 564 " --> pdb=" O ILE E 571 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 618 through 620 removed outlier: 6.587A pdb=" N ARG E 668 " --> pdb=" O LEU E 741 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 654 through 659 removed outlier: 3.514A pdb=" N SER E 683 " --> pdb=" O THR E 695 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 768 through 771 Processing sheet with id=AG2, first strand: chain 'E' and resid 816 through 822 removed outlier: 5.123A pdb=" N ASP E 817 " --> pdb=" O ALA E 808 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA E 808 " --> pdb=" O ASP E 817 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N GLY E 819 " --> pdb=" O VAL E 806 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL E 806 " --> pdb=" O GLY E 819 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS E 803 " --> pdb=" O TYR E 861 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS E 856 " --> pdb=" O LEU E 871 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU E 871 " --> pdb=" O LYS E 856 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU E 858 " --> pdb=" O GLU E 869 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 824 through 827 Processing sheet with id=AG4, first strand: chain 'F' and resid 235 through 238 Processing sheet with id=AG5, first strand: chain 'F' and resid 298 through 311 removed outlier: 3.506A pdb=" N ILE F 299 " --> pdb=" O THR F 398 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG F 394 " --> pdb=" O GLY F 303 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN F 392 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU F 307 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASN F 390 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE F 309 " --> pdb=" O TYR F 388 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR F 388 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 437 through 439 removed outlier: 3.761A pdb=" N ASP F 437 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR F 439 " --> pdb=" O TYR F 395 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 420 through 423 removed outlier: 3.898A pdb=" N SER F 420 " --> pdb=" O LEU F 412 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS F 405 " --> pdb=" O GLY F 485 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLY F 485 " --> pdb=" O LYS F 405 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR F 407 " --> pdb=" O VAL F 483 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL F 483 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N THR F 409 " --> pdb=" O THR F 481 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 489 through 490 removed outlier: 3.552A pdb=" N THR F 489 " --> pdb=" O VAL F 497 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 525 through 531 Processing sheet with id=AH1, first strand: chain 'F' and resid 558 through 560 removed outlier: 3.697A pdb=" N THR F 558 " --> pdb=" O TYR F 565 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU F 564 " --> pdb=" O ILE F 571 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 651 through 659 Processing sheet with id=AH3, first strand: chain 'F' and resid 707 through 712 removed outlier: 3.629A pdb=" N PHE F 711 " --> pdb=" O TYR F 669 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR F 669 " --> pdb=" O PHE F 711 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 770 through 775 removed outlier: 6.733A pdb=" N ASP F 771 " --> pdb=" O ASN F 784 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN F 775 " --> pdb=" O ASN F 780 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASN F 780 " --> pdb=" O ASN F 775 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET F 786 " --> pdb=" O VAL F 840 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL F 840 " --> pdb=" O MET F 786 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 820 through 822 removed outlier: 3.558A pdb=" N LYS F 821 " --> pdb=" O TYR F 804 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR F 804 " --> pdb=" O LYS F 821 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS F 803 " --> pdb=" O TYR F 861 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS F 856 " --> pdb=" O LEU F 871 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU F 871 " --> pdb=" O LYS F 856 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU F 858 " --> pdb=" O GLU F 869 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 826 through 827 Processing sheet with id=AH7, first strand: chain 'G' and resid 235 through 238 Processing sheet with id=AH8, first strand: chain 'G' and resid 418 through 422 removed outlier: 6.993A pdb=" N LEU G 412 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N THR G 421 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR G 410 " --> pdb=" O THR G 421 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE G 476 " --> pdb=" O THR G 365 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER G 364 " --> pdb=" O SER G 330 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER G 330 " --> pdb=" O SER G 364 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLU G 305 " --> pdb=" O THR G 327 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ASN G 329 " --> pdb=" O GLY G 303 " (cutoff:3.500A) removed outlier: 9.486A pdb=" N GLY G 303 " --> pdb=" O ASN G 329 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N MET G 304 " --> pdb=" O ARG G 394 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG G 394 " --> pdb=" O MET G 304 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS G 306 " --> pdb=" O ASN G 392 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE G 460 " --> pdb=" O ILE G 389 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 352 through 353 removed outlier: 6.098A pdb=" N ASN G 352 " --> pdb=" O PHE G 580 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER G 516 " --> pdb=" O ILE G 611 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ILE G 613 " --> pdb=" O SER G 516 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE G 518 " --> pdb=" O ILE G 613 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 489 through 490 Processing sheet with id=AI2, first strand: chain 'G' and resid 558 through 559 removed outlier: 3.690A pdb=" N LEU G 564 " --> pdb=" O ILE G 571 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'G' and resid 618 through 620 removed outlier: 6.568A pdb=" N ARG G 668 " --> pdb=" O LEU G 741 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 654 through 659 Processing sheet with id=AI5, first strand: chain 'G' and resid 768 through 771 Processing sheet with id=AI6, first strand: chain 'G' and resid 816 through 822 removed outlier: 3.542A pdb=" N ALA G 808 " --> pdb=" O LYS G 816 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL G 806 " --> pdb=" O ILE G 818 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR G 820 " --> pdb=" O TYR G 804 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TYR G 804 " --> pdb=" O THR G 820 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS G 803 " --> pdb=" O TYR G 861 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS G 856 " --> pdb=" O LEU G 871 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU G 871 " --> pdb=" O LYS G 856 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU G 858 " --> pdb=" O GLU G 869 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'G' and resid 824 through 827 Processing sheet with id=AI8, first strand: chain 'H' and resid 235 through 238 Processing sheet with id=AI9, first strand: chain 'H' and resid 303 through 311 removed outlier: 6.822A pdb=" N ASN H 392 " --> pdb=" O GLU H 305 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU H 307 " --> pdb=" O ASN H 390 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN H 390 " --> pdb=" O LEU H 307 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ILE H 309 " --> pdb=" O TYR H 388 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TYR H 388 " --> pdb=" O ILE H 309 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'H' and resid 420 through 423 removed outlier: 3.744A pdb=" N SER H 420 " --> pdb=" O LEU H 412 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LYS H 405 " --> pdb=" O ASN H 486 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASN H 486 " --> pdb=" O LYS H 405 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLN H 482 " --> pdb=" O THR H 409 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASN H 411 " --> pdb=" O THR H 480 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N THR H 480 " --> pdb=" O ASN H 411 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL H 413 " --> pdb=" O LEU H 478 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LEU H 478 " --> pdb=" O VAL H 413 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'H' and resid 489 through 490 removed outlier: 3.572A pdb=" N THR H 489 " --> pdb=" O VAL H 497 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'H' and resid 525 through 531 Processing sheet with id=AJ4, first strand: chain 'H' and resid 564 through 565 removed outlier: 4.095A pdb=" N LEU H 564 " --> pdb=" O ILE H 571 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'H' and resid 651 through 659 Processing sheet with id=AJ6, first strand: chain 'H' and resid 707 through 710 Processing sheet with id=AJ7, first strand: chain 'H' and resid 770 through 775 removed outlier: 6.682A pdb=" N ASP H 771 " --> pdb=" O ASN H 784 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASN H 780 " --> pdb=" O ASN H 775 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'H' and resid 816 through 820 removed outlier: 5.429A pdb=" N ASP H 817 " --> pdb=" O ALA H 808 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ALA H 808 " --> pdb=" O ASP H 817 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLY H 819 " --> pdb=" O VAL H 806 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL H 806 " --> pdb=" O GLY H 819 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS H 803 " --> pdb=" O TYR H 861 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU H 858 " --> pdb=" O GLU H 869 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'H' and resid 826 through 827 Processing sheet with id=AK1, first strand: chain 'I' and resid 235 through 238 Processing sheet with id=AK2, first strand: chain 'I' and resid 366 through 367 removed outlier: 5.171A pdb=" N GLU I 305 " --> pdb=" O THR I 327 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N VAL I 302 " --> pdb=" O TYR I 396 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TYR I 396 " --> pdb=" O VAL I 302 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N MET I 304 " --> pdb=" O ARG I 394 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG I 394 " --> pdb=" O MET I 304 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS I 306 " --> pdb=" O ASN I 392 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE I 460 " --> pdb=" O ILE I 389 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'I' and resid 352 through 353 removed outlier: 5.970A pdb=" N ASN I 352 " --> pdb=" O PHE I 580 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER I 516 " --> pdb=" O ILE I 611 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ILE I 613 " --> pdb=" O SER I 516 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE I 518 " --> pdb=" O ILE I 613 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'I' and resid 362 through 364 removed outlier: 3.796A pdb=" N SER I 420 " --> pdb=" O LEU I 412 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'I' and resid 489 through 490 removed outlier: 3.547A pdb=" N THR I 489 " --> pdb=" O VAL I 497 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL I 497 " --> pdb=" O THR I 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK5 Processing sheet with id=AK6, first strand: chain 'I' and resid 558 through 559 removed outlier: 3.753A pdb=" N LEU I 564 " --> pdb=" O ILE I 571 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'I' and resid 618 through 620 removed outlier: 6.594A pdb=" N ARG I 668 " --> pdb=" O LEU I 741 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'I' and resid 654 through 659 removed outlier: 3.680A pdb=" N SER I 683 " --> pdb=" O THR I 695 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR I 695 " --> pdb=" O SER I 683 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'I' and resid 768 through 771 Processing sheet with id=AL1, first strand: chain 'I' and resid 816 through 822 removed outlier: 3.583A pdb=" N ALA I 808 " --> pdb=" O LYS I 816 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL I 806 " --> pdb=" O ILE I 818 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N THR I 820 " --> pdb=" O TYR I 804 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TYR I 804 " --> pdb=" O THR I 820 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS I 803 " --> pdb=" O TYR I 861 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS I 856 " --> pdb=" O LEU I 871 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU I 871 " --> pdb=" O LYS I 856 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU I 858 " --> pdb=" O GLU I 869 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'I' and resid 824 through 827 Processing sheet with id=AL3, first strand: chain 'J' and resid 235 through 238 Processing sheet with id=AL4, first strand: chain 'J' and resid 298 through 300 Processing sheet with id=AL5, first strand: chain 'J' and resid 303 through 311 removed outlier: 5.712A pdb=" N MET J 304 " --> pdb=" O ARG J 394 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ARG J 394 " --> pdb=" O MET J 304 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'J' and resid 303 through 311 removed outlier: 5.712A pdb=" N MET J 304 " --> pdb=" O ARG J 394 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ARG J 394 " --> pdb=" O MET J 304 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'J' and resid 420 through 423 removed outlier: 3.856A pdb=" N SER J 420 " --> pdb=" O LEU J 412 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS J 405 " --> pdb=" O GLY J 485 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLY J 485 " --> pdb=" O LYS J 405 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR J 407 " --> pdb=" O VAL J 483 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N VAL J 483 " --> pdb=" O THR J 407 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N THR J 409 " --> pdb=" O THR J 481 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'J' and resid 489 through 490 removed outlier: 3.535A pdb=" N THR J 489 " --> pdb=" O VAL J 497 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'J' and resid 525 through 531 Processing sheet with id=AM1, first strand: chain 'J' and resid 558 through 560 removed outlier: 3.601A pdb=" N THR J 558 " --> pdb=" O TYR J 565 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU J 564 " --> pdb=" O ILE J 571 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'J' and resid 652 through 659 Processing sheet with id=AM3, first strand: chain 'J' and resid 707 through 712 Processing sheet with id=AM4, first strand: chain 'J' and resid 770 through 775 removed outlier: 6.799A pdb=" N ASP J 771 " --> pdb=" O ASN J 784 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN J 775 " --> pdb=" O ASN J 780 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN J 780 " --> pdb=" O ASN J 775 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'J' and resid 820 through 822 removed outlier: 3.509A pdb=" N LYS J 821 " --> pdb=" O TYR J 804 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR J 804 " --> pdb=" O LYS J 821 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS J 803 " --> pdb=" O TYR J 861 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LYS J 856 " --> pdb=" O LEU J 871 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU J 871 " --> pdb=" O LYS J 856 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU J 858 " --> pdb=" O GLU J 869 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'J' and resid 824 through 827 Processing sheet with id=AM7, first strand: chain 'K' and resid 235 through 238 Processing sheet with id=AM8, first strand: chain 'K' and resid 418 through 422 removed outlier: 6.920A pdb=" N LEU K 412 " --> pdb=" O LEU K 419 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N THR K 421 " --> pdb=" O THR K 410 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR K 410 " --> pdb=" O THR K 421 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE K 476 " --> pdb=" O THR K 365 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER K 364 " --> pdb=" O SER K 330 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER K 330 " --> pdb=" O SER K 364 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLU K 305 " --> pdb=" O THR K 327 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ASN K 329 " --> pdb=" O GLY K 303 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N GLY K 303 " --> pdb=" O ASN K 329 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL K 302 " --> pdb=" O TYR K 396 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TYR K 396 " --> pdb=" O VAL K 302 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N MET K 304 " --> pdb=" O ARG K 394 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG K 394 " --> pdb=" O MET K 304 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS K 306 " --> pdb=" O ASN K 392 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE K 460 " --> pdb=" O ILE K 389 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'K' and resid 352 through 353 removed outlier: 5.925A pdb=" N ASN K 352 " --> pdb=" O PHE K 580 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER K 516 " --> pdb=" O ILE K 611 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE K 613 " --> pdb=" O SER K 516 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE K 518 " --> pdb=" O ILE K 613 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'K' and resid 489 through 490 Processing sheet with id=AN2, first strand: chain 'K' and resid 558 through 559 removed outlier: 3.594A pdb=" N LEU K 564 " --> pdb=" O ILE K 571 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'K' and resid 618 through 620 removed outlier: 6.563A pdb=" N ARG K 668 " --> pdb=" O LEU K 741 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'K' and resid 654 through 659 removed outlier: 3.609A pdb=" N SER K 683 " --> pdb=" O THR K 695 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR K 695 " --> pdb=" O SER K 683 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'K' and resid 768 through 771 Processing sheet with id=AN6, first strand: chain 'K' and resid 816 through 822 removed outlier: 3.751A pdb=" N ALA K 808 " --> pdb=" O LYS K 816 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL K 806 " --> pdb=" O ILE K 818 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR K 820 " --> pdb=" O TYR K 804 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR K 804 " --> pdb=" O THR K 820 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS K 856 " --> pdb=" O LEU K 871 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU K 871 " --> pdb=" O LYS K 856 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU K 858 " --> pdb=" O GLU K 869 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'K' and resid 824 through 827 Processing sheet with id=AN8, first strand: chain 'L' and resid 235 through 238 Processing sheet with id=AN9, first strand: chain 'L' and resid 300 through 311 removed outlier: 3.714A pdb=" N GLY L 301 " --> pdb=" O TYR L 396 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN L 392 " --> pdb=" O GLU L 305 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU L 307 " --> pdb=" O ASN L 390 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASN L 390 " --> pdb=" O LEU L 307 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ILE L 309 " --> pdb=" O TYR L 388 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TYR L 388 " --> pdb=" O ILE L 309 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'L' and resid 437 through 439 removed outlier: 3.747A pdb=" N ASP L 437 " --> pdb=" O ASN L 397 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR L 439 " --> pdb=" O TYR L 395 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'L' and resid 420 through 423 removed outlier: 3.842A pdb=" N SER L 420 " --> pdb=" O LEU L 412 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LYS L 405 " --> pdb=" O GLY L 485 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY L 485 " --> pdb=" O LYS L 405 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR L 407 " --> pdb=" O VAL L 483 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL L 483 " --> pdb=" O THR L 407 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR L 409 " --> pdb=" O THR L 481 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'L' and resid 489 through 490 removed outlier: 3.577A pdb=" N THR L 489 " --> pdb=" O VAL L 497 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'L' and resid 525 through 531 Processing sheet with id=AO5, first strand: chain 'L' and resid 558 through 560 removed outlier: 3.812A pdb=" N THR L 558 " --> pdb=" O TYR L 565 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU L 564 " --> pdb=" O ILE L 571 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'L' and resid 652 through 659 removed outlier: 3.808A pdb=" N THR L 695 " --> pdb=" O SER L 683 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'L' and resid 707 through 709 Processing sheet with id=AO8, first strand: chain 'L' and resid 770 through 775 removed outlier: 7.159A pdb=" N ASP L 771 " --> pdb=" O ASN L 784 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN L 780 " --> pdb=" O ASN L 775 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'L' and resid 820 through 822 removed outlier: 3.762A pdb=" N TYR L 804 " --> pdb=" O LYS L 821 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS L 803 " --> pdb=" O TYR L 861 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS L 856 " --> pdb=" O VAL L 872 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL L 872 " --> pdb=" O LYS L 856 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ILE L 860 " --> pdb=" O ARG L 868 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ARG L 868 " --> pdb=" O ILE L 860 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'L' and resid 824 through 827 Processing sheet with id=AP2, first strand: chain 'M' and resid 235 through 238 Processing sheet with id=AP3, first strand: chain 'M' and resid 418 through 422 removed outlier: 3.683A pdb=" N SER M 420 " --> pdb=" O LEU M 412 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE M 476 " --> pdb=" O THR M 365 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLU M 305 " --> pdb=" O THR M 327 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N MET M 304 " --> pdb=" O ARG M 394 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG M 394 " --> pdb=" O MET M 304 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS M 306 " --> pdb=" O ASN M 392 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA M 391 " --> pdb=" O LEU M 449 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL M 393 " --> pdb=" O LEU M 447 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'M' and resid 418 through 422 removed outlier: 3.683A pdb=" N SER M 420 " --> pdb=" O LEU M 412 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE M 476 " --> pdb=" O THR M 365 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLU M 305 " --> pdb=" O THR M 327 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N MET M 304 " --> pdb=" O ARG M 394 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG M 394 " --> pdb=" O MET M 304 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS M 306 " --> pdb=" O ASN M 392 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE M 460 " --> pdb=" O ILE M 389 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'M' and resid 352 through 353 removed outlier: 5.885A pdb=" N ASN M 352 " --> pdb=" O PHE M 580 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER M 516 " --> pdb=" O ILE M 611 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE M 613 " --> pdb=" O SER M 516 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE M 518 " --> pdb=" O ILE M 613 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'M' and resid 489 through 490 Processing sheet with id=AP7, first strand: chain 'M' and resid 558 through 559 removed outlier: 3.635A pdb=" N LEU M 564 " --> pdb=" O ILE M 571 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'M' and resid 618 through 621 removed outlier: 5.291A pdb=" N ASN M 735 " --> pdb=" O TYR M 674 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR M 674 " --> pdb=" O ASN M 735 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG M 668 " --> pdb=" O LEU M 741 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'M' and resid 654 through 659 removed outlier: 3.706A pdb=" N SER M 683 " --> pdb=" O THR M 695 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR M 695 " --> pdb=" O SER M 683 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'M' and resid 768 through 771 Processing sheet with id=AQ2, first strand: chain 'M' and resid 816 through 822 removed outlier: 3.846A pdb=" N VAL M 806 " --> pdb=" O ILE M 818 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR M 820 " --> pdb=" O TYR M 804 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR M 804 " --> pdb=" O THR M 820 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS M 803 " --> pdb=" O TYR M 861 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR M 861 " --> pdb=" O LYS M 803 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS M 856 " --> pdb=" O LEU M 871 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU M 871 " --> pdb=" O LYS M 856 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU M 858 " --> pdb=" O GLU M 869 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'M' and resid 824 through 827 Processing sheet with id=AQ4, first strand: chain 'Z' and resid 235 through 238 Processing sheet with id=AQ5, first strand: chain 'Z' and resid 418 through 422 removed outlier: 3.899A pdb=" N SER Z 420 " --> pdb=" O LEU Z 412 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE Z 476 " --> pdb=" O THR Z 365 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER Z 364 " --> pdb=" O SER Z 330 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER Z 330 " --> pdb=" O SER Z 364 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLU Z 305 " --> pdb=" O THR Z 327 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N ASN Z 329 " --> pdb=" O GLY Z 303 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N GLY Z 303 " --> pdb=" O ASN Z 329 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL Z 302 " --> pdb=" O TYR Z 396 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TYR Z 396 " --> pdb=" O VAL Z 302 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N MET Z 304 " --> pdb=" O ARG Z 394 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG Z 394 " --> pdb=" O MET Z 304 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS Z 306 " --> pdb=" O ASN Z 392 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE Z 460 " --> pdb=" O ILE Z 389 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'Z' and resid 352 through 353 removed outlier: 6.030A pdb=" N ASN Z 352 " --> pdb=" O PHE Z 580 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER Z 516 " --> pdb=" O ILE Z 611 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE Z 613 " --> pdb=" O SER Z 516 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE Z 518 " --> pdb=" O ILE Z 613 " (cutoff:3.500A) Processing sheet with id=AQ7, first strand: chain 'Z' and resid 489 through 490 Processing sheet with id=AQ8, first strand: chain 'Z' and resid 558 through 559 removed outlier: 3.660A pdb=" N LEU Z 564 " --> pdb=" O ILE Z 571 " (cutoff:3.500A) Processing sheet with id=AQ9, first strand: chain 'Z' and resid 618 through 620 removed outlier: 6.481A pdb=" N ARG Z 668 " --> pdb=" O LEU Z 741 " (cutoff:3.500A) Processing sheet with id=AR1, first strand: chain 'Z' and resid 654 through 659 Processing sheet with id=AR2, first strand: chain 'Z' and resid 768 through 771 removed outlier: 3.503A pdb=" N MET Z 786 " --> pdb=" O VAL Z 840 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE Z 788 " --> pdb=" O ASN Z 838 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASN Z 838 " --> pdb=" O PHE Z 788 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 'Z' and resid 816 through 822 removed outlier: 3.791A pdb=" N VAL Z 806 " --> pdb=" O ILE Z 818 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR Z 820 " --> pdb=" O TYR Z 804 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TYR Z 804 " --> pdb=" O THR Z 820 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS Z 803 " --> pdb=" O TYR Z 861 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR Z 861 " --> pdb=" O LYS Z 803 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS Z 856 " --> pdb=" O LEU Z 871 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU Z 871 " --> pdb=" O LYS Z 856 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU Z 858 " --> pdb=" O GLU Z 869 " (cutoff:3.500A) 1917 hydrogen bonds defined for protein. 4992 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: 30.01 Time building geometry restraints manager: 15.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 22620 1.33 - 1.45: 11035 1.45 - 1.57: 40067 1.57 - 1.69: 7 1.69 - 1.81: 266 Bond restraints: 73995 Sorted by residual: bond pdb=" CA HIS L 314 " pdb=" CB HIS L 314 " ideal model delta sigma weight residual 1.522 1.478 0.044 1.27e-02 6.20e+03 1.20e+01 bond pdb=" CA ASP K 749 " pdb=" CB ASP K 749 " ideal model delta sigma weight residual 1.536 1.661 -0.125 4.10e-02 5.95e+02 9.25e+00 bond pdb=" CA ASP I 749 " pdb=" CB ASP I 749 " ideal model delta sigma weight residual 1.536 1.655 -0.119 4.10e-02 5.95e+02 8.43e+00 bond pdb=" CA ASP Z 749 " pdb=" CB ASP Z 749 " ideal model delta sigma weight residual 1.539 1.670 -0.131 4.88e-02 4.20e+02 7.21e+00 bond pdb=" C ASP C 677 " pdb=" N PRO C 678 " ideal model delta sigma weight residual 1.334 1.356 -0.022 8.40e-03 1.42e+04 6.92e+00 ... (remaining 73990 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 99593 3.47 - 6.94: 751 6.94 - 10.41: 86 10.41 - 13.88: 8 13.88 - 17.34: 7 Bond angle restraints: 100445 Sorted by residual: angle pdb=" N GLY F 652 " pdb=" CA GLY F 652 " pdb=" C GLY F 652 " ideal model delta sigma weight residual 111.21 116.85 -5.64 1.04e+00 9.25e-01 2.94e+01 angle pdb=" N THR E 864 " pdb=" CA THR E 864 " pdb=" C THR E 864 " ideal model delta sigma weight residual 109.81 121.77 -11.96 2.21e+00 2.05e-01 2.93e+01 angle pdb=" N THR C 864 " pdb=" CA THR C 864 " pdb=" C THR C 864 " ideal model delta sigma weight residual 109.81 121.72 -11.91 2.21e+00 2.05e-01 2.90e+01 angle pdb=" N THR Z 864 " pdb=" CA THR Z 864 " pdb=" C THR Z 864 " ideal model delta sigma weight residual 109.81 121.68 -11.87 2.21e+00 2.05e-01 2.89e+01 angle pdb=" N THR M 864 " pdb=" CA THR M 864 " pdb=" C THR M 864 " ideal model delta sigma weight residual 109.81 121.59 -11.78 2.21e+00 2.05e-01 2.84e+01 ... (remaining 100440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 39623 18.00 - 36.00: 4365 36.00 - 54.00: 781 54.00 - 72.00: 83 72.00 - 89.99: 33 Dihedral angle restraints: 44885 sinusoidal: 17819 harmonic: 27066 Sorted by residual: dihedral pdb=" CA ILE G 863 " pdb=" C ILE G 863 " pdb=" N THR G 864 " pdb=" CA THR G 864 " ideal model delta harmonic sigma weight residual -180.00 -136.54 -43.46 0 5.00e+00 4.00e-02 7.55e+01 dihedral pdb=" CA ILE Z 863 " pdb=" C ILE Z 863 " pdb=" N THR Z 864 " pdb=" CA THR Z 864 " ideal model delta harmonic sigma weight residual -180.00 -137.10 -42.90 0 5.00e+00 4.00e-02 7.36e+01 dihedral pdb=" CA ILE I 863 " pdb=" C ILE I 863 " pdb=" N THR I 864 " pdb=" CA THR I 864 " ideal model delta harmonic sigma weight residual -180.00 -138.05 -41.95 0 5.00e+00 4.00e-02 7.04e+01 ... (remaining 44882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 9350 0.074 - 0.148: 1700 0.148 - 0.222: 165 0.222 - 0.296: 32 0.296 - 0.370: 15 Chirality restraints: 11262 Sorted by residual: chirality pdb=" CB ILE B 761 " pdb=" CA ILE B 761 " pdb=" CG1 ILE B 761 " pdb=" CG2 ILE B 761 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CB THR D 864 " pdb=" CA THR D 864 " pdb=" OG1 THR D 864 " pdb=" CG2 THR D 864 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CB THR A 864 " pdb=" CA THR A 864 " pdb=" OG1 THR A 864 " pdb=" CG2 THR A 864 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 11259 not shown) Planarity restraints: 13130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR J 230 " -0.026 2.00e-02 2.50e+03 2.06e-02 8.45e+00 pdb=" CG TYR J 230 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR J 230 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR J 230 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR J 230 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR J 230 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR J 230 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR J 230 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP Z 291 " -0.045 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO Z 292 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO Z 292 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO Z 292 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP K 291 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.69e+00 pdb=" N PRO K 292 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO K 292 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO K 292 " -0.036 5.00e-02 4.00e+02 ... (remaining 13127 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 18685 2.79 - 3.32: 60115 3.32 - 3.85: 110666 3.85 - 4.37: 119536 4.37 - 4.90: 218788 Nonbonded interactions: 527790 Sorted by model distance: nonbonded pdb=" O TYR B 618 " pdb=" OG SER B 737 " model vdw 2.266 3.040 nonbonded pdb=" OG1 THR E 266 " pdb=" O PRO E 292 " model vdw 2.273 3.040 nonbonded pdb=" OG SER Z 334 " pdb=" OG SER Z 358 " model vdw 2.278 3.040 nonbonded pdb=" OG SER E 334 " pdb=" OG SER E 358 " model vdw 2.282 3.040 nonbonded pdb=" OG SER G 334 " pdb=" OG SER G 358 " model vdw 2.283 3.040 ... (remaining 527785 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 216 through 872) selection = (chain 'B' and resid 216 through 872) selection = (chain 'C' and resid 216 through 872) selection = (chain 'D' and resid 216 through 872) selection = (chain 'E' and resid 216 through 872) selection = (chain 'F' and resid 216 through 872) selection = (chain 'G' and resid 216 through 872) selection = (chain 'H' and resid 216 through 872) selection = (chain 'I' and resid 216 through 872) selection = (chain 'J' and resid 216 through 872) selection = (chain 'K' and resid 216 through 872) selection = (chain 'L' and resid 216 through 872) selection = (chain 'M' and resid 216 through 872) selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 0.050 Extract box with map and model: 1.920 Check model and map are aligned: 0.400 Set scattering table: 0.500 Process input model: 125.690 Find NCS groups from input model: 3.080 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 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 : 0.006 0.131 73995 Z= 0.395 Angle : 0.931 17.344 100445 Z= 0.517 Chirality : 0.058 0.370 11262 Planarity : 0.006 0.069 13130 Dihedral : 14.998 89.994 27597 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 0.55 % Allowed : 11.62 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -4.61 (0.07), residues: 9190 helix: -4.58 (0.06), residues: 959 sheet: -1.73 (0.10), residues: 2318 loop : -3.58 (0.06), residues: 5913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 503 HIS 0.007 0.002 HIS H 765 PHE 0.029 0.003 PHE G 249 TYR 0.050 0.002 TYR J 230 ARG 0.005 0.001 ARG J 394 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 664 time to evaluate : 6.297 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 228 ASP cc_start: 0.7288 (t0) cc_final: 0.7045 (t0) REVERT: B 709 TYR cc_start: 0.7338 (m-80) cc_final: 0.7087 (m-80) REVERT: C 455 PHE cc_start: 0.7469 (m-80) cc_final: 0.7217 (m-80) REVERT: C 625 TYR cc_start: 0.7345 (t80) cc_final: 0.6426 (t80) REVERT: C 632 TRP cc_start: 0.7020 (m100) cc_final: 0.6732 (m100) REVERT: C 692 GLU cc_start: 0.5699 (mt-10) cc_final: 0.4650 (tm-30) REVERT: C 758 ASP cc_start: 0.7383 (t0) cc_final: 0.7169 (t0) REVERT: D 228 ASP cc_start: 0.7438 (t0) cc_final: 0.7192 (t70) REVERT: D 403 MET cc_start: 0.8799 (ttp) cc_final: 0.8486 (ttp) REVERT: D 632 TRP cc_start: 0.7064 (t-100) cc_final: 0.6583 (t-100) REVERT: D 660 MET cc_start: 0.7600 (mmp) cc_final: 0.7343 (mmm) REVERT: E 333 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7436 (mm-30) REVERT: E 460 ILE cc_start: 0.9180 (mp) cc_final: 0.8851 (mt) REVERT: E 569 ILE cc_start: 0.9029 (mp) cc_final: 0.8653 (mt) REVERT: E 694 LYS cc_start: 0.6999 (tttm) cc_final: 0.6744 (ttpp) REVERT: E 712 GLU cc_start: 0.8281 (pt0) cc_final: 0.8036 (mt-10) REVERT: E 794 ASN cc_start: 0.7191 (p0) cc_final: 0.6938 (p0) REVERT: F 586 ASN cc_start: 0.7762 (t0) cc_final: 0.7497 (t0) REVERT: F 604 LYS cc_start: 0.8592 (tmtt) cc_final: 0.8057 (pttp) REVERT: F 762 MET cc_start: 0.7721 (ppp) cc_final: 0.7373 (ppp) REVERT: F 861 TYR cc_start: 0.6987 (m-10) cc_final: 0.6488 (m-80) REVERT: G 442 LYS cc_start: 0.8611 (ttmt) cc_final: 0.8382 (ttmm) REVERT: G 454 GLN cc_start: 0.7845 (tp40) cc_final: 0.7623 (pt0) REVERT: H 385 GLU cc_start: 0.6679 (tt0) cc_final: 0.6305 (mt-10) REVERT: H 604 LYS cc_start: 0.8435 (tmtt) cc_final: 0.7926 (pttm) REVERT: H 632 TRP cc_start: 0.6486 (t-100) cc_final: 0.6206 (t-100) REVERT: H 660 MET cc_start: 0.7161 (mmp) cc_final: 0.6787 (mmt) REVERT: H 778 THR cc_start: 0.7985 (OUTLIER) cc_final: 0.7702 (m) REVERT: H 825 MET cc_start: 0.8511 (mmt) cc_final: 0.7852 (mmt) REVERT: I 758 ASP cc_start: 0.7586 (t0) cc_final: 0.7292 (t0) REVERT: J 660 MET cc_start: 0.7031 (mmp) cc_final: 0.6483 (mmm) REVERT: K 442 LYS cc_start: 0.8828 (ttmt) cc_final: 0.8573 (ttmm) REVERT: K 452 MET cc_start: 0.6551 (mpp) cc_final: 0.5765 (mmt) REVERT: K 479 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7253 (tm-30) REVERT: K 825 MET cc_start: 0.8086 (tpt) cc_final: 0.7742 (tpt) REVERT: L 762 MET cc_start: 0.7940 (ppp) cc_final: 0.7424 (ppp) REVERT: L 825 MET cc_start: 0.8672 (mmt) cc_final: 0.8109 (mmt) REVERT: M 403 MET cc_start: 0.8641 (mtp) cc_final: 0.8166 (mtm) REVERT: M 442 LYS cc_start: 0.8311 (ttmt) cc_final: 0.7970 (ttmm) REVERT: M 712 GLU cc_start: 0.8179 (pt0) cc_final: 0.7932 (mt-10) REVERT: M 762 MET cc_start: 0.8584 (ttp) cc_final: 0.8348 (ttm) REVERT: M 786 MET cc_start: 0.7587 (tpp) cc_final: 0.7336 (tpp) REVERT: M 794 ASN cc_start: 0.7584 (p0) cc_final: 0.7187 (p0) REVERT: Z 442 LYS cc_start: 0.8507 (ttmt) cc_final: 0.8299 (ttpt) REVERT: Z 692 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6042 (mm-30) REVERT: Z 794 ASN cc_start: 0.7290 (p0) cc_final: 0.7070 (p0) outliers start: 45 outliers final: 23 residues processed: 707 average time/residue: 0.6945 time to fit residues: 848.6502 Evaluate side-chains 478 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 454 time to evaluate : 6.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 864 THR Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain H residue 332 THR Chi-restraints excluded: chain H residue 453 ASP Chi-restraints excluded: chain H residue 778 THR Chi-restraints excluded: chain I residue 421 THR Chi-restraints excluded: chain J residue 257 TYR Chi-restraints excluded: chain J residue 332 THR Chi-restraints excluded: chain J residue 341 VAL Chi-restraints excluded: chain J residue 864 THR Chi-restraints excluded: chain L residue 302 VAL Chi-restraints excluded: chain L residue 864 THR Chi-restraints excluded: chain M residue 431 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 768 optimal weight: 6.9990 chunk 689 optimal weight: 4.9990 chunk 382 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 465 optimal weight: 20.0000 chunk 368 optimal weight: 0.9990 chunk 713 optimal weight: 10.0000 chunk 276 optimal weight: 9.9990 chunk 433 optimal weight: 8.9990 chunk 530 optimal weight: 0.4980 chunk 826 optimal weight: 1.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN A 602 ASN ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN A 735 ASN A 765 HIS A 792 GLN B 397 ASN B 432 ASN B 509 GLN ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 651 ASN B 682 ASN B 735 ASN ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN C 640 GLN C 682 ASN D 636 ASN D 644 GLN D 651 ASN D 682 ASN D 720 ASN D 735 ASN D 792 GLN D 794 ASN E 682 ASN E 735 ASN E 838 ASN E 841 ASN F 432 ASN F 648 ASN F 651 ASN F 735 ASN ** G 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 450 ASN G 651 ASN G 735 ASN G 838 ASN G 841 ASN H 397 ASN ** H 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 644 GLN H 651 ASN H 735 ASN H 838 ASN I 335 ASN I 486 ASN I 640 GLN I 735 ASN ** I 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 841 ASN J 428 GLN J 644 GLN J 651 ASN J 735 ASN J 792 GLN ** K 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 682 ASN K 735 ASN K 838 ASN ** L 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 644 GLN L 651 ASN L 735 ASN M 335 ASN ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 450 ASN M 636 ASN M 682 ASN M 735 ASN M 827 ASN M 838 ASN M 841 ASN ** Z 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 735 ASN Z 838 ASN Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 73995 Z= 0.192 Angle : 0.615 11.251 100445 Z= 0.325 Chirality : 0.045 0.211 11262 Planarity : 0.004 0.056 13130 Dihedral : 6.134 48.329 10002 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 1.41 % Allowed : 14.24 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.88 (0.07), residues: 9190 helix: -3.57 (0.11), residues: 962 sheet: -1.07 (0.10), residues: 2471 loop : -3.29 (0.07), residues: 5757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 632 HIS 0.005 0.001 HIS C 765 PHE 0.019 0.002 PHE G 249 TYR 0.022 0.001 TYR L 230 ARG 0.006 0.000 ARG K 868 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 515 time to evaluate : 6.403 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: A 228 ASP cc_start: 0.7172 (t0) cc_final: 0.6907 (t0) REVERT: A 564 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7581 (pp) REVERT: A 632 TRP cc_start: 0.6320 (t-100) cc_final: 0.6102 (t-100) REVERT: A 793 THR cc_start: 0.8103 (OUTLIER) cc_final: 0.7862 (m) REVERT: A 868 ARG cc_start: 0.7907 (tmm-80) cc_final: 0.7393 (tmm-80) REVERT: B 709 TYR cc_start: 0.7225 (m-80) cc_final: 0.7002 (m-80) REVERT: C 625 TYR cc_start: 0.7261 (t80) cc_final: 0.6405 (t80) REVERT: C 632 TRP cc_start: 0.7061 (m100) cc_final: 0.6623 (m100) REVERT: C 692 GLU cc_start: 0.5656 (mt-10) cc_final: 0.4722 (tm-30) REVERT: C 870 LEU cc_start: 0.8311 (tt) cc_final: 0.8030 (tp) REVERT: D 403 MET cc_start: 0.8866 (ttp) cc_final: 0.8593 (ttp) REVERT: D 825 MET cc_start: 0.8862 (mmp) cc_final: 0.8583 (mmm) REVERT: E 460 ILE cc_start: 0.9136 (mp) cc_final: 0.8796 (mt) REVERT: E 694 LYS cc_start: 0.6751 (tttm) cc_final: 0.6397 (ttpp) REVERT: E 868 ARG cc_start: 0.6937 (ptm160) cc_final: 0.6671 (ttm170) REVERT: F 604 LYS cc_start: 0.8542 (tmtt) cc_final: 0.8026 (pttp) REVERT: F 709 TYR cc_start: 0.7039 (m-80) cc_final: 0.6728 (m-80) REVERT: F 762 MET cc_start: 0.7894 (ppp) cc_final: 0.6907 (ppp) REVERT: F 861 TYR cc_start: 0.7084 (OUTLIER) cc_final: 0.6701 (m-10) REVERT: G 442 LYS cc_start: 0.8627 (ttmt) cc_final: 0.8393 (ttmm) REVERT: H 545 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8677 (pp) REVERT: H 740 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6905 (tm-30) REVERT: H 861 TYR cc_start: 0.6758 (OUTLIER) cc_final: 0.6384 (m-10) REVERT: I 455 PHE cc_start: 0.7912 (m-80) cc_final: 0.7186 (m-80) REVERT: J 564 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7392 (pp) REVERT: J 861 TYR cc_start: 0.6979 (OUTLIER) cc_final: 0.6625 (m-10) REVERT: K 335 ASN cc_start: 0.8799 (t0) cc_final: 0.8358 (t0) REVERT: K 442 LYS cc_start: 0.8859 (ttmt) cc_final: 0.8598 (ttmm) REVERT: K 452 MET cc_start: 0.6401 (mpp) cc_final: 0.5681 (mmt) REVERT: K 454 GLN cc_start: 0.7877 (tp40) cc_final: 0.7409 (pt0) REVERT: K 625 TYR cc_start: 0.7733 (t80) cc_final: 0.7242 (t80) REVERT: K 632 TRP cc_start: 0.6966 (m100) cc_final: 0.6718 (m100) REVERT: L 740 GLU cc_start: 0.8421 (tp30) cc_final: 0.8208 (tm-30) REVERT: L 762 MET cc_start: 0.8111 (ppp) cc_final: 0.7559 (ppp) REVERT: L 861 TYR cc_start: 0.6931 (OUTLIER) cc_final: 0.6719 (m-80) REVERT: M 442 LYS cc_start: 0.8409 (ttmt) cc_final: 0.8123 (ttmm) REVERT: M 786 MET cc_start: 0.7535 (tpp) cc_final: 0.7265 (tpp) REVERT: M 794 ASN cc_start: 0.7404 (p0) cc_final: 0.7017 (p0) REVERT: Z 335 ASN cc_start: 0.8833 (t0) cc_final: 0.8489 (t0) REVERT: Z 403 MET cc_start: 0.8635 (mtm) cc_final: 0.8330 (mtp) REVERT: Z 692 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6505 (mm-30) outliers start: 115 outliers final: 67 residues processed: 611 average time/residue: 0.6575 time to fit residues: 708.1760 Evaluate side-chains 505 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 429 time to evaluate : 6.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 864 THR Chi-restraints excluded: chain E residue 489 THR Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 861 TYR Chi-restraints excluded: chain F residue 864 THR Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 651 ASN Chi-restraints excluded: chain G residue 724 THR Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain H residue 332 THR Chi-restraints excluded: chain H residue 545 LEU Chi-restraints excluded: chain H residue 547 ILE Chi-restraints excluded: chain H residue 714 THR Chi-restraints excluded: chain H residue 740 GLU Chi-restraints excluded: chain H residue 772 LEU Chi-restraints excluded: chain H residue 793 THR Chi-restraints excluded: chain H residue 861 TYR Chi-restraints excluded: chain I residue 421 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 654 THR Chi-restraints excluded: chain J residue 257 TYR Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 332 THR Chi-restraints excluded: chain J residue 428 GLN Chi-restraints excluded: chain J residue 437 ASP Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 564 LEU Chi-restraints excluded: chain J residue 772 LEU Chi-restraints excluded: chain J residue 861 TYR Chi-restraints excluded: chain J residue 864 THR Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 791 THR Chi-restraints excluded: chain L residue 302 VAL Chi-restraints excluded: chain L residue 332 THR Chi-restraints excluded: chain L residue 377 THR Chi-restraints excluded: chain L residue 545 LEU Chi-restraints excluded: chain L residue 861 TYR Chi-restraints excluded: chain L residue 864 THR Chi-restraints excluded: chain M residue 293 LEU Chi-restraints excluded: chain M residue 489 THR Chi-restraints excluded: chain M residue 623 ASP Chi-restraints excluded: chain Z residue 451 THR Chi-restraints excluded: chain Z residue 454 GLN Chi-restraints excluded: chain Z residue 569 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 459 optimal weight: 6.9990 chunk 256 optimal weight: 8.9990 chunk 687 optimal weight: 20.0000 chunk 562 optimal weight: 10.0000 chunk 227 optimal weight: 0.9980 chunk 827 optimal weight: 8.9990 chunk 894 optimal weight: 10.0000 chunk 737 optimal weight: 6.9990 chunk 820 optimal weight: 10.0000 chunk 282 optimal weight: 0.0770 chunk 664 optimal weight: 5.9990 overall best weight: 4.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 ASN ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN ** C 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 ASN D 794 ASN E 432 ASN E 450 ASN E 454 GLN E 640 GLN E 742 ASN F 397 ASN ** F 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 792 GLN ** G 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 636 ASN ** I 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 432 ASN I 454 GLN ** I 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 794 ASN K 329 ASN K 486 ASN K 742 ASN L 636 ASN ** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 742 ASN ** Z 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 742 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 73995 Z= 0.281 Angle : 0.633 10.299 100445 Z= 0.334 Chirality : 0.046 0.296 11262 Planarity : 0.004 0.055 13130 Dihedral : 6.012 52.133 9995 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 2.54 % Allowed : 15.93 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.47 (0.08), residues: 9190 helix: -2.91 (0.13), residues: 925 sheet: -0.94 (0.10), residues: 2590 loop : -3.04 (0.07), residues: 5675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 632 HIS 0.006 0.001 HIS C 765 PHE 0.020 0.002 PHE A 788 TYR 0.026 0.001 TYR L 230 ARG 0.005 0.000 ARG F 668 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 457 time to evaluate : 6.218 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 257 TYR cc_start: 0.8682 (OUTLIER) cc_final: 0.6043 (p90) REVERT: A 564 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7466 (pp) REVERT: A 632 TRP cc_start: 0.6156 (t-100) cc_final: 0.5879 (t-100) REVERT: A 793 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7991 (m) REVERT: A 861 TYR cc_start: 0.7053 (OUTLIER) cc_final: 0.6756 (m-10) REVERT: A 869 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6211 (mt-10) REVERT: B 232 ARG cc_start: 0.8127 (tpp80) cc_final: 0.7924 (tpp80) REVERT: C 625 TYR cc_start: 0.7476 (t80) cc_final: 0.6534 (t80) REVERT: C 692 GLU cc_start: 0.5657 (mt-10) cc_final: 0.4651 (tm-30) REVERT: C 870 LEU cc_start: 0.8251 (tt) cc_final: 0.8019 (tp) REVERT: D 293 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8461 (mt) REVERT: D 403 MET cc_start: 0.8772 (ttp) cc_final: 0.8505 (ttp) REVERT: D 656 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7614 (mm) REVERT: D 663 LEU cc_start: 0.4235 (OUTLIER) cc_final: 0.3939 (pp) REVERT: D 825 MET cc_start: 0.8978 (mmp) cc_final: 0.8748 (mmm) REVERT: E 460 ILE cc_start: 0.9176 (mp) cc_final: 0.8827 (mt) REVERT: E 569 ILE cc_start: 0.9030 (mp) cc_final: 0.8679 (mt) REVERT: E 632 TRP cc_start: 0.6605 (m100) cc_final: 0.6224 (m100) REVERT: E 868 ARG cc_start: 0.7137 (ptm160) cc_final: 0.6736 (ttm-80) REVERT: F 362 ASP cc_start: 0.8253 (t70) cc_final: 0.8038 (t0) REVERT: F 604 LYS cc_start: 0.8445 (tmtt) cc_final: 0.7972 (pttp) REVERT: F 709 TYR cc_start: 0.7059 (m-80) cc_final: 0.6796 (m-80) REVERT: F 762 MET cc_start: 0.8063 (ppp) cc_final: 0.7167 (ppp) REVERT: F 861 TYR cc_start: 0.7070 (OUTLIER) cc_final: 0.6676 (m-10) REVERT: G 442 LYS cc_start: 0.8690 (ttmt) cc_final: 0.8470 (ttmm) REVERT: G 651 ASN cc_start: 0.7462 (OUTLIER) cc_final: 0.6277 (p0) REVERT: H 545 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8707 (pp) REVERT: H 861 TYR cc_start: 0.6969 (OUTLIER) cc_final: 0.6563 (m-10) REVERT: I 455 PHE cc_start: 0.7889 (m-80) cc_final: 0.7376 (m-80) REVERT: I 632 TRP cc_start: 0.6566 (m100) cc_final: 0.6173 (m100) REVERT: J 293 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8203 (mm) REVERT: J 663 LEU cc_start: 0.4021 (OUTLIER) cc_final: 0.3713 (pp) REVERT: J 754 LYS cc_start: 0.3222 (OUTLIER) cc_final: 0.2679 (ttpp) REVERT: J 861 TYR cc_start: 0.7012 (OUTLIER) cc_final: 0.6611 (m-10) REVERT: K 335 ASN cc_start: 0.8854 (t0) cc_final: 0.8612 (t0) REVERT: K 442 LYS cc_start: 0.8908 (ttmt) cc_final: 0.8619 (ttmm) REVERT: K 452 MET cc_start: 0.6213 (mpp) cc_final: 0.5617 (mmt) REVERT: K 453 ASP cc_start: 0.8424 (p0) cc_final: 0.8152 (p0) REVERT: K 454 GLN cc_start: 0.7886 (tp40) cc_final: 0.7551 (pt0) REVERT: K 825 MET cc_start: 0.8115 (tpt) cc_final: 0.7872 (tpt) REVERT: L 632 TRP cc_start: 0.6405 (t-100) cc_final: 0.5838 (t-100) REVERT: L 762 MET cc_start: 0.8214 (ppp) cc_final: 0.7576 (ppp) REVERT: L 820 THR cc_start: 0.9507 (OUTLIER) cc_final: 0.8949 (p) REVERT: L 825 MET cc_start: 0.8468 (mmt) cc_final: 0.8063 (mmt) REVERT: L 861 TYR cc_start: 0.6746 (OUTLIER) cc_final: 0.6433 (m-10) REVERT: L 868 ARG cc_start: 0.7864 (tmm-80) cc_final: 0.7663 (tmm-80) REVERT: M 442 LYS cc_start: 0.8541 (ttmt) cc_final: 0.8220 (ttmm) REVERT: M 786 MET cc_start: 0.7551 (tpp) cc_final: 0.7278 (tpp) REVERT: M 794 ASN cc_start: 0.7459 (p0) cc_final: 0.7174 (p0) REVERT: Z 335 ASN cc_start: 0.8891 (t0) cc_final: 0.8656 (t0) REVERT: Z 742 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.7974 (m-40) outliers start: 208 outliers final: 133 residues processed: 639 average time/residue: 0.6313 time to fit residues: 712.7013 Evaluate side-chains 576 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 424 time to evaluate : 6.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 861 TYR Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 455 PHE Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain D residue 852 ILE Chi-restraints excluded: chain D residue 864 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 403 MET Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 801 ILE Chi-restraints excluded: chain E residue 856 LYS Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 792 GLN Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 861 TYR Chi-restraints excluded: chain F residue 864 THR Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain G residue 418 THR Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 651 ASN Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 817 ASP Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain H residue 332 THR Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 545 LEU Chi-restraints excluded: chain H residue 547 ILE Chi-restraints excluded: chain H residue 636 ASN Chi-restraints excluded: chain H residue 638 THR Chi-restraints excluded: chain H residue 714 THR Chi-restraints excluded: chain H residue 772 LEU Chi-restraints excluded: chain H residue 793 THR Chi-restraints excluded: chain H residue 861 TYR Chi-restraints excluded: chain I residue 297 TYR Chi-restraints excluded: chain I residue 299 ILE Chi-restraints excluded: chain I residue 421 THR Chi-restraints excluded: chain I residue 462 ILE Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 576 VAL Chi-restraints excluded: chain I residue 654 THR Chi-restraints excluded: chain I residue 721 ILE Chi-restraints excluded: chain J residue 257 TYR Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 332 THR Chi-restraints excluded: chain J residue 341 VAL Chi-restraints excluded: chain J residue 393 VAL Chi-restraints excluded: chain J residue 437 ASP Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 663 LEU Chi-restraints excluded: chain J residue 699 VAL Chi-restraints excluded: chain J residue 754 LYS Chi-restraints excluded: chain J residue 772 LEU Chi-restraints excluded: chain J residue 791 THR Chi-restraints excluded: chain J residue 861 TYR Chi-restraints excluded: chain J residue 864 THR Chi-restraints excluded: chain K residue 462 ILE Chi-restraints excluded: chain K residue 479 GLU Chi-restraints excluded: chain K residue 643 LEU Chi-restraints excluded: chain K residue 656 ILE Chi-restraints excluded: chain K residue 783 ILE Chi-restraints excluded: chain K residue 791 THR Chi-restraints excluded: chain K residue 817 ASP Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 302 VAL Chi-restraints excluded: chain L residue 332 THR Chi-restraints excluded: chain L residue 377 THR Chi-restraints excluded: chain L residue 393 VAL Chi-restraints excluded: chain L residue 410 THR Chi-restraints excluded: chain L residue 545 LEU Chi-restraints excluded: chain L residue 654 THR Chi-restraints excluded: chain L residue 670 VAL Chi-restraints excluded: chain L residue 739 THR Chi-restraints excluded: chain L residue 791 THR Chi-restraints excluded: chain L residue 793 THR Chi-restraints excluded: chain L residue 820 THR Chi-restraints excluded: chain L residue 861 TYR Chi-restraints excluded: chain L residue 864 THR Chi-restraints excluded: chain M residue 293 LEU Chi-restraints excluded: chain M residue 362 ASP Chi-restraints excluded: chain M residue 422 ILE Chi-restraints excluded: chain M residue 489 THR Chi-restraints excluded: chain M residue 558 THR Chi-restraints excluded: chain M residue 721 ILE Chi-restraints excluded: chain Z residue 421 THR Chi-restraints excluded: chain Z residue 451 THR Chi-restraints excluded: chain Z residue 454 GLN Chi-restraints excluded: chain Z residue 489 THR Chi-restraints excluded: chain Z residue 569 ILE Chi-restraints excluded: chain Z residue 670 VAL Chi-restraints excluded: chain Z residue 680 THR Chi-restraints excluded: chain Z residue 742 ASN Chi-restraints excluded: chain Z residue 856 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 817 optimal weight: 9.9990 chunk 622 optimal weight: 6.9990 chunk 429 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 395 optimal weight: 7.9990 chunk 555 optimal weight: 0.6980 chunk 830 optimal weight: 9.9990 chunk 879 optimal weight: 5.9990 chunk 434 optimal weight: 10.0000 chunk 787 optimal weight: 0.9980 chunk 237 optimal weight: 30.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 ASN B 636 ASN ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 ASN D 794 ASN E 450 ASN F 765 HIS ** F 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 636 ASN ** I 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 742 ASN ** I 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 329 ASN ** K 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 765 HIS L 397 ASN L 636 ASN ** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 486 ASN M 765 HIS ** Z 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 73995 Z= 0.262 Angle : 0.615 10.741 100445 Z= 0.324 Chirality : 0.045 0.338 11262 Planarity : 0.004 0.055 13130 Dihedral : 5.879 51.263 9995 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.35 % Allowed : 17.06 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.25 (0.08), residues: 9190 helix: -2.62 (0.14), residues: 925 sheet: -0.81 (0.10), residues: 2597 loop : -2.90 (0.07), residues: 5668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 632 HIS 0.005 0.001 HIS C 765 PHE 0.020 0.002 PHE G 249 TYR 0.025 0.001 TYR F 230 ARG 0.004 0.000 ARG Z 868 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 451 time to evaluate : 6.308 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: A 257 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.5923 (p90) REVERT: A 564 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7562 (pp) REVERT: A 632 TRP cc_start: 0.5996 (t-100) cc_final: 0.5725 (t-100) REVERT: A 861 TYR cc_start: 0.7094 (OUTLIER) cc_final: 0.6787 (m-10) REVERT: A 869 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6200 (mt-10) REVERT: B 426 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7687 (pp20) REVERT: B 861 TYR cc_start: 0.7020 (m-10) cc_final: 0.6775 (m-10) REVERT: C 625 TYR cc_start: 0.7464 (t80) cc_final: 0.6538 (t80) REVERT: C 632 TRP cc_start: 0.7150 (m100) cc_final: 0.6819 (m100) REVERT: C 692 GLU cc_start: 0.5611 (mt-10) cc_final: 0.4538 (tm-30) REVERT: C 791 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8365 (p) REVERT: D 293 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8492 (mt) REVERT: D 403 MET cc_start: 0.8733 (ttp) cc_final: 0.8443 (ttp) REVERT: D 656 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7686 (mm) REVERT: D 663 LEU cc_start: 0.4245 (OUTLIER) cc_final: 0.4015 (pp) REVERT: D 861 TYR cc_start: 0.7004 (OUTLIER) cc_final: 0.6417 (m-10) REVERT: E 460 ILE cc_start: 0.9247 (mp) cc_final: 0.8916 (mt) REVERT: E 569 ILE cc_start: 0.9048 (mp) cc_final: 0.8650 (mt) REVERT: E 632 TRP cc_start: 0.6610 (m100) cc_final: 0.6130 (m100) REVERT: E 868 ARG cc_start: 0.7129 (ptm160) cc_final: 0.6662 (ttm-80) REVERT: F 604 LYS cc_start: 0.8441 (tmtt) cc_final: 0.7913 (pttp) REVERT: F 709 TYR cc_start: 0.7039 (m-80) cc_final: 0.6808 (m-80) REVERT: F 762 MET cc_start: 0.8169 (ppp) cc_final: 0.6983 (ppp) REVERT: F 861 TYR cc_start: 0.7129 (OUTLIER) cc_final: 0.6751 (m-10) REVERT: G 442 LYS cc_start: 0.8674 (ttmt) cc_final: 0.8440 (ttmm) REVERT: H 447 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8483 (tp) REVERT: H 545 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8717 (pp) REVERT: H 861 TYR cc_start: 0.6973 (OUTLIER) cc_final: 0.6554 (m-10) REVERT: I 455 PHE cc_start: 0.7928 (m-80) cc_final: 0.7193 (m-80) REVERT: I 632 TRP cc_start: 0.6457 (m100) cc_final: 0.5960 (m100) REVERT: I 801 ILE cc_start: 0.9501 (OUTLIER) cc_final: 0.9276 (mt) REVERT: J 293 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8109 (mm) REVERT: J 426 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7408 (pp20) REVERT: J 663 LEU cc_start: 0.4068 (OUTLIER) cc_final: 0.3685 (pp) REVERT: J 754 LYS cc_start: 0.2550 (OUTLIER) cc_final: 0.1791 (ttpp) REVERT: J 861 TYR cc_start: 0.7013 (OUTLIER) cc_final: 0.6601 (m-10) REVERT: K 335 ASN cc_start: 0.8875 (t0) cc_final: 0.8656 (t0) REVERT: K 442 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8637 (ttmm) REVERT: K 452 MET cc_start: 0.6319 (mpp) cc_final: 0.5944 (mmm) REVERT: K 453 ASP cc_start: 0.8359 (p0) cc_final: 0.8080 (p0) REVERT: K 454 GLN cc_start: 0.7882 (tp40) cc_final: 0.7545 (pt0) REVERT: K 825 MET cc_start: 0.8103 (tpt) cc_final: 0.7886 (tpt) REVERT: L 257 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.8230 (p90) REVERT: L 632 TRP cc_start: 0.6209 (t-100) cc_final: 0.5681 (t-100) REVERT: L 762 MET cc_start: 0.8175 (ppp) cc_final: 0.7548 (ppp) REVERT: L 820 THR cc_start: 0.9509 (OUTLIER) cc_final: 0.8936 (p) REVERT: L 861 TYR cc_start: 0.6921 (OUTLIER) cc_final: 0.6535 (m-10) REVERT: M 442 LYS cc_start: 0.8546 (ttmt) cc_final: 0.8229 (ttmm) REVERT: M 462 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8681 (mt) REVERT: M 786 MET cc_start: 0.7532 (tpp) cc_final: 0.7265 (tpp) REVERT: M 794 ASN cc_start: 0.7462 (p0) cc_final: 0.7167 (p0) REVERT: Z 335 ASN cc_start: 0.8876 (t0) cc_final: 0.8658 (t0) outliers start: 274 outliers final: 181 residues processed: 695 average time/residue: 0.6322 time to fit residues: 781.1664 Evaluate side-chains 631 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 426 time to evaluate : 6.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 861 TYR Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 601 TYR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 455 PHE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 TYR Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 656 ILE Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain D residue 852 ILE Chi-restraints excluded: chain D residue 861 TYR Chi-restraints excluded: chain D residue 864 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 403 MET Chi-restraints excluded: chain E residue 489 THR Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 801 ILE Chi-restraints excluded: chain E residue 856 LYS Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 579 ILE Chi-restraints excluded: chain F residue 654 THR Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 861 TYR Chi-restraints excluded: chain F residue 864 THR Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain G residue 418 THR Chi-restraints excluded: chain G residue 454 GLN Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 479 GLU Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 531 THR Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 650 LEU Chi-restraints excluded: chain G residue 654 THR Chi-restraints excluded: chain G residue 739 THR Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 817 ASP Chi-restraints excluded: chain G residue 818 ILE Chi-restraints excluded: chain H residue 257 TYR Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain H residue 332 THR Chi-restraints excluded: chain H residue 341 VAL Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 447 LEU Chi-restraints excluded: chain H residue 545 LEU Chi-restraints excluded: chain H residue 547 ILE Chi-restraints excluded: chain H residue 564 LEU Chi-restraints excluded: chain H residue 636 ASN Chi-restraints excluded: chain H residue 714 THR Chi-restraints excluded: chain H residue 772 LEU Chi-restraints excluded: chain H residue 791 THR Chi-restraints excluded: chain H residue 793 THR Chi-restraints excluded: chain H residue 861 TYR Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 297 TYR Chi-restraints excluded: chain I residue 299 ILE Chi-restraints excluded: chain I residue 421 THR Chi-restraints excluded: chain I residue 558 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 576 VAL Chi-restraints excluded: chain I residue 654 THR Chi-restraints excluded: chain I residue 721 ILE Chi-restraints excluded: chain I residue 801 ILE Chi-restraints excluded: chain I residue 855 TYR Chi-restraints excluded: chain I residue 856 LYS Chi-restraints excluded: chain J residue 257 TYR Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 332 THR Chi-restraints excluded: chain J residue 341 VAL Chi-restraints excluded: chain J residue 360 THR Chi-restraints excluded: chain J residue 426 GLU Chi-restraints excluded: chain J residue 437 ASP Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 663 LEU Chi-restraints excluded: chain J residue 699 VAL Chi-restraints excluded: chain J residue 714 THR Chi-restraints excluded: chain J residue 739 THR Chi-restraints excluded: chain J residue 754 LYS Chi-restraints excluded: chain J residue 772 LEU Chi-restraints excluded: chain J residue 791 THR Chi-restraints excluded: chain J residue 854 THR Chi-restraints excluded: chain J residue 861 TYR Chi-restraints excluded: chain J residue 864 THR Chi-restraints excluded: chain K residue 418 THR Chi-restraints excluded: chain K residue 462 ILE Chi-restraints excluded: chain K residue 479 GLU Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 643 LEU Chi-restraints excluded: chain K residue 650 LEU Chi-restraints excluded: chain K residue 670 VAL Chi-restraints excluded: chain K residue 783 ILE Chi-restraints excluded: chain K residue 791 THR Chi-restraints excluded: chain K residue 793 THR Chi-restraints excluded: chain K residue 817 ASP Chi-restraints excluded: chain K residue 818 ILE Chi-restraints excluded: chain L residue 257 TYR Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 302 VAL Chi-restraints excluded: chain L residue 332 THR Chi-restraints excluded: chain L residue 360 THR Chi-restraints excluded: chain L residue 377 THR Chi-restraints excluded: chain L residue 393 VAL Chi-restraints excluded: chain L residue 409 THR Chi-restraints excluded: chain L residue 428 GLN Chi-restraints excluded: chain L residue 545 LEU Chi-restraints excluded: chain L residue 654 THR Chi-restraints excluded: chain L residue 670 VAL Chi-restraints excluded: chain L residue 725 LEU Chi-restraints excluded: chain L residue 730 THR Chi-restraints excluded: chain L residue 739 THR Chi-restraints excluded: chain L residue 791 THR Chi-restraints excluded: chain L residue 793 THR Chi-restraints excluded: chain L residue 820 THR Chi-restraints excluded: chain L residue 861 TYR Chi-restraints excluded: chain L residue 864 THR Chi-restraints excluded: chain M residue 293 LEU Chi-restraints excluded: chain M residue 422 ILE Chi-restraints excluded: chain M residue 462 ILE Chi-restraints excluded: chain M residue 483 VAL Chi-restraints excluded: chain M residue 489 THR Chi-restraints excluded: chain M residue 531 THR Chi-restraints excluded: chain M residue 558 THR Chi-restraints excluded: chain M residue 623 ASP Chi-restraints excluded: chain M residue 679 LEU Chi-restraints excluded: chain M residue 721 ILE Chi-restraints excluded: chain Z residue 339 VAL Chi-restraints excluded: chain Z residue 421 THR Chi-restraints excluded: chain Z residue 451 THR Chi-restraints excluded: chain Z residue 489 THR Chi-restraints excluded: chain Z residue 569 ILE Chi-restraints excluded: chain Z residue 680 THR Chi-restraints excluded: chain Z residue 856 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 732 optimal weight: 9.9990 chunk 499 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 654 optimal weight: 4.9990 chunk 362 optimal weight: 2.9990 chunk 750 optimal weight: 9.9990 chunk 608 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 449 optimal weight: 0.9980 chunk 789 optimal weight: 10.0000 chunk 221 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 ASN ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN ** C 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 ASN D 794 ASN E 450 ASN F 346 GLN F 792 GLN F 794 ASN G 651 ASN ** G 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 223 ASN H 346 GLN H 636 ASN ** I 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 454 GLN ** I 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 509 GLN ** K 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 636 ASN ** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 GLN M 765 HIS ** Z 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 73995 Z= 0.289 Angle : 0.630 11.251 100445 Z= 0.330 Chirality : 0.046 0.337 11262 Planarity : 0.004 0.055 13130 Dihedral : 5.867 53.419 9995 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 3.89 % Allowed : 17.77 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.15 (0.08), residues: 9190 helix: -2.41 (0.15), residues: 925 sheet: -0.89 (0.10), residues: 2623 loop : -2.78 (0.08), residues: 5642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 632 HIS 0.005 0.001 HIS Z 765 PHE 0.020 0.002 PHE G 249 TYR 0.025 0.001 TYR F 230 ARG 0.005 0.000 ARG B 805 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 318 poor density : 458 time to evaluate : 6.374 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: A 257 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.6151 (p90) REVERT: A 632 TRP cc_start: 0.6107 (t-100) cc_final: 0.5832 (t-100) REVERT: A 861 TYR cc_start: 0.7110 (OUTLIER) cc_final: 0.6819 (m-10) REVERT: A 869 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6402 (mt-10) REVERT: B 426 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7700 (pp20) REVERT: B 868 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7500 (tmm-80) REVERT: C 452 MET cc_start: 0.7594 (mmt) cc_final: 0.7368 (mmt) REVERT: C 625 TYR cc_start: 0.7517 (t80) cc_final: 0.6301 (t80) REVERT: C 632 TRP cc_start: 0.7144 (m100) cc_final: 0.6828 (m100) REVERT: C 692 GLU cc_start: 0.5643 (mt-10) cc_final: 0.4543 (tm-30) REVERT: C 791 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8472 (p) REVERT: D 293 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8469 (mt) REVERT: D 403 MET cc_start: 0.8738 (ttp) cc_final: 0.8459 (ttp) REVERT: D 663 LEU cc_start: 0.4298 (OUTLIER) cc_final: 0.4089 (pp) REVERT: D 861 TYR cc_start: 0.6985 (OUTLIER) cc_final: 0.6665 (m-10) REVERT: E 460 ILE cc_start: 0.9312 (mp) cc_final: 0.8995 (mt) REVERT: E 569 ILE cc_start: 0.9072 (mp) cc_final: 0.8658 (mt) REVERT: E 868 ARG cc_start: 0.7086 (ptm160) cc_final: 0.6599 (ttm170) REVERT: F 240 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8998 (tp) REVERT: F 426 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7409 (pp20) REVERT: F 604 LYS cc_start: 0.8530 (tmtt) cc_final: 0.7978 (pttp) REVERT: F 709 TYR cc_start: 0.7047 (m-80) cc_final: 0.6845 (m-80) REVERT: F 762 MET cc_start: 0.8144 (ppp) cc_final: 0.7441 (ppp) REVERT: F 861 TYR cc_start: 0.7181 (OUTLIER) cc_final: 0.6835 (m-10) REVERT: G 482 GLN cc_start: 0.9354 (OUTLIER) cc_final: 0.8800 (pm20) REVERT: H 257 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.7995 (p90) REVERT: H 447 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8527 (tp) REVERT: H 545 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8847 (pp) REVERT: H 740 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7453 (tm-30) REVERT: H 861 TYR cc_start: 0.6992 (OUTLIER) cc_final: 0.6561 (m-10) REVERT: I 454 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7901 (tm-30) REVERT: I 455 PHE cc_start: 0.7827 (m-80) cc_final: 0.7365 (m-80) REVERT: I 632 TRP cc_start: 0.6494 (m100) cc_final: 0.6016 (m100) REVERT: I 801 ILE cc_start: 0.9505 (OUTLIER) cc_final: 0.9284 (mt) REVERT: J 293 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8090 (mm) REVERT: J 426 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7469 (pp20) REVERT: J 663 LEU cc_start: 0.4197 (OUTLIER) cc_final: 0.3831 (pp) REVERT: J 688 ILE cc_start: 0.5763 (OUTLIER) cc_final: 0.5447 (pt) REVERT: J 754 LYS cc_start: 0.2655 (OUTLIER) cc_final: 0.1882 (ttpp) REVERT: J 861 TYR cc_start: 0.7033 (OUTLIER) cc_final: 0.6610 (m-10) REVERT: K 263 GLU cc_start: 0.6242 (tt0) cc_final: 0.5931 (tt0) REVERT: K 335 ASN cc_start: 0.8888 (t0) cc_final: 0.8673 (t0) REVERT: K 442 LYS cc_start: 0.8983 (ttmt) cc_final: 0.8664 (ttmm) REVERT: K 452 MET cc_start: 0.6326 (mpp) cc_final: 0.5993 (mmm) REVERT: K 453 ASP cc_start: 0.8390 (p0) cc_final: 0.8090 (p0) REVERT: K 454 GLN cc_start: 0.7915 (tp40) cc_final: 0.7594 (pt0) REVERT: K 679 LEU cc_start: -0.2500 (OUTLIER) cc_final: -0.2967 (mt) REVERT: L 257 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.8180 (p90) REVERT: L 632 TRP cc_start: 0.6304 (t-100) cc_final: 0.5845 (t-100) REVERT: L 762 MET cc_start: 0.8181 (ppp) cc_final: 0.7386 (ppp) REVERT: L 820 THR cc_start: 0.9529 (OUTLIER) cc_final: 0.9025 (p) REVERT: L 825 MET cc_start: 0.8360 (mmt) cc_final: 0.8105 (mmt) REVERT: L 861 TYR cc_start: 0.6919 (OUTLIER) cc_final: 0.6541 (m-10) REVERT: M 433 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8587 (tt) REVERT: M 462 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8621 (mt) REVERT: M 786 MET cc_start: 0.7532 (tpp) cc_final: 0.7273 (tpp) REVERT: M 794 ASN cc_start: 0.7623 (p0) cc_final: 0.7330 (p0) REVERT: Z 455 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7873 (m-10) REVERT: Z 686 VAL cc_start: 0.8336 (t) cc_final: 0.7929 (t) REVERT: Z 692 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6208 (mm-30) outliers start: 318 outliers final: 235 residues processed: 734 average time/residue: 0.6266 time to fit residues: 818.6204 Evaluate side-chains 704 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 436 time to evaluate : 6.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 861 TYR Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 601 TYR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 868 ARG Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 455 PHE Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 TYR Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 542 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain D residue 852 ILE Chi-restraints excluded: chain D residue 861 TYR Chi-restraints excluded: chain D residue 864 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 403 MET Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 489 THR Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 801 ILE Chi-restraints excluded: chain E residue 856 LYS Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 426 GLU Chi-restraints excluded: chain F residue 451 THR Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 579 ILE Chi-restraints excluded: chain F residue 654 THR Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 852 ILE Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 861 TYR Chi-restraints excluded: chain F residue 864 THR Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain G residue 418 THR Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 454 GLN Chi-restraints excluded: chain G residue 479 GLU Chi-restraints excluded: chain G residue 482 GLN Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 531 THR Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 650 LEU Chi-restraints excluded: chain G residue 651 ASN Chi-restraints excluded: chain G residue 654 THR Chi-restraints excluded: chain G residue 739 THR Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 817 ASP Chi-restraints excluded: chain G residue 818 ILE Chi-restraints excluded: chain G residue 855 TYR Chi-restraints excluded: chain H residue 257 TYR Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain H residue 332 THR Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 409 THR Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 447 LEU Chi-restraints excluded: chain H residue 545 LEU Chi-restraints excluded: chain H residue 547 ILE Chi-restraints excluded: chain H residue 564 LEU Chi-restraints excluded: chain H residue 636 ASN Chi-restraints excluded: chain H residue 654 THR Chi-restraints excluded: chain H residue 670 VAL Chi-restraints excluded: chain H residue 714 THR Chi-restraints excluded: chain H residue 740 GLU Chi-restraints excluded: chain H residue 759 GLN Chi-restraints excluded: chain H residue 772 LEU Chi-restraints excluded: chain H residue 791 THR Chi-restraints excluded: chain H residue 793 THR Chi-restraints excluded: chain H residue 852 ILE Chi-restraints excluded: chain H residue 861 TYR Chi-restraints excluded: chain H residue 872 VAL Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 297 TYR Chi-restraints excluded: chain I residue 299 ILE Chi-restraints excluded: chain I residue 421 THR Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain I residue 462 ILE Chi-restraints excluded: chain I residue 558 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 576 VAL Chi-restraints excluded: chain I residue 590 ASP Chi-restraints excluded: chain I residue 721 ILE Chi-restraints excluded: chain I residue 739 THR Chi-restraints excluded: chain I residue 801 ILE Chi-restraints excluded: chain I residue 855 TYR Chi-restraints excluded: chain I residue 856 LYS Chi-restraints excluded: chain J residue 257 TYR Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 332 THR Chi-restraints excluded: chain J residue 341 VAL Chi-restraints excluded: chain J residue 360 THR Chi-restraints excluded: chain J residue 393 VAL Chi-restraints excluded: chain J residue 426 GLU Chi-restraints excluded: chain J residue 437 ASP Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 650 LEU Chi-restraints excluded: chain J residue 663 LEU Chi-restraints excluded: chain J residue 688 ILE Chi-restraints excluded: chain J residue 699 VAL Chi-restraints excluded: chain J residue 714 THR Chi-restraints excluded: chain J residue 739 THR Chi-restraints excluded: chain J residue 753 VAL Chi-restraints excluded: chain J residue 754 LYS Chi-restraints excluded: chain J residue 762 MET Chi-restraints excluded: chain J residue 772 LEU Chi-restraints excluded: chain J residue 791 THR Chi-restraints excluded: chain J residue 861 TYR Chi-restraints excluded: chain J residue 864 THR Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 418 THR Chi-restraints excluded: chain K residue 451 THR Chi-restraints excluded: chain K residue 462 ILE Chi-restraints excluded: chain K residue 479 GLU Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 643 LEU Chi-restraints excluded: chain K residue 650 LEU Chi-restraints excluded: chain K residue 679 LEU Chi-restraints excluded: chain K residue 783 ILE Chi-restraints excluded: chain K residue 791 THR Chi-restraints excluded: chain K residue 793 THR Chi-restraints excluded: chain K residue 817 ASP Chi-restraints excluded: chain K residue 818 ILE Chi-restraints excluded: chain K residue 855 TYR Chi-restraints excluded: chain L residue 257 TYR Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 302 VAL Chi-restraints excluded: chain L residue 332 THR Chi-restraints excluded: chain L residue 341 VAL Chi-restraints excluded: chain L residue 360 THR Chi-restraints excluded: chain L residue 377 THR Chi-restraints excluded: chain L residue 393 VAL Chi-restraints excluded: chain L residue 409 THR Chi-restraints excluded: chain L residue 410 THR Chi-restraints excluded: chain L residue 428 GLN Chi-restraints excluded: chain L residue 545 LEU Chi-restraints excluded: chain L residue 636 ASN Chi-restraints excluded: chain L residue 638 THR Chi-restraints excluded: chain L residue 654 THR Chi-restraints excluded: chain L residue 663 LEU Chi-restraints excluded: chain L residue 670 VAL Chi-restraints excluded: chain L residue 725 LEU Chi-restraints excluded: chain L residue 730 THR Chi-restraints excluded: chain L residue 737 SER Chi-restraints excluded: chain L residue 739 THR Chi-restraints excluded: chain L residue 791 THR Chi-restraints excluded: chain L residue 793 THR Chi-restraints excluded: chain L residue 820 THR Chi-restraints excluded: chain L residue 861 TYR Chi-restraints excluded: chain L residue 864 THR Chi-restraints excluded: chain M residue 293 LEU Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain M residue 422 ILE Chi-restraints excluded: chain M residue 433 LEU Chi-restraints excluded: chain M residue 462 ILE Chi-restraints excluded: chain M residue 483 VAL Chi-restraints excluded: chain M residue 489 THR Chi-restraints excluded: chain M residue 531 THR Chi-restraints excluded: chain M residue 558 THR Chi-restraints excluded: chain M residue 623 ASP Chi-restraints excluded: chain M residue 679 LEU Chi-restraints excluded: chain M residue 721 ILE Chi-restraints excluded: chain Z residue 287 THR Chi-restraints excluded: chain Z residue 339 VAL Chi-restraints excluded: chain Z residue 421 THR Chi-restraints excluded: chain Z residue 422 ILE Chi-restraints excluded: chain Z residue 451 THR Chi-restraints excluded: chain Z residue 455 PHE Chi-restraints excluded: chain Z residue 489 THR Chi-restraints excluded: chain Z residue 569 ILE Chi-restraints excluded: chain Z residue 590 ASP Chi-restraints excluded: chain Z residue 670 VAL Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain Z residue 855 TYR Chi-restraints excluded: chain Z residue 856 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 295 optimal weight: 3.9990 chunk 792 optimal weight: 5.9990 chunk 173 optimal weight: 0.0170 chunk 516 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 chunk 880 optimal weight: 2.9990 chunk 730 optimal weight: 7.9990 chunk 407 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 291 optimal weight: 1.9990 chunk 462 optimal weight: 5.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 ASN B 636 ASN C 335 ASN C 651 ASN C 742 ASN D 636 ASN D 794 ASN F 794 ASN G 742 ASN H 636 ASN ** I 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 794 ASN ** K 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 765 HIS L 636 ASN ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 450 ASN ** Z 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 495 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 73995 Z= 0.173 Angle : 0.578 11.292 100445 Z= 0.302 Chirality : 0.044 0.316 11262 Planarity : 0.003 0.055 13130 Dihedral : 5.539 52.904 9995 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.57 % Allowed : 18.76 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.96 (0.08), residues: 9190 helix: -2.26 (0.15), residues: 928 sheet: -0.74 (0.10), residues: 2592 loop : -2.66 (0.08), residues: 5670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 632 HIS 0.004 0.001 HIS Z 765 PHE 0.020 0.001 PHE I 455 TYR 0.020 0.001 TYR F 230 ARG 0.004 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 466 time to evaluate : 6.278 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 257 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.5830 (p90) REVERT: A 632 TRP cc_start: 0.6056 (t-100) cc_final: 0.5789 (t-100) REVERT: A 853 MET cc_start: 0.6120 (tmm) cc_final: 0.5855 (ttm) REVERT: A 861 TYR cc_start: 0.7056 (OUTLIER) cc_final: 0.6727 (m-10) REVERT: A 869 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.6140 (mt-10) REVERT: B 868 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7529 (tmm-80) REVERT: C 452 MET cc_start: 0.7481 (mmt) cc_final: 0.7213 (mmt) REVERT: C 625 TYR cc_start: 0.7425 (t80) cc_final: 0.6282 (t80) REVERT: C 632 TRP cc_start: 0.7194 (m100) cc_final: 0.6857 (m100) REVERT: C 692 GLU cc_start: 0.5642 (mt-10) cc_final: 0.4270 (tm-30) REVERT: C 791 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8364 (p) REVERT: D 293 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8367 (mt) REVERT: D 403 MET cc_start: 0.8692 (ttp) cc_final: 0.8412 (ttp) REVERT: D 426 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7409 (pp20) REVERT: D 663 LEU cc_start: 0.4247 (OUTLIER) cc_final: 0.4001 (pp) REVERT: D 861 TYR cc_start: 0.7018 (OUTLIER) cc_final: 0.6714 (m-10) REVERT: E 460 ILE cc_start: 0.9272 (mp) cc_final: 0.8952 (mt) REVERT: E 569 ILE cc_start: 0.9063 (mp) cc_final: 0.8682 (mt) REVERT: E 625 TYR cc_start: 0.7887 (t80) cc_final: 0.7087 (t80) REVERT: E 632 TRP cc_start: 0.6597 (m100) cc_final: 0.6146 (m100) REVERT: E 868 ARG cc_start: 0.7302 (ptm160) cc_final: 0.6857 (ttm170) REVERT: F 240 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8937 (tp) REVERT: F 426 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7337 (pp20) REVERT: F 604 LYS cc_start: 0.8544 (tmtt) cc_final: 0.8013 (pttp) REVERT: F 709 TYR cc_start: 0.7042 (m-80) cc_final: 0.6841 (m-80) REVERT: F 762 MET cc_start: 0.8020 (ppp) cc_final: 0.7374 (ppp) REVERT: F 861 TYR cc_start: 0.7147 (OUTLIER) cc_final: 0.6797 (m-10) REVERT: G 482 GLN cc_start: 0.9324 (OUTLIER) cc_final: 0.8728 (pm20) REVERT: G 623 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7507 (m-30) REVERT: G 651 ASN cc_start: 0.7760 (OUTLIER) cc_final: 0.6965 (p0) REVERT: H 293 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8498 (mt) REVERT: H 447 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8374 (tp) REVERT: H 545 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8864 (pp) REVERT: H 740 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7605 (tm-30) REVERT: H 861 TYR cc_start: 0.6906 (OUTLIER) cc_final: 0.6520 (m-10) REVERT: I 455 PHE cc_start: 0.7831 (m-80) cc_final: 0.7232 (m-80) REVERT: I 632 TRP cc_start: 0.6451 (m100) cc_final: 0.5887 (m100) REVERT: I 801 ILE cc_start: 0.9484 (OUTLIER) cc_final: 0.9253 (mt) REVERT: J 293 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8065 (mm) REVERT: J 426 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7375 (pp20) REVERT: J 663 LEU cc_start: 0.4133 (OUTLIER) cc_final: 0.3781 (pp) REVERT: J 688 ILE cc_start: 0.5647 (OUTLIER) cc_final: 0.5346 (pt) REVERT: J 861 TYR cc_start: 0.6988 (OUTLIER) cc_final: 0.6566 (m-10) REVERT: J 868 ARG cc_start: 0.8042 (tmm-80) cc_final: 0.7673 (tmm-80) REVERT: K 442 LYS cc_start: 0.8908 (ttmt) cc_final: 0.8588 (ttmm) REVERT: K 452 MET cc_start: 0.6260 (mpp) cc_final: 0.5794 (mmt) REVERT: K 453 ASP cc_start: 0.8383 (p0) cc_final: 0.8107 (p0) REVERT: K 454 GLN cc_start: 0.7983 (tp40) cc_final: 0.7607 (pt0) REVERT: K 856 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8544 (ttpp) REVERT: L 257 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.8137 (p90) REVERT: L 632 TRP cc_start: 0.6180 (t-100) cc_final: 0.5757 (t-100) REVERT: L 759 GLN cc_start: 0.6394 (OUTLIER) cc_final: 0.5971 (tp40) REVERT: L 762 MET cc_start: 0.8053 (ppp) cc_final: 0.7451 (ppp) REVERT: L 820 THR cc_start: 0.9517 (OUTLIER) cc_final: 0.8994 (p) REVERT: L 861 TYR cc_start: 0.6908 (OUTLIER) cc_final: 0.6509 (m-10) REVERT: M 433 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8565 (tt) REVERT: M 462 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8608 (mt) REVERT: M 514 SER cc_start: 0.9084 (m) cc_final: 0.8853 (p) REVERT: M 786 MET cc_start: 0.7396 (tpp) cc_final: 0.7112 (tpp) REVERT: M 794 ASN cc_start: 0.7510 (p0) cc_final: 0.7224 (p0) REVERT: Z 455 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.7814 (m-10) REVERT: Z 482 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8248 (pp30) REVERT: Z 679 LEU cc_start: -0.1828 (OUTLIER) cc_final: -0.2341 (tp) outliers start: 292 outliers final: 187 residues processed: 721 average time/residue: 0.6144 time to fit residues: 788.7275 Evaluate side-chains 653 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 430 time to evaluate : 6.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 861 TYR Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 601 TYR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 868 ARG Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 651 ASN Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 855 TYR Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain D residue 861 TYR Chi-restraints excluded: chain D residue 864 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 489 THR Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 679 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 426 GLU Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain F residue 451 THR Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 654 THR Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 861 TYR Chi-restraints excluded: chain F residue 864 THR Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 418 THR Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 454 GLN Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 479 GLU Chi-restraints excluded: chain G residue 482 GLN Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 623 ASP Chi-restraints excluded: chain G residue 650 LEU Chi-restraints excluded: chain G residue 651 ASN Chi-restraints excluded: chain G residue 654 THR Chi-restraints excluded: chain G residue 679 LEU Chi-restraints excluded: chain G residue 739 THR Chi-restraints excluded: chain G residue 744 THR Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 818 ILE Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain H residue 332 THR Chi-restraints excluded: chain H residue 341 VAL Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 410 THR Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 447 LEU Chi-restraints excluded: chain H residue 545 LEU Chi-restraints excluded: chain H residue 547 ILE Chi-restraints excluded: chain H residue 564 LEU Chi-restraints excluded: chain H residue 636 ASN Chi-restraints excluded: chain H residue 654 THR Chi-restraints excluded: chain H residue 670 VAL Chi-restraints excluded: chain H residue 714 THR Chi-restraints excluded: chain H residue 721 ILE Chi-restraints excluded: chain H residue 740 GLU Chi-restraints excluded: chain H residue 759 GLN Chi-restraints excluded: chain H residue 772 LEU Chi-restraints excluded: chain H residue 791 THR Chi-restraints excluded: chain H residue 793 THR Chi-restraints excluded: chain H residue 818 ILE Chi-restraints excluded: chain H residue 861 TYR Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 299 ILE Chi-restraints excluded: chain I residue 421 THR Chi-restraints excluded: chain I residue 462 ILE Chi-restraints excluded: chain I residue 558 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 576 VAL Chi-restraints excluded: chain I residue 588 ILE Chi-restraints excluded: chain I residue 590 ASP Chi-restraints excluded: chain I residue 654 THR Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 801 ILE Chi-restraints excluded: chain I residue 855 TYR Chi-restraints excluded: chain J residue 257 TYR Chi-restraints excluded: chain J residue 262 LEU Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 332 THR Chi-restraints excluded: chain J residue 360 THR Chi-restraints excluded: chain J residue 364 SER Chi-restraints excluded: chain J residue 393 VAL Chi-restraints excluded: chain J residue 426 GLU Chi-restraints excluded: chain J residue 437 ASP Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 663 LEU Chi-restraints excluded: chain J residue 688 ILE Chi-restraints excluded: chain J residue 699 VAL Chi-restraints excluded: chain J residue 714 THR Chi-restraints excluded: chain J residue 753 VAL Chi-restraints excluded: chain J residue 772 LEU Chi-restraints excluded: chain J residue 791 THR Chi-restraints excluded: chain J residue 861 TYR Chi-restraints excluded: chain J residue 864 THR Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 462 ILE Chi-restraints excluded: chain K residue 479 GLU Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 643 LEU Chi-restraints excluded: chain K residue 650 LEU Chi-restraints excluded: chain K residue 656 ILE Chi-restraints excluded: chain K residue 738 ILE Chi-restraints excluded: chain K residue 783 ILE Chi-restraints excluded: chain K residue 791 THR Chi-restraints excluded: chain K residue 793 THR Chi-restraints excluded: chain K residue 855 TYR Chi-restraints excluded: chain K residue 856 LYS Chi-restraints excluded: chain L residue 257 TYR Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 302 VAL Chi-restraints excluded: chain L residue 332 THR Chi-restraints excluded: chain L residue 360 THR Chi-restraints excluded: chain L residue 380 SER Chi-restraints excluded: chain L residue 410 THR Chi-restraints excluded: chain L residue 428 GLN Chi-restraints excluded: chain L residue 545 LEU Chi-restraints excluded: chain L residue 636 ASN Chi-restraints excluded: chain L residue 663 LEU Chi-restraints excluded: chain L residue 670 VAL Chi-restraints excluded: chain L residue 730 THR Chi-restraints excluded: chain L residue 737 SER Chi-restraints excluded: chain L residue 759 GLN Chi-restraints excluded: chain L residue 772 LEU Chi-restraints excluded: chain L residue 820 THR Chi-restraints excluded: chain L residue 861 TYR Chi-restraints excluded: chain L residue 864 THR Chi-restraints excluded: chain M residue 293 LEU Chi-restraints excluded: chain M residue 403 MET Chi-restraints excluded: chain M residue 422 ILE Chi-restraints excluded: chain M residue 433 LEU Chi-restraints excluded: chain M residue 462 ILE Chi-restraints excluded: chain M residue 558 THR Chi-restraints excluded: chain M residue 623 ASP Chi-restraints excluded: chain M residue 679 LEU Chi-restraints excluded: chain M residue 721 ILE Chi-restraints excluded: chain Z residue 339 VAL Chi-restraints excluded: chain Z residue 421 THR Chi-restraints excluded: chain Z residue 451 THR Chi-restraints excluded: chain Z residue 455 PHE Chi-restraints excluded: chain Z residue 482 GLN Chi-restraints excluded: chain Z residue 489 THR Chi-restraints excluded: chain Z residue 569 ILE Chi-restraints excluded: chain Z residue 590 ASP Chi-restraints excluded: chain Z residue 654 THR Chi-restraints excluded: chain Z residue 670 VAL Chi-restraints excluded: chain Z residue 679 LEU Chi-restraints excluded: chain Z residue 680 THR Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain Z residue 744 THR Chi-restraints excluded: chain Z residue 856 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 848 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 501 optimal weight: 8.9990 chunk 642 optimal weight: 0.6980 chunk 498 optimal weight: 40.0000 chunk 741 optimal weight: 9.9990 chunk 491 optimal weight: 8.9990 chunk 877 optimal weight: 9.9990 chunk 548 optimal weight: 9.9990 chunk 534 optimal weight: 10.0000 chunk 404 optimal weight: 0.0070 overall best weight: 3.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 ASN ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN C 486 ASN D 636 ASN D 794 ASN E 486 ASN H 636 ASN ** I 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 454 GLN I 838 ASN ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 495 GLN ** K 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 636 ASN ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 651 ASN ** Z 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 73995 Z= 0.263 Angle : 0.614 12.053 100445 Z= 0.320 Chirality : 0.045 0.293 11262 Planarity : 0.004 0.054 13130 Dihedral : 5.584 51.644 9994 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 3.91 % Allowed : 18.98 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.90 (0.08), residues: 9190 helix: -2.13 (0.15), residues: 922 sheet: -0.73 (0.10), residues: 2592 loop : -2.62 (0.08), residues: 5676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP Z 632 HIS 0.005 0.001 HIS Z 765 PHE 0.018 0.002 PHE G 249 TYR 0.026 0.001 TYR F 230 ARG 0.006 0.000 ARG J 668 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 320 poor density : 443 time to evaluate : 6.266 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 257 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.6109 (p90) REVERT: A 632 TRP cc_start: 0.6076 (t-100) cc_final: 0.5796 (t-100) REVERT: A 861 TYR cc_start: 0.7131 (OUTLIER) cc_final: 0.6806 (m-10) REVERT: A 869 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6306 (mt-10) REVERT: B 426 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7713 (pp20) REVERT: B 663 LEU cc_start: 0.4158 (OUTLIER) cc_final: 0.3881 (pp) REVERT: B 868 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7501 (tmm-80) REVERT: C 452 MET cc_start: 0.7585 (mmt) cc_final: 0.7369 (mmt) REVERT: C 625 TYR cc_start: 0.7467 (t80) cc_final: 0.6293 (t80) REVERT: C 651 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.6843 (p0) REVERT: C 692 GLU cc_start: 0.5677 (mt-10) cc_final: 0.4315 (tm-30) REVERT: C 717 ASP cc_start: 0.4232 (OUTLIER) cc_final: 0.3803 (m-30) REVERT: C 791 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8452 (p) REVERT: D 293 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8234 (mt) REVERT: D 403 MET cc_start: 0.8729 (ttp) cc_final: 0.8460 (ttp) REVERT: D 426 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7440 (pp20) REVERT: D 663 LEU cc_start: 0.4319 (OUTLIER) cc_final: 0.4104 (pp) REVERT: D 861 TYR cc_start: 0.7037 (OUTLIER) cc_final: 0.6729 (m-10) REVERT: E 455 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7249 (m-80) REVERT: E 460 ILE cc_start: 0.9302 (mp) cc_final: 0.8973 (mt) REVERT: E 569 ILE cc_start: 0.9081 (mp) cc_final: 0.8647 (mt) REVERT: E 868 ARG cc_start: 0.7200 (ptm160) cc_final: 0.6969 (ttm170) REVERT: F 240 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8999 (tp) REVERT: F 347 ASN cc_start: 0.8431 (m-40) cc_final: 0.8165 (t0) REVERT: F 426 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7355 (pp20) REVERT: F 604 LYS cc_start: 0.8550 (tttt) cc_final: 0.8028 (pttp) REVERT: F 695 THR cc_start: 0.6751 (p) cc_final: 0.6358 (m) REVERT: F 762 MET cc_start: 0.8070 (ppp) cc_final: 0.7389 (ppp) REVERT: F 861 TYR cc_start: 0.7200 (OUTLIER) cc_final: 0.6847 (m-10) REVERT: G 334 SER cc_start: 0.8069 (OUTLIER) cc_final: 0.7783 (p) REVERT: G 482 GLN cc_start: 0.9336 (OUTLIER) cc_final: 0.8775 (pm20) REVERT: G 623 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7456 (m-30) REVERT: H 447 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8455 (tp) REVERT: H 545 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8876 (pp) REVERT: H 740 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7586 (tm-30) REVERT: H 861 TYR cc_start: 0.6941 (OUTLIER) cc_final: 0.6520 (m-10) REVERT: I 453 ASP cc_start: 0.8056 (p0) cc_final: 0.7816 (p0) REVERT: I 455 PHE cc_start: 0.7859 (m-80) cc_final: 0.7239 (m-80) REVERT: I 632 TRP cc_start: 0.6483 (m100) cc_final: 0.5908 (m100) REVERT: I 801 ILE cc_start: 0.9498 (OUTLIER) cc_final: 0.9282 (mt) REVERT: J 293 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8087 (mm) REVERT: J 426 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7420 (pp20) REVERT: J 663 LEU cc_start: 0.4184 (OUTLIER) cc_final: 0.3816 (pp) REVERT: J 688 ILE cc_start: 0.5719 (OUTLIER) cc_final: 0.5408 (pt) REVERT: J 754 LYS cc_start: 0.2831 (OUTLIER) cc_final: 0.2283 (ttpp) REVERT: J 861 TYR cc_start: 0.7020 (OUTLIER) cc_final: 0.6599 (m-10) REVERT: J 868 ARG cc_start: 0.8173 (tmm-80) cc_final: 0.7703 (tmm-80) REVERT: K 263 GLU cc_start: 0.5961 (tt0) cc_final: 0.5738 (tt0) REVERT: K 442 LYS cc_start: 0.8936 (ttmt) cc_final: 0.8612 (ttmm) REVERT: K 452 MET cc_start: 0.6285 (mpp) cc_final: 0.5851 (mmt) REVERT: K 453 ASP cc_start: 0.8354 (p0) cc_final: 0.8138 (p0) REVERT: K 454 GLN cc_start: 0.7823 (tp40) cc_final: 0.7533 (pt0) REVERT: K 856 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8560 (ttpp) REVERT: L 257 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.8137 (p90) REVERT: L 632 TRP cc_start: 0.6091 (t-100) cc_final: 0.5671 (t-100) REVERT: L 762 MET cc_start: 0.8165 (ppp) cc_final: 0.7390 (ppp) REVERT: L 820 THR cc_start: 0.9538 (OUTLIER) cc_final: 0.8998 (p) REVERT: L 861 TYR cc_start: 0.6974 (OUTLIER) cc_final: 0.6569 (m-10) REVERT: M 433 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8565 (tt) REVERT: M 462 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8644 (mt) REVERT: M 514 SER cc_start: 0.9117 (m) cc_final: 0.8900 (p) REVERT: M 786 MET cc_start: 0.7479 (tpp) cc_final: 0.7196 (tpp) REVERT: M 794 ASN cc_start: 0.7548 (p0) cc_final: 0.7266 (p0) REVERT: Z 455 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7732 (m-10) REVERT: Z 482 GLN cc_start: 0.9230 (OUTLIER) cc_final: 0.8296 (pp30) outliers start: 320 outliers final: 249 residues processed: 728 average time/residue: 0.6110 time to fit residues: 796.3395 Evaluate side-chains 716 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 428 time to evaluate : 6.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 861 TYR Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 601 TYR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 868 ARG Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 651 ASN Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 717 ASP Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 783 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 855 TYR Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 636 ASN Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain D residue 852 ILE Chi-restraints excluded: chain D residue 861 TYR Chi-restraints excluded: chain D residue 864 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 455 PHE Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 489 THR Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 679 LEU Chi-restraints excluded: chain E residue 801 ILE Chi-restraints excluded: chain E residue 856 LYS Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 426 GLU Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain F residue 451 THR Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 579 ILE Chi-restraints excluded: chain F residue 654 THR Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 847 THR Chi-restraints excluded: chain F residue 852 ILE Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 861 TYR Chi-restraints excluded: chain F residue 864 THR Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 418 THR Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 454 GLN Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 479 GLU Chi-restraints excluded: chain G residue 482 GLN Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 531 THR Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 603 VAL Chi-restraints excluded: chain G residue 623 ASP Chi-restraints excluded: chain G residue 650 LEU Chi-restraints excluded: chain G residue 654 THR Chi-restraints excluded: chain G residue 679 LEU Chi-restraints excluded: chain G residue 739 THR Chi-restraints excluded: chain G residue 744 THR Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 817 ASP Chi-restraints excluded: chain G residue 818 ILE Chi-restraints excluded: chain G residue 855 TYR Chi-restraints excluded: chain H residue 257 TYR Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain H residue 332 THR Chi-restraints excluded: chain H residue 341 VAL Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain H residue 410 THR Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 447 LEU Chi-restraints excluded: chain H residue 545 LEU Chi-restraints excluded: chain H residue 547 ILE Chi-restraints excluded: chain H residue 564 LEU Chi-restraints excluded: chain H residue 636 ASN Chi-restraints excluded: chain H residue 654 THR Chi-restraints excluded: chain H residue 670 VAL Chi-restraints excluded: chain H residue 714 THR Chi-restraints excluded: chain H residue 721 ILE Chi-restraints excluded: chain H residue 739 THR Chi-restraints excluded: chain H residue 740 GLU Chi-restraints excluded: chain H residue 759 GLN Chi-restraints excluded: chain H residue 772 LEU Chi-restraints excluded: chain H residue 791 THR Chi-restraints excluded: chain H residue 793 THR Chi-restraints excluded: chain H residue 818 ILE Chi-restraints excluded: chain H residue 861 TYR Chi-restraints excluded: chain H residue 872 VAL Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 297 TYR Chi-restraints excluded: chain I residue 299 ILE Chi-restraints excluded: chain I residue 421 THR Chi-restraints excluded: chain I residue 462 ILE Chi-restraints excluded: chain I residue 558 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 576 VAL Chi-restraints excluded: chain I residue 590 ASP Chi-restraints excluded: chain I residue 610 ASN Chi-restraints excluded: chain I residue 650 LEU Chi-restraints excluded: chain I residue 654 THR Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 679 LEU Chi-restraints excluded: chain I residue 721 ILE Chi-restraints excluded: chain I residue 739 THR Chi-restraints excluded: chain I residue 801 ILE Chi-restraints excluded: chain I residue 855 TYR Chi-restraints excluded: chain I residue 856 LYS Chi-restraints excluded: chain J residue 257 TYR Chi-restraints excluded: chain J residue 262 LEU Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 332 THR Chi-restraints excluded: chain J residue 341 VAL Chi-restraints excluded: chain J residue 360 THR Chi-restraints excluded: chain J residue 364 SER Chi-restraints excluded: chain J residue 393 VAL Chi-restraints excluded: chain J residue 426 GLU Chi-restraints excluded: chain J residue 437 ASP Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 663 LEU Chi-restraints excluded: chain J residue 688 ILE Chi-restraints excluded: chain J residue 699 VAL Chi-restraints excluded: chain J residue 714 THR Chi-restraints excluded: chain J residue 753 VAL Chi-restraints excluded: chain J residue 754 LYS Chi-restraints excluded: chain J residue 772 LEU Chi-restraints excluded: chain J residue 791 THR Chi-restraints excluded: chain J residue 861 TYR Chi-restraints excluded: chain J residue 864 THR Chi-restraints excluded: chain J residue 872 VAL Chi-restraints excluded: chain K residue 330 SER Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 418 THR Chi-restraints excluded: chain K residue 451 THR Chi-restraints excluded: chain K residue 462 ILE Chi-restraints excluded: chain K residue 479 GLU Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 501 ASN Chi-restraints excluded: chain K residue 643 LEU Chi-restraints excluded: chain K residue 650 LEU Chi-restraints excluded: chain K residue 656 ILE Chi-restraints excluded: chain K residue 679 LEU Chi-restraints excluded: chain K residue 686 VAL Chi-restraints excluded: chain K residue 738 ILE Chi-restraints excluded: chain K residue 783 ILE Chi-restraints excluded: chain K residue 791 THR Chi-restraints excluded: chain K residue 793 THR Chi-restraints excluded: chain K residue 817 ASP Chi-restraints excluded: chain K residue 818 ILE Chi-restraints excluded: chain K residue 855 TYR Chi-restraints excluded: chain K residue 856 LYS Chi-restraints excluded: chain L residue 257 TYR Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 302 VAL Chi-restraints excluded: chain L residue 332 THR Chi-restraints excluded: chain L residue 360 THR Chi-restraints excluded: chain L residue 377 THR Chi-restraints excluded: chain L residue 380 SER Chi-restraints excluded: chain L residue 409 THR Chi-restraints excluded: chain L residue 410 THR Chi-restraints excluded: chain L residue 428 GLN Chi-restraints excluded: chain L residue 545 LEU Chi-restraints excluded: chain L residue 636 ASN Chi-restraints excluded: chain L residue 663 LEU Chi-restraints excluded: chain L residue 670 VAL Chi-restraints excluded: chain L residue 733 LEU Chi-restraints excluded: chain L residue 737 SER Chi-restraints excluded: chain L residue 772 LEU Chi-restraints excluded: chain L residue 820 THR Chi-restraints excluded: chain L residue 861 TYR Chi-restraints excluded: chain L residue 864 THR Chi-restraints excluded: chain M residue 293 LEU Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain M residue 422 ILE Chi-restraints excluded: chain M residue 433 LEU Chi-restraints excluded: chain M residue 462 ILE Chi-restraints excluded: chain M residue 476 ILE Chi-restraints excluded: chain M residue 489 THR Chi-restraints excluded: chain M residue 531 THR Chi-restraints excluded: chain M residue 558 THR Chi-restraints excluded: chain M residue 623 ASP Chi-restraints excluded: chain M residue 679 LEU Chi-restraints excluded: chain M residue 721 ILE Chi-restraints excluded: chain M residue 753 VAL Chi-restraints excluded: chain Z residue 339 VAL Chi-restraints excluded: chain Z residue 421 THR Chi-restraints excluded: chain Z residue 422 ILE Chi-restraints excluded: chain Z residue 451 THR Chi-restraints excluded: chain Z residue 455 PHE Chi-restraints excluded: chain Z residue 482 GLN Chi-restraints excluded: chain Z residue 489 THR Chi-restraints excluded: chain Z residue 569 ILE Chi-restraints excluded: chain Z residue 590 ASP Chi-restraints excluded: chain Z residue 670 VAL Chi-restraints excluded: chain Z residue 679 LEU Chi-restraints excluded: chain Z residue 680 THR Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain Z residue 744 THR Chi-restraints excluded: chain Z residue 856 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 542 optimal weight: 4.9990 chunk 350 optimal weight: 0.8980 chunk 523 optimal weight: 8.9990 chunk 264 optimal weight: 0.8980 chunk 172 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 557 optimal weight: 20.0000 chunk 597 optimal weight: 5.9990 chunk 433 optimal weight: 30.0000 chunk 81 optimal weight: 10.0000 chunk 689 optimal weight: 10.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 ASN ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 ASN D 794 ASN ** G 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 223 ASN H 636 ASN ** I 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 636 ASN ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 742 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 73995 Z= 0.253 Angle : 0.613 13.871 100445 Z= 0.320 Chirality : 0.045 0.287 11262 Planarity : 0.004 0.054 13130 Dihedral : 5.591 51.493 9994 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 4.24 % Allowed : 18.98 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.85 (0.08), residues: 9190 helix: -2.04 (0.15), residues: 922 sheet: -0.62 (0.10), residues: 2550 loop : -2.62 (0.08), residues: 5718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP Z 632 HIS 0.005 0.001 HIS Z 765 PHE 0.019 0.002 PHE G 249 TYR 0.026 0.001 TYR F 230 ARG 0.005 0.000 ARG J 668 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 347 poor density : 432 time to evaluate : 6.343 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 257 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.6128 (p90) REVERT: A 632 TRP cc_start: 0.6136 (t-100) cc_final: 0.5873 (t-100) REVERT: A 853 MET cc_start: 0.5874 (tmm) cc_final: 0.5652 (ttm) REVERT: A 861 TYR cc_start: 0.7154 (OUTLIER) cc_final: 0.6801 (m-10) REVERT: A 869 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6204 (mt-10) REVERT: B 426 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7702 (pp20) REVERT: B 442 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8173 (ttpp) REVERT: B 663 LEU cc_start: 0.4236 (OUTLIER) cc_final: 0.3917 (pp) REVERT: B 868 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7504 (tmm-80) REVERT: C 452 MET cc_start: 0.7597 (mmt) cc_final: 0.7384 (mmt) REVERT: C 625 TYR cc_start: 0.7453 (t80) cc_final: 0.6282 (t80) REVERT: C 632 TRP cc_start: 0.6743 (m100) cc_final: 0.6421 (m100) REVERT: C 692 GLU cc_start: 0.5677 (mt-10) cc_final: 0.4313 (tm-30) REVERT: C 717 ASP cc_start: 0.4256 (OUTLIER) cc_final: 0.3818 (m-30) REVERT: C 791 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8450 (p) REVERT: D 293 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8222 (mt) REVERT: D 403 MET cc_start: 0.8723 (ttp) cc_final: 0.8461 (ttp) REVERT: D 426 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7438 (pp20) REVERT: D 861 TYR cc_start: 0.7035 (OUTLIER) cc_final: 0.6713 (m-10) REVERT: E 455 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7249 (m-80) REVERT: E 460 ILE cc_start: 0.9340 (mp) cc_final: 0.9032 (mt) REVERT: E 868 ARG cc_start: 0.7205 (ptm160) cc_final: 0.6956 (ttm170) REVERT: F 240 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9011 (tp) REVERT: F 426 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7324 (pp20) REVERT: F 604 LYS cc_start: 0.8504 (tttt) cc_final: 0.7964 (pttp) REVERT: F 762 MET cc_start: 0.8055 (ppp) cc_final: 0.7386 (ppp) REVERT: F 861 TYR cc_start: 0.7174 (OUTLIER) cc_final: 0.6815 (m-10) REVERT: G 334 SER cc_start: 0.8094 (OUTLIER) cc_final: 0.7806 (p) REVERT: G 482 GLN cc_start: 0.9351 (OUTLIER) cc_final: 0.8804 (pm20) REVERT: H 447 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8452 (tp) REVERT: H 545 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8871 (pp) REVERT: H 740 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: H 825 MET cc_start: 0.8412 (mmt) cc_final: 0.7866 (mmt) REVERT: H 861 TYR cc_start: 0.6939 (OUTLIER) cc_final: 0.6516 (m-10) REVERT: I 455 PHE cc_start: 0.7764 (m-80) cc_final: 0.7161 (m-80) REVERT: I 632 TRP cc_start: 0.6488 (m100) cc_final: 0.5897 (m100) REVERT: I 801 ILE cc_start: 0.9503 (OUTLIER) cc_final: 0.9290 (mt) REVERT: J 293 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8025 (mm) REVERT: J 313 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6740 (tt0) REVERT: J 426 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7406 (pp20) REVERT: J 663 LEU cc_start: 0.4192 (OUTLIER) cc_final: 0.3821 (pp) REVERT: J 688 ILE cc_start: 0.5703 (OUTLIER) cc_final: 0.5391 (pt) REVERT: J 754 LYS cc_start: 0.2819 (OUTLIER) cc_final: 0.2236 (ttpp) REVERT: J 861 TYR cc_start: 0.7021 (OUTLIER) cc_final: 0.6591 (m-10) REVERT: J 868 ARG cc_start: 0.8168 (tmm-80) cc_final: 0.7702 (tmm-80) REVERT: K 263 GLU cc_start: 0.5973 (tt0) cc_final: 0.5745 (tt0) REVERT: K 442 LYS cc_start: 0.8944 (ttmt) cc_final: 0.8610 (ttmm) REVERT: K 452 MET cc_start: 0.6284 (mpp) cc_final: 0.5785 (mmt) REVERT: K 454 GLN cc_start: 0.7783 (tp40) cc_final: 0.7476 (pt0) REVERT: K 856 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8554 (ttpp) REVERT: L 257 TYR cc_start: 0.8795 (OUTLIER) cc_final: 0.8151 (p90) REVERT: L 632 TRP cc_start: 0.6073 (t-100) cc_final: 0.5657 (t-100) REVERT: L 762 MET cc_start: 0.8187 (ppp) cc_final: 0.7392 (ppp) REVERT: L 820 THR cc_start: 0.9549 (OUTLIER) cc_final: 0.9025 (p) REVERT: L 861 TYR cc_start: 0.6998 (OUTLIER) cc_final: 0.6583 (m-10) REVERT: L 868 ARG cc_start: 0.7822 (tmm-80) cc_final: 0.7465 (tmm-80) REVERT: M 433 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8552 (tt) REVERT: M 462 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8640 (mt) REVERT: M 514 SER cc_start: 0.9115 (m) cc_final: 0.8904 (p) REVERT: M 786 MET cc_start: 0.7458 (tpp) cc_final: 0.7186 (tpp) REVERT: M 794 ASN cc_start: 0.7514 (p0) cc_final: 0.7249 (p0) REVERT: Z 455 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7743 (m-10) REVERT: Z 482 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8246 (pp30) REVERT: Z 742 ASN cc_start: 0.8337 (OUTLIER) cc_final: 0.8042 (m-40) outliers start: 347 outliers final: 275 residues processed: 743 average time/residue: 0.6135 time to fit residues: 814.9362 Evaluate side-chains 736 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 423 time to evaluate : 6.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 861 TYR Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 601 TYR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 868 ARG Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 717 ASP Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 783 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 855 TYR Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain D residue 852 ILE Chi-restraints excluded: chain D residue 861 TYR Chi-restraints excluded: chain D residue 864 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 455 PHE Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 489 THR Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 679 LEU Chi-restraints excluded: chain E residue 744 THR Chi-restraints excluded: chain E residue 801 ILE Chi-restraints excluded: chain E residue 856 LYS Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 426 GLU Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain F residue 451 THR Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 579 ILE Chi-restraints excluded: chain F residue 654 THR Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain F residue 733 LEU Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 847 THR Chi-restraints excluded: chain F residue 852 ILE Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 861 TYR Chi-restraints excluded: chain F residue 864 THR Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 418 THR Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 454 GLN Chi-restraints excluded: chain G residue 476 ILE Chi-restraints excluded: chain G residue 479 GLU Chi-restraints excluded: chain G residue 482 GLN Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 531 THR Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 595 LEU Chi-restraints excluded: chain G residue 603 VAL Chi-restraints excluded: chain G residue 623 ASP Chi-restraints excluded: chain G residue 650 LEU Chi-restraints excluded: chain G residue 654 THR Chi-restraints excluded: chain G residue 679 LEU Chi-restraints excluded: chain G residue 739 THR Chi-restraints excluded: chain G residue 744 THR Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 817 ASP Chi-restraints excluded: chain G residue 818 ILE Chi-restraints excluded: chain G residue 855 TYR Chi-restraints excluded: chain H residue 257 TYR Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain H residue 332 THR Chi-restraints excluded: chain H residue 341 VAL Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain H residue 410 THR Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 447 LEU Chi-restraints excluded: chain H residue 545 LEU Chi-restraints excluded: chain H residue 547 ILE Chi-restraints excluded: chain H residue 636 ASN Chi-restraints excluded: chain H residue 638 THR Chi-restraints excluded: chain H residue 654 THR Chi-restraints excluded: chain H residue 670 VAL Chi-restraints excluded: chain H residue 714 THR Chi-restraints excluded: chain H residue 721 ILE Chi-restraints excluded: chain H residue 739 THR Chi-restraints excluded: chain H residue 740 GLU Chi-restraints excluded: chain H residue 759 GLN Chi-restraints excluded: chain H residue 772 LEU Chi-restraints excluded: chain H residue 791 THR Chi-restraints excluded: chain H residue 793 THR Chi-restraints excluded: chain H residue 818 ILE Chi-restraints excluded: chain H residue 852 ILE Chi-restraints excluded: chain H residue 861 TYR Chi-restraints excluded: chain H residue 872 VAL Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 297 TYR Chi-restraints excluded: chain I residue 299 ILE Chi-restraints excluded: chain I residue 421 THR Chi-restraints excluded: chain I residue 462 ILE Chi-restraints excluded: chain I residue 479 GLU Chi-restraints excluded: chain I residue 558 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 576 VAL Chi-restraints excluded: chain I residue 590 ASP Chi-restraints excluded: chain I residue 610 ASN Chi-restraints excluded: chain I residue 650 LEU Chi-restraints excluded: chain I residue 654 THR Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 679 LEU Chi-restraints excluded: chain I residue 721 ILE Chi-restraints excluded: chain I residue 739 THR Chi-restraints excluded: chain I residue 744 THR Chi-restraints excluded: chain I residue 801 ILE Chi-restraints excluded: chain I residue 855 TYR Chi-restraints excluded: chain I residue 856 LYS Chi-restraints excluded: chain J residue 229 SER Chi-restraints excluded: chain J residue 257 TYR Chi-restraints excluded: chain J residue 262 LEU Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 332 THR Chi-restraints excluded: chain J residue 341 VAL Chi-restraints excluded: chain J residue 360 THR Chi-restraints excluded: chain J residue 364 SER Chi-restraints excluded: chain J residue 393 VAL Chi-restraints excluded: chain J residue 410 THR Chi-restraints excluded: chain J residue 426 GLU Chi-restraints excluded: chain J residue 437 ASP Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 579 ILE Chi-restraints excluded: chain J residue 650 LEU Chi-restraints excluded: chain J residue 663 LEU Chi-restraints excluded: chain J residue 688 ILE Chi-restraints excluded: chain J residue 699 VAL Chi-restraints excluded: chain J residue 714 THR Chi-restraints excluded: chain J residue 739 THR Chi-restraints excluded: chain J residue 753 VAL Chi-restraints excluded: chain J residue 754 LYS Chi-restraints excluded: chain J residue 772 LEU Chi-restraints excluded: chain J residue 791 THR Chi-restraints excluded: chain J residue 861 TYR Chi-restraints excluded: chain J residue 864 THR Chi-restraints excluded: chain J residue 872 VAL Chi-restraints excluded: chain K residue 330 SER Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 418 THR Chi-restraints excluded: chain K residue 451 THR Chi-restraints excluded: chain K residue 462 ILE Chi-restraints excluded: chain K residue 479 GLU Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 501 ASN Chi-restraints excluded: chain K residue 643 LEU Chi-restraints excluded: chain K residue 650 LEU Chi-restraints excluded: chain K residue 656 ILE Chi-restraints excluded: chain K residue 679 LEU Chi-restraints excluded: chain K residue 738 ILE Chi-restraints excluded: chain K residue 739 THR Chi-restraints excluded: chain K residue 783 ILE Chi-restraints excluded: chain K residue 791 THR Chi-restraints excluded: chain K residue 793 THR Chi-restraints excluded: chain K residue 817 ASP Chi-restraints excluded: chain K residue 818 ILE Chi-restraints excluded: chain K residue 856 LYS Chi-restraints excluded: chain L residue 257 TYR Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 302 VAL Chi-restraints excluded: chain L residue 332 THR Chi-restraints excluded: chain L residue 341 VAL Chi-restraints excluded: chain L residue 360 THR Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain L residue 377 THR Chi-restraints excluded: chain L residue 380 SER Chi-restraints excluded: chain L residue 393 VAL Chi-restraints excluded: chain L residue 409 THR Chi-restraints excluded: chain L residue 410 THR Chi-restraints excluded: chain L residue 428 GLN Chi-restraints excluded: chain L residue 545 LEU Chi-restraints excluded: chain L residue 636 ASN Chi-restraints excluded: chain L residue 654 THR Chi-restraints excluded: chain L residue 663 LEU Chi-restraints excluded: chain L residue 670 VAL Chi-restraints excluded: chain L residue 725 LEU Chi-restraints excluded: chain L residue 733 LEU Chi-restraints excluded: chain L residue 737 SER Chi-restraints excluded: chain L residue 772 LEU Chi-restraints excluded: chain L residue 820 THR Chi-restraints excluded: chain L residue 861 TYR Chi-restraints excluded: chain L residue 864 THR Chi-restraints excluded: chain M residue 293 LEU Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain M residue 422 ILE Chi-restraints excluded: chain M residue 433 LEU Chi-restraints excluded: chain M residue 462 ILE Chi-restraints excluded: chain M residue 476 ILE Chi-restraints excluded: chain M residue 483 VAL Chi-restraints excluded: chain M residue 489 THR Chi-restraints excluded: chain M residue 531 THR Chi-restraints excluded: chain M residue 558 THR Chi-restraints excluded: chain M residue 623 ASP Chi-restraints excluded: chain M residue 679 LEU Chi-restraints excluded: chain M residue 721 ILE Chi-restraints excluded: chain M residue 753 VAL Chi-restraints excluded: chain Z residue 287 THR Chi-restraints excluded: chain Z residue 330 SER Chi-restraints excluded: chain Z residue 339 VAL Chi-restraints excluded: chain Z residue 421 THR Chi-restraints excluded: chain Z residue 422 ILE Chi-restraints excluded: chain Z residue 451 THR Chi-restraints excluded: chain Z residue 455 PHE Chi-restraints excluded: chain Z residue 482 GLN Chi-restraints excluded: chain Z residue 489 THR Chi-restraints excluded: chain Z residue 569 ILE Chi-restraints excluded: chain Z residue 590 ASP Chi-restraints excluded: chain Z residue 670 VAL Chi-restraints excluded: chain Z residue 679 LEU Chi-restraints excluded: chain Z residue 680 THR Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain Z residue 742 ASN Chi-restraints excluded: chain Z residue 744 THR Chi-restraints excluded: chain Z residue 856 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 797 optimal weight: 9.9990 chunk 840 optimal weight: 7.9990 chunk 766 optimal weight: 20.0000 chunk 817 optimal weight: 9.9990 chunk 491 optimal weight: 9.9990 chunk 356 optimal weight: 7.9990 chunk 641 optimal weight: 7.9990 chunk 250 optimal weight: 8.9990 chunk 738 optimal weight: 2.9990 chunk 773 optimal weight: 8.9990 chunk 814 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 ASN B 636 ASN ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 ASN D 794 ASN F 794 ASN ** G 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 651 ASN H 509 GLN H 636 ASN ** I 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 223 ASN J 610 ASN ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 811 GLN L 432 ASN ** L 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 73995 Z= 0.421 Angle : 0.713 15.439 100445 Z= 0.373 Chirality : 0.048 0.297 11262 Planarity : 0.004 0.056 13130 Dihedral : 6.038 50.384 9994 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer: Outliers : 4.40 % Allowed : 19.32 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.96 (0.08), residues: 9190 helix: -2.07 (0.15), residues: 916 sheet: -0.54 (0.11), residues: 2424 loop : -2.76 (0.07), residues: 5850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP Z 632 HIS 0.006 0.002 HIS Z 765 PHE 0.026 0.003 PHE A 788 TYR 0.028 0.002 TYR F 230 ARG 0.005 0.001 ARG M 868 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 360 poor density : 435 time to evaluate : 6.345 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: A 257 TYR cc_start: 0.8796 (OUTLIER) cc_final: 0.6454 (p90) REVERT: A 853 MET cc_start: 0.6119 (tmm) cc_final: 0.5820 (ttm) REVERT: A 861 TYR cc_start: 0.7257 (OUTLIER) cc_final: 0.6920 (m-10) REVERT: A 869 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6629 (mt-10) REVERT: B 426 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7721 (pp20) REVERT: B 442 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8262 (ttpp) REVERT: B 663 LEU cc_start: 0.4544 (OUTLIER) cc_final: 0.4259 (pp) REVERT: B 868 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7429 (tmm-80) REVERT: C 625 TYR cc_start: 0.7455 (t80) cc_final: 0.5928 (t80) REVERT: C 692 GLU cc_start: 0.5779 (mt-10) cc_final: 0.4349 (tm-30) REVERT: C 717 ASP cc_start: 0.5037 (OUTLIER) cc_final: 0.4709 (m-30) REVERT: C 791 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8565 (p) REVERT: D 293 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8369 (mt) REVERT: D 426 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7575 (pp20) REVERT: D 861 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.6774 (m-10) REVERT: E 403 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8333 (mtm) REVERT: E 455 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7286 (m-80) REVERT: E 460 ILE cc_start: 0.9411 (mp) cc_final: 0.9090 (mt) REVERT: E 868 ARG cc_start: 0.7240 (ptm160) cc_final: 0.6933 (ttm170) REVERT: F 240 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9055 (tp) REVERT: F 426 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7409 (pp20) REVERT: F 604 LYS cc_start: 0.8595 (tttt) cc_final: 0.8051 (pttp) REVERT: F 762 MET cc_start: 0.8182 (ppp) cc_final: 0.7487 (ppp) REVERT: F 861 TYR cc_start: 0.7214 (OUTLIER) cc_final: 0.6877 (m-10) REVERT: G 334 SER cc_start: 0.8211 (OUTLIER) cc_final: 0.7898 (p) REVERT: G 452 MET cc_start: 0.7309 (mmt) cc_final: 0.7073 (mmm) REVERT: G 482 GLN cc_start: 0.9356 (OUTLIER) cc_final: 0.8821 (pm20) REVERT: H 447 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8640 (tp) REVERT: H 545 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8865 (pp) REVERT: H 740 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7710 (tm-30) REVERT: H 861 TYR cc_start: 0.7051 (OUTLIER) cc_final: 0.6620 (m-10) REVERT: I 455 PHE cc_start: 0.7863 (m-80) cc_final: 0.7325 (m-80) REVERT: I 632 TRP cc_start: 0.6537 (m100) cc_final: 0.5994 (m100) REVERT: J 293 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.7967 (mm) REVERT: J 313 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7014 (tt0) REVERT: J 426 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7606 (pp20) REVERT: J 663 LEU cc_start: 0.4297 (OUTLIER) cc_final: 0.3917 (pp) REVERT: J 688 ILE cc_start: 0.5702 (OUTLIER) cc_final: 0.5381 (pt) REVERT: J 754 LYS cc_start: 0.2615 (OUTLIER) cc_final: 0.2056 (ttpp) REVERT: J 861 TYR cc_start: 0.7099 (OUTLIER) cc_final: 0.6672 (m-10) REVERT: K 263 GLU cc_start: 0.6235 (tt0) cc_final: 0.5970 (tt0) REVERT: K 442 LYS cc_start: 0.9045 (ttmt) cc_final: 0.8706 (ttmm) REVERT: K 452 MET cc_start: 0.6357 (mpp) cc_final: 0.5728 (mmt) REVERT: K 632 TRP cc_start: 0.6942 (m100) cc_final: 0.6506 (m100) REVERT: K 679 LEU cc_start: -0.2672 (OUTLIER) cc_final: -0.3087 (tp) REVERT: K 856 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8684 (ttpp) REVERT: L 257 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.8168 (p90) REVERT: L 632 TRP cc_start: 0.6155 (t-100) cc_final: 0.5760 (t-100) REVERT: L 762 MET cc_start: 0.8211 (ppp) cc_final: 0.7224 (ppp) REVERT: L 861 TYR cc_start: 0.7028 (OUTLIER) cc_final: 0.6675 (m-10) REVERT: L 868 ARG cc_start: 0.7971 (tmm-80) cc_final: 0.7610 (tmm-80) REVERT: M 433 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8615 (tt) REVERT: M 786 MET cc_start: 0.7608 (tpp) cc_final: 0.7334 (tpp) REVERT: M 794 ASN cc_start: 0.7532 (p0) cc_final: 0.7235 (p0) REVERT: Z 335 ASN cc_start: 0.9014 (t0) cc_final: 0.8766 (t0) REVERT: Z 455 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.7681 (m-10) REVERT: Z 482 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8542 (pt0) REVERT: Z 794 ASN cc_start: 0.7468 (p0) cc_final: 0.7203 (p0) outliers start: 360 outliers final: 290 residues processed: 754 average time/residue: 0.6150 time to fit residues: 827.9342 Evaluate side-chains 747 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 326 poor density : 421 time to evaluate : 6.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 861 TYR Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 601 TYR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 868 ARG Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 717 ASP Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 783 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 855 TYR Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 542 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 636 ASN Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain D residue 852 ILE Chi-restraints excluded: chain D residue 861 TYR Chi-restraints excluded: chain D residue 864 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 403 MET Chi-restraints excluded: chain E residue 455 PHE Chi-restraints excluded: chain E residue 462 ILE Chi-restraints excluded: chain E residue 479 GLU Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 489 THR Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 679 LEU Chi-restraints excluded: chain E residue 744 THR Chi-restraints excluded: chain E residue 801 ILE Chi-restraints excluded: chain E residue 856 LYS Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 426 GLU Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain F residue 451 THR Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 579 ILE Chi-restraints excluded: chain F residue 654 THR Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 847 THR Chi-restraints excluded: chain F residue 852 ILE Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 861 TYR Chi-restraints excluded: chain F residue 864 THR Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 418 THR Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 454 GLN Chi-restraints excluded: chain G residue 479 GLU Chi-restraints excluded: chain G residue 482 GLN Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 531 THR Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 595 LEU Chi-restraints excluded: chain G residue 603 VAL Chi-restraints excluded: chain G residue 650 LEU Chi-restraints excluded: chain G residue 654 THR Chi-restraints excluded: chain G residue 679 LEU Chi-restraints excluded: chain G residue 739 THR Chi-restraints excluded: chain G residue 744 THR Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 817 ASP Chi-restraints excluded: chain G residue 818 ILE Chi-restraints excluded: chain G residue 855 TYR Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain H residue 332 THR Chi-restraints excluded: chain H residue 341 VAL Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain H residue 409 THR Chi-restraints excluded: chain H residue 410 THR Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 437 ASP Chi-restraints excluded: chain H residue 447 LEU Chi-restraints excluded: chain H residue 545 LEU Chi-restraints excluded: chain H residue 547 ILE Chi-restraints excluded: chain H residue 636 ASN Chi-restraints excluded: chain H residue 638 THR Chi-restraints excluded: chain H residue 654 THR Chi-restraints excluded: chain H residue 670 VAL Chi-restraints excluded: chain H residue 714 THR Chi-restraints excluded: chain H residue 721 ILE Chi-restraints excluded: chain H residue 739 THR Chi-restraints excluded: chain H residue 740 GLU Chi-restraints excluded: chain H residue 759 GLN Chi-restraints excluded: chain H residue 772 LEU Chi-restraints excluded: chain H residue 791 THR Chi-restraints excluded: chain H residue 793 THR Chi-restraints excluded: chain H residue 818 ILE Chi-restraints excluded: chain H residue 852 ILE Chi-restraints excluded: chain H residue 861 TYR Chi-restraints excluded: chain H residue 872 VAL Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 297 TYR Chi-restraints excluded: chain I residue 299 ILE Chi-restraints excluded: chain I residue 421 THR Chi-restraints excluded: chain I residue 462 ILE Chi-restraints excluded: chain I residue 558 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 576 VAL Chi-restraints excluded: chain I residue 590 ASP Chi-restraints excluded: chain I residue 650 LEU Chi-restraints excluded: chain I residue 654 THR Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 679 LEU Chi-restraints excluded: chain I residue 721 ILE Chi-restraints excluded: chain I residue 744 THR Chi-restraints excluded: chain I residue 855 TYR Chi-restraints excluded: chain I residue 856 LYS Chi-restraints excluded: chain J residue 229 SER Chi-restraints excluded: chain J residue 257 TYR Chi-restraints excluded: chain J residue 262 LEU Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 332 THR Chi-restraints excluded: chain J residue 341 VAL Chi-restraints excluded: chain J residue 360 THR Chi-restraints excluded: chain J residue 364 SER Chi-restraints excluded: chain J residue 365 THR Chi-restraints excluded: chain J residue 393 VAL Chi-restraints excluded: chain J residue 409 THR Chi-restraints excluded: chain J residue 410 THR Chi-restraints excluded: chain J residue 426 GLU Chi-restraints excluded: chain J residue 437 ASP Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 579 ILE Chi-restraints excluded: chain J residue 650 LEU Chi-restraints excluded: chain J residue 663 LEU Chi-restraints excluded: chain J residue 688 ILE Chi-restraints excluded: chain J residue 699 VAL Chi-restraints excluded: chain J residue 714 THR Chi-restraints excluded: chain J residue 739 THR Chi-restraints excluded: chain J residue 753 VAL Chi-restraints excluded: chain J residue 754 LYS Chi-restraints excluded: chain J residue 772 LEU Chi-restraints excluded: chain J residue 791 THR Chi-restraints excluded: chain J residue 861 TYR Chi-restraints excluded: chain J residue 864 THR Chi-restraints excluded: chain J residue 872 VAL Chi-restraints excluded: chain K residue 297 TYR Chi-restraints excluded: chain K residue 330 SER Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 418 THR Chi-restraints excluded: chain K residue 451 THR Chi-restraints excluded: chain K residue 462 ILE Chi-restraints excluded: chain K residue 479 GLU Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 501 ASN Chi-restraints excluded: chain K residue 643 LEU Chi-restraints excluded: chain K residue 650 LEU Chi-restraints excluded: chain K residue 656 ILE Chi-restraints excluded: chain K residue 679 LEU Chi-restraints excluded: chain K residue 686 VAL Chi-restraints excluded: chain K residue 738 ILE Chi-restraints excluded: chain K residue 739 THR Chi-restraints excluded: chain K residue 791 THR Chi-restraints excluded: chain K residue 793 THR Chi-restraints excluded: chain K residue 817 ASP Chi-restraints excluded: chain K residue 818 ILE Chi-restraints excluded: chain K residue 856 LYS Chi-restraints excluded: chain L residue 257 TYR Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 302 VAL Chi-restraints excluded: chain L residue 332 THR Chi-restraints excluded: chain L residue 341 VAL Chi-restraints excluded: chain L residue 360 THR Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain L residue 377 THR Chi-restraints excluded: chain L residue 380 SER Chi-restraints excluded: chain L residue 393 VAL Chi-restraints excluded: chain L residue 409 THR Chi-restraints excluded: chain L residue 410 THR Chi-restraints excluded: chain L residue 428 GLN Chi-restraints excluded: chain L residue 545 LEU Chi-restraints excluded: chain L residue 654 THR Chi-restraints excluded: chain L residue 663 LEU Chi-restraints excluded: chain L residue 670 VAL Chi-restraints excluded: chain L residue 725 LEU Chi-restraints excluded: chain L residue 737 SER Chi-restraints excluded: chain L residue 739 THR Chi-restraints excluded: chain L residue 772 LEU Chi-restraints excluded: chain L residue 791 THR Chi-restraints excluded: chain L residue 861 TYR Chi-restraints excluded: chain L residue 864 THR Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain M residue 293 LEU Chi-restraints excluded: chain M residue 297 TYR Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain M residue 362 ASP Chi-restraints excluded: chain M residue 422 ILE Chi-restraints excluded: chain M residue 433 LEU Chi-restraints excluded: chain M residue 476 ILE Chi-restraints excluded: chain M residue 483 VAL Chi-restraints excluded: chain M residue 489 THR Chi-restraints excluded: chain M residue 531 THR Chi-restraints excluded: chain M residue 558 THR Chi-restraints excluded: chain M residue 623 ASP Chi-restraints excluded: chain M residue 679 LEU Chi-restraints excluded: chain M residue 721 ILE Chi-restraints excluded: chain M residue 753 VAL Chi-restraints excluded: chain M residue 793 THR Chi-restraints excluded: chain M residue 855 TYR Chi-restraints excluded: chain Z residue 287 THR Chi-restraints excluded: chain Z residue 330 SER Chi-restraints excluded: chain Z residue 339 VAL Chi-restraints excluded: chain Z residue 421 THR Chi-restraints excluded: chain Z residue 422 ILE Chi-restraints excluded: chain Z residue 451 THR Chi-restraints excluded: chain Z residue 455 PHE Chi-restraints excluded: chain Z residue 482 GLN Chi-restraints excluded: chain Z residue 489 THR Chi-restraints excluded: chain Z residue 569 ILE Chi-restraints excluded: chain Z residue 590 ASP Chi-restraints excluded: chain Z residue 670 VAL Chi-restraints excluded: chain Z residue 679 LEU Chi-restraints excluded: chain Z residue 680 THR Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain Z residue 744 THR Chi-restraints excluded: chain Z residue 855 TYR Chi-restraints excluded: chain Z residue 856 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 536 optimal weight: 7.9990 chunk 864 optimal weight: 0.9990 chunk 527 optimal weight: 0.9990 chunk 410 optimal weight: 0.7980 chunk 600 optimal weight: 9.9990 chunk 906 optimal weight: 5.9990 chunk 834 optimal weight: 10.0000 chunk 721 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 557 optimal weight: 9.9990 chunk 442 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 ASN A 794 ASN B 636 ASN C 335 ASN ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 ASN D 794 ASN F 794 ASN ** G 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 636 ASN H 794 ASN I 454 GLN J 314 HIS ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 794 ASN ** K 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 794 ASN ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 450 ASN ** Z 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 73995 Z= 0.216 Angle : 0.618 16.681 100445 Z= 0.322 Chirality : 0.045 0.284 11262 Planarity : 0.004 0.055 13130 Dihedral : 5.697 51.646 9994 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.84 % Allowed : 20.14 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.78 (0.08), residues: 9190 helix: -1.88 (0.16), residues: 898 sheet: -0.65 (0.10), residues: 2550 loop : -2.55 (0.08), residues: 5742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP Z 632 HIS 0.005 0.001 HIS Z 765 PHE 0.019 0.002 PHE G 249 TYR 0.024 0.001 TYR F 230 ARG 0.011 0.000 ARG K 868 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 445 time to evaluate : 7.013 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: A 257 TYR cc_start: 0.8701 (OUTLIER) cc_final: 0.6177 (p90) REVERT: A 853 MET cc_start: 0.5716 (tmm) cc_final: 0.5466 (ttm) REVERT: A 861 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6850 (m-10) REVERT: A 869 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6216 (mt-10) REVERT: B 426 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7628 (pp20) REVERT: B 442 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8132 (ttpp) REVERT: B 663 LEU cc_start: 0.4131 (OUTLIER) cc_final: 0.3840 (pp) REVERT: B 868 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7511 (tmm-80) REVERT: C 625 TYR cc_start: 0.7440 (t80) cc_final: 0.6210 (t80) REVERT: C 692 GLU cc_start: 0.5698 (mt-10) cc_final: 0.4281 (tm-30) REVERT: C 717 ASP cc_start: 0.4407 (OUTLIER) cc_final: 0.3982 (m-30) REVERT: C 791 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8443 (p) REVERT: D 293 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8288 (mt) REVERT: D 426 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7479 (pp20) REVERT: D 861 TYR cc_start: 0.7022 (OUTLIER) cc_final: 0.6697 (m-10) REVERT: E 403 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8409 (mtm) REVERT: E 455 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7163 (m-80) REVERT: E 460 ILE cc_start: 0.9331 (mp) cc_final: 0.9008 (mt) REVERT: E 625 TYR cc_start: 0.7879 (t80) cc_final: 0.7599 (t80) REVERT: E 868 ARG cc_start: 0.7262 (ptm160) cc_final: 0.6599 (ttm-80) REVERT: F 240 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9016 (tp) REVERT: F 426 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7370 (pp20) REVERT: F 604 LYS cc_start: 0.8506 (tttt) cc_final: 0.7964 (pttp) REVERT: F 762 MET cc_start: 0.7997 (ppp) cc_final: 0.7558 (ppp) REVERT: F 861 TYR cc_start: 0.7174 (OUTLIER) cc_final: 0.6823 (m-10) REVERT: G 334 SER cc_start: 0.8128 (OUTLIER) cc_final: 0.7843 (p) REVERT: G 452 MET cc_start: 0.7278 (mmt) cc_final: 0.7032 (mmm) REVERT: G 482 GLN cc_start: 0.9349 (OUTLIER) cc_final: 0.8792 (pm20) REVERT: G 623 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7576 (m-30) REVERT: H 293 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8494 (mt) REVERT: H 447 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8487 (tp) REVERT: H 545 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8850 (pp) REVERT: H 740 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: H 825 MET cc_start: 0.8382 (mmt) cc_final: 0.7837 (mmt) REVERT: H 861 TYR cc_start: 0.6952 (OUTLIER) cc_final: 0.6516 (m-10) REVERT: I 632 TRP cc_start: 0.6507 (m100) cc_final: 0.5901 (m100) REVERT: I 853 MET cc_start: 0.7000 (tmm) cc_final: 0.6793 (tmm) REVERT: J 293 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8069 (mm) REVERT: J 313 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6749 (tt0) REVERT: J 426 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7314 (pp20) REVERT: J 581 ASP cc_start: 0.7773 (p0) cc_final: 0.7149 (p0) REVERT: J 663 LEU cc_start: 0.4203 (OUTLIER) cc_final: 0.3850 (pp) REVERT: J 688 ILE cc_start: 0.5604 (OUTLIER) cc_final: 0.5295 (pt) REVERT: J 754 LYS cc_start: 0.2811 (OUTLIER) cc_final: 0.2244 (ttpp) REVERT: J 861 TYR cc_start: 0.7042 (OUTLIER) cc_final: 0.6604 (m-10) REVERT: J 868 ARG cc_start: 0.8028 (tmm-80) cc_final: 0.7583 (tmm-80) REVERT: K 263 GLU cc_start: 0.6186 (tt0) cc_final: 0.5907 (tt0) REVERT: K 442 LYS cc_start: 0.8906 (ttmt) cc_final: 0.8569 (ttmm) REVERT: K 452 MET cc_start: 0.6281 (mpp) cc_final: 0.5692 (mmt) REVERT: K 632 TRP cc_start: 0.6888 (m100) cc_final: 0.6229 (m100) REVERT: K 825 MET cc_start: 0.8369 (mmt) cc_final: 0.7633 (mmm) REVERT: K 856 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8440 (ttpp) REVERT: L 257 TYR cc_start: 0.8806 (OUTLIER) cc_final: 0.8140 (p90) REVERT: L 632 TRP cc_start: 0.6206 (t-100) cc_final: 0.5779 (t-100) REVERT: L 762 MET cc_start: 0.8214 (ppp) cc_final: 0.7471 (ppp) REVERT: L 861 TYR cc_start: 0.7022 (OUTLIER) cc_final: 0.6719 (m-10) REVERT: L 868 ARG cc_start: 0.7897 (tmm-80) cc_final: 0.7402 (tmm-80) REVERT: M 433 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8533 (tt) REVERT: M 514 SER cc_start: 0.9123 (m) cc_final: 0.8909 (p) REVERT: M 794 ASN cc_start: 0.7469 (p0) cc_final: 0.7170 (p0) REVERT: Z 335 ASN cc_start: 0.8987 (t0) cc_final: 0.8741 (t0) REVERT: Z 455 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.7664 (m-10) REVERT: Z 482 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8271 (pp30) outliers start: 314 outliers final: 253 residues processed: 722 average time/residue: 0.6249 time to fit residues: 804.4472 Evaluate side-chains 720 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 430 time to evaluate : 6.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 861 TYR Chi-restraints excluded: chain A residue 864 THR Chi-restraints excluded: chain A residue 869 GLU Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 601 TYR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 868 ARG Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 717 ASP Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 783 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 793 THR Chi-restraints excluded: chain C residue 855 TYR Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 257 TYR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 426 GLU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 772 LEU Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain D residue 852 ILE Chi-restraints excluded: chain D residue 861 TYR Chi-restraints excluded: chain D residue 864 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 403 MET Chi-restraints excluded: chain E residue 455 PHE Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 489 THR Chi-restraints excluded: chain E residue 578 LEU Chi-restraints excluded: chain E residue 650 LEU Chi-restraints excluded: chain E residue 679 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 257 TYR Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 393 VAL Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 426 GLU Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain F residue 451 THR Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 535 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 579 ILE Chi-restraints excluded: chain F residue 654 THR Chi-restraints excluded: chain F residue 699 VAL Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 847 THR Chi-restraints excluded: chain F residue 852 ILE Chi-restraints excluded: chain F residue 858 LEU Chi-restraints excluded: chain F residue 861 TYR Chi-restraints excluded: chain F residue 864 THR Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 247 ASP Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 297 TYR Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 451 THR Chi-restraints excluded: chain G residue 454 GLN Chi-restraints excluded: chain G residue 479 GLU Chi-restraints excluded: chain G residue 482 GLN Chi-restraints excluded: chain G residue 489 THR Chi-restraints excluded: chain G residue 531 THR Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 595 LEU Chi-restraints excluded: chain G residue 623 ASP Chi-restraints excluded: chain G residue 650 LEU Chi-restraints excluded: chain G residue 654 THR Chi-restraints excluded: chain G residue 679 LEU Chi-restraints excluded: chain G residue 744 THR Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 817 ASP Chi-restraints excluded: chain G residue 818 ILE Chi-restraints excluded: chain G residue 855 TYR Chi-restraints excluded: chain H residue 257 TYR Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain H residue 332 THR Chi-restraints excluded: chain H residue 341 VAL Chi-restraints excluded: chain H residue 360 THR Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain H residue 410 THR Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 429 ILE Chi-restraints excluded: chain H residue 447 LEU Chi-restraints excluded: chain H residue 545 LEU Chi-restraints excluded: chain H residue 547 ILE Chi-restraints excluded: chain H residue 636 ASN Chi-restraints excluded: chain H residue 670 VAL Chi-restraints excluded: chain H residue 714 THR Chi-restraints excluded: chain H residue 739 THR Chi-restraints excluded: chain H residue 740 GLU Chi-restraints excluded: chain H residue 759 GLN Chi-restraints excluded: chain H residue 772 LEU Chi-restraints excluded: chain H residue 791 THR Chi-restraints excluded: chain H residue 793 THR Chi-restraints excluded: chain H residue 818 ILE Chi-restraints excluded: chain H residue 852 ILE Chi-restraints excluded: chain H residue 861 TYR Chi-restraints excluded: chain H residue 872 VAL Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 297 TYR Chi-restraints excluded: chain I residue 299 ILE Chi-restraints excluded: chain I residue 421 THR Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain I residue 462 ILE Chi-restraints excluded: chain I residue 558 THR Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 576 VAL Chi-restraints excluded: chain I residue 590 ASP Chi-restraints excluded: chain I residue 650 LEU Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 679 LEU Chi-restraints excluded: chain I residue 721 ILE Chi-restraints excluded: chain I residue 855 TYR Chi-restraints excluded: chain J residue 229 SER Chi-restraints excluded: chain J residue 257 TYR Chi-restraints excluded: chain J residue 262 LEU Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 332 THR Chi-restraints excluded: chain J residue 341 VAL Chi-restraints excluded: chain J residue 360 THR Chi-restraints excluded: chain J residue 364 SER Chi-restraints excluded: chain J residue 393 VAL Chi-restraints excluded: chain J residue 409 THR Chi-restraints excluded: chain J residue 410 THR Chi-restraints excluded: chain J residue 426 GLU Chi-restraints excluded: chain J residue 437 ASP Chi-restraints excluded: chain J residue 545 LEU Chi-restraints excluded: chain J residue 579 ILE Chi-restraints excluded: chain J residue 650 LEU Chi-restraints excluded: chain J residue 663 LEU Chi-restraints excluded: chain J residue 688 ILE Chi-restraints excluded: chain J residue 699 VAL Chi-restraints excluded: chain J residue 714 THR Chi-restraints excluded: chain J residue 739 THR Chi-restraints excluded: chain J residue 753 VAL Chi-restraints excluded: chain J residue 754 LYS Chi-restraints excluded: chain J residue 772 LEU Chi-restraints excluded: chain J residue 791 THR Chi-restraints excluded: chain J residue 861 TYR Chi-restraints excluded: chain J residue 864 THR Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 418 THR Chi-restraints excluded: chain K residue 451 THR Chi-restraints excluded: chain K residue 462 ILE Chi-restraints excluded: chain K residue 479 GLU Chi-restraints excluded: chain K residue 489 THR Chi-restraints excluded: chain K residue 501 ASN Chi-restraints excluded: chain K residue 643 LEU Chi-restraints excluded: chain K residue 650 LEU Chi-restraints excluded: chain K residue 656 ILE Chi-restraints excluded: chain K residue 679 LEU Chi-restraints excluded: chain K residue 686 VAL Chi-restraints excluded: chain K residue 738 ILE Chi-restraints excluded: chain K residue 739 THR Chi-restraints excluded: chain K residue 783 ILE Chi-restraints excluded: chain K residue 791 THR Chi-restraints excluded: chain K residue 793 THR Chi-restraints excluded: chain K residue 817 ASP Chi-restraints excluded: chain K residue 818 ILE Chi-restraints excluded: chain K residue 856 LYS Chi-restraints excluded: chain L residue 257 TYR Chi-restraints excluded: chain L residue 262 LEU Chi-restraints excluded: chain L residue 293 LEU Chi-restraints excluded: chain L residue 302 VAL Chi-restraints excluded: chain L residue 332 THR Chi-restraints excluded: chain L residue 341 VAL Chi-restraints excluded: chain L residue 360 THR Chi-restraints excluded: chain L residue 377 THR Chi-restraints excluded: chain L residue 380 SER Chi-restraints excluded: chain L residue 393 VAL Chi-restraints excluded: chain L residue 409 THR Chi-restraints excluded: chain L residue 410 THR Chi-restraints excluded: chain L residue 428 GLN Chi-restraints excluded: chain L residue 545 LEU Chi-restraints excluded: chain L residue 654 THR Chi-restraints excluded: chain L residue 663 LEU Chi-restraints excluded: chain L residue 670 VAL Chi-restraints excluded: chain L residue 733 LEU Chi-restraints excluded: chain L residue 737 SER Chi-restraints excluded: chain L residue 772 LEU Chi-restraints excluded: chain L residue 791 THR Chi-restraints excluded: chain L residue 794 ASN Chi-restraints excluded: chain L residue 861 TYR Chi-restraints excluded: chain L residue 864 THR Chi-restraints excluded: chain M residue 287 THR Chi-restraints excluded: chain M residue 293 LEU Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain M residue 422 ILE Chi-restraints excluded: chain M residue 433 LEU Chi-restraints excluded: chain M residue 489 THR Chi-restraints excluded: chain M residue 531 THR Chi-restraints excluded: chain M residue 558 THR Chi-restraints excluded: chain M residue 623 ASP Chi-restraints excluded: chain M residue 679 LEU Chi-restraints excluded: chain M residue 721 ILE Chi-restraints excluded: chain M residue 753 VAL Chi-restraints excluded: chain M residue 793 THR Chi-restraints excluded: chain M residue 855 TYR Chi-restraints excluded: chain Z residue 287 THR Chi-restraints excluded: chain Z residue 339 VAL Chi-restraints excluded: chain Z residue 421 THR Chi-restraints excluded: chain Z residue 422 ILE Chi-restraints excluded: chain Z residue 451 THR Chi-restraints excluded: chain Z residue 455 PHE Chi-restraints excluded: chain Z residue 482 GLN Chi-restraints excluded: chain Z residue 489 THR Chi-restraints excluded: chain Z residue 569 ILE Chi-restraints excluded: chain Z residue 590 ASP Chi-restraints excluded: chain Z residue 670 VAL Chi-restraints excluded: chain Z residue 679 LEU Chi-restraints excluded: chain Z residue 680 THR Chi-restraints excluded: chain Z residue 739 THR Chi-restraints excluded: chain Z residue 855 TYR Chi-restraints excluded: chain Z residue 856 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 573 optimal weight: 0.0370 chunk 769 optimal weight: 6.9990 chunk 221 optimal weight: 9.9990 chunk 665 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 723 optimal weight: 2.9990 chunk 302 optimal weight: 8.9990 chunk 742 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 794 ASN ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 ASN D 794 ASN F 794 ASN ** G 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 794 ASN I 454 GLN ** J 765 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 794 ASN ** K 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 794 ASN ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.112234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.088876 restraints weight = 159475.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.090522 restraints weight = 84798.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.090823 restraints weight = 58233.683| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.254 73995 Z= 0.275 Angle : 0.759 59.199 100445 Z= 0.436 Chirality : 0.046 0.499 11262 Planarity : 0.005 0.148 13130 Dihedral : 5.693 51.858 9994 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.58 % Favored : 92.40 % Rotamer: Outliers : 3.78 % Allowed : 20.33 % Favored : 75.90 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.77 (0.08), residues: 9190 helix: -1.87 (0.16), residues: 898 sheet: -0.64 (0.10), residues: 2550 loop : -2.55 (0.08), residues: 5742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP Z 632 HIS 0.005 0.001 HIS Z 765 PHE 0.019 0.002 PHE G 249 TYR 0.024 0.001 TYR F 230 ARG 0.068 0.001 ARG M 859 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13254.94 seconds wall clock time: 233 minutes 46.23 seconds (14026.23 seconds total)