Starting phenix.real_space_refine on Thu Jun 19 18:52:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jp5_9866/06_2025/6jp5_9866.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jp5_9866/06_2025/6jp5_9866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6jp5_9866/06_2025/6jp5_9866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jp5_9866/06_2025/6jp5_9866.map" model { file = "/net/cci-nas-00/data/ceres_data/6jp5_9866/06_2025/6jp5_9866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jp5_9866/06_2025/6jp5_9866.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 P 9 5.49 5 S 126 5.16 5 C 14268 2.51 5 N 3596 2.21 5 O 4066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.72s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22068 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 10219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1274, 10219 Classifications: {'peptide': 1274} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 38, 'TRANS': 1235} Chain breaks: 6 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 57 Chain: "E" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1326 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 4 Chain: "F" Number of atoms: 7804 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 bond proxies already assigned to first conformer: 7954 Chain: "B" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 710 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 91} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1367 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 308 Unusual residues: {' CA': 3, '3PE': 8, 'C5U': 1, 'NAG': 1, 'PC1': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'3PE:plan-1': 1, '3PE:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 116 Unusual residues: {'ETA': 1, 'NAG': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 16.33, per 1000 atoms: 0.74 Number of scatterers: 22068 At special positions: 0 Unit cell: (171.287, 184.379, 164.741, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 126 16.00 P 9 15.00 O 4066 8.00 N 3596 7.00 C 14268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 254 " distance=2.23 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=1.78 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 968 " distance=2.02 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1352 " distance=2.36 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 80 " distance=2.05 Simple disulfide: pdb=" SG CYS F 305 " - pdb=" SG CYS F1047 " distance=2.03 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F1062 " distance=2.77 Simple disulfide: pdb=" SG CYS F 406 " - pdb=" SG CYS F1074 " distance=2.27 Simple disulfide: pdb=" SG CYS F 670 " - pdb=" SG CYS F 700 " distance=2.02 Simple disulfide: pdb=" SG CYS F 844 " - pdb=" SG CYS F 853 " distance=1.50 Simple disulfide: pdb=" SG CYS F 907 " - pdb=" SG CYS F 977 " distance=2.04 Simple disulfide: pdb=" SG CYS F 999 " - pdb=" SG CYS F1029 " distance=2.03 Simple disulfide: pdb=" SG CYS F1002 " - pdb=" SG CYS F1027 " distance=2.02 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 Atom "HETATM21968 O5 NAG F1104 .*. O " rejected from bonding due to valence issues. Atom "HETATM21996 O5 NAG F1114 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-3 " NAG D 1 " - " NAG D 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG L 1 " - " NAG F1125 " NAG-ASN " NAG A1901 " - " ASN A 257 " " NAG F1104 " - " ASN F 326 " " NAG F1107 " - " ASN F 891 " " NAG F1114 " - " ASN F 92 " " NAG F1115 " - " ASN F 606 " " NAG F1120 " - " ASN F 784 " " NAG F1121 " - " ASN F1001 " " NAG F1122 " - " ASN F 988 " " NAG F1125 " - " ASN F 827 " " NAG G 1 " - " ASN F 615 " " NAG H 1 " - " ASN F 186 " " NAG I 1 " - " ASN F 470 " " NAG J 1 " - " ASN F 898 " " NAG K 1 " - " ASN F 678 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.33 Conformation dependent library (CDL) restraints added in 3.8 seconds 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5110 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 19 sheets defined 53.7% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 removed outlier: 3.733A pdb=" N GLU A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 70 removed outlier: 3.565A pdb=" N ILE A 57 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 61 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 78 removed outlier: 4.278A pdb=" N ASP A 77 " --> pdb=" O MET A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 101 removed outlier: 4.095A pdb=" N PHE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE A 97 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 120 removed outlier: 3.503A pdb=" N SER A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 144 removed outlier: 3.907A pdb=" N VAL A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 144 " --> pdb=" O GLU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 176 Proline residue: A 172 - end of helix Processing helix chain 'A' and resid 179 through 192 removed outlier: 4.395A pdb=" N VAL A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN A 187 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 196 through 219 removed outlier: 3.536A pdb=" N LEU A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 290 removed outlier: 3.884A pdb=" N CYS A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 306 removed outlier: 3.947A pdb=" N VAL A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 298 " --> pdb=" O TRP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 322 removed outlier: 3.680A pdb=" N PHE A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 346 Processing helix chain 'A' and resid 349 through 372 removed outlier: 4.012A pdb=" N LEU A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 431 removed outlier: 3.615A pdb=" N TRP A 423 " --> pdb=" O ARG A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 438 through 451 removed outlier: 3.502A pdb=" N ALA A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 486 removed outlier: 3.540A pdb=" N THR A 461 " --> pdb=" O PRO A 457 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 473 " --> pdb=" O ARG A 469 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 494 removed outlier: 3.677A pdb=" N TYR A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER A 494 " --> pdb=" O GLN A 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 487 through 494' Processing helix chain 'A' and resid 496 through 514 removed outlier: 3.522A pdb=" N PHE A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 504 " --> pdb=" O ASP A 500 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS A 505 " --> pdb=" O CYS A 501 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 517 No H-bonds generated for 'chain 'A' and resid 515 through 517' Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 529 through 542 removed outlier: 3.809A pdb=" N ARG A 534 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU A 535 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE A 538 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 540 " --> pdb=" O LYS A 537 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TRP A 542 " --> pdb=" O THR A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 555 removed outlier: 3.542A pdb=" N SER A 555 " --> pdb=" O SER A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 582 removed outlier: 4.034A pdb=" N SER A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU A 562 " --> pdb=" O SER A 558 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 612 removed outlier: 3.526A pdb=" N ALA A 603 " --> pdb=" O ASN A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 627 removed outlier: 3.572A pdb=" N VAL A 619 " --> pdb=" O ASP A 615 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN A 622 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 623 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR A 627 " --> pdb=" O GLY A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 647 removed outlier: 4.395A pdb=" N TYR A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 645 " --> pdb=" O PHE A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 655 Processing helix chain 'A' and resid 655 through 663 Processing helix chain 'A' and resid 665 through 677 removed outlier: 3.564A pdb=" N THR A 671 " --> pdb=" O ALA A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 687 removed outlier: 3.545A pdb=" N LYS A 682 " --> pdb=" O ALA A 678 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG A 684 " --> pdb=" O GLU A 680 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS A 685 " --> pdb=" O ARG A 681 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET A 686 " --> pdb=" O LYS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 798 removed outlier: 4.125A pdb=" N HIS A 793 " --> pdb=" O ARG A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 806 Processing helix chain 'A' and resid 808 through 816 removed outlier: 3.897A pdb=" N ALA A 814 " --> pdb=" O LEU A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 832 Processing helix chain 'A' and resid 832 through 854 removed outlier: 3.667A pdb=" N PHE A 839 " --> pdb=" O PHE A 835 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER A 841 " --> pdb=" O ILE A 837 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 883 removed outlier: 3.514A pdb=" N LEU A 873 " --> pdb=" O ASN A 869 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 874 " --> pdb=" O ILE A 870 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL A 876 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 879 " --> pdb=" O VAL A 875 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 880 " --> pdb=" O VAL A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 899 removed outlier: 3.848A pdb=" N VAL A 898 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 899 " --> pdb=" O ILE A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 911 removed outlier: 3.651A pdb=" N ARG A 906 " --> pdb=" O LEU A 902 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A 907 " --> pdb=" O ARG A 903 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE A 908 " --> pdb=" O PRO A 904 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASN A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A 910 " --> pdb=" O ARG A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 924 removed outlier: 3.710A pdb=" N VAL A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 951 removed outlier: 3.596A pdb=" N GLN A 948 " --> pdb=" O CYS A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 979 No H-bonds generated for 'chain 'A' and resid 977 through 979' Processing helix chain 'A' and resid 999 through 1012 Processing helix chain 'A' and resid 1015 through 1025 Processing helix chain 'A' and resid 1038 through 1040 No H-bonds generated for 'chain 'A' and resid 1038 through 1040' Processing helix chain 'A' and resid 1041 through 1052 removed outlier: 4.404A pdb=" N PHE A1045 " --> pdb=" O MET A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1070 removed outlier: 3.764A pdb=" N PHE A1063 " --> pdb=" O ILE A1059 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A1066 " --> pdb=" O GLY A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1095 removed outlier: 3.763A pdb=" N CYS A1088 " --> pdb=" O ASN A1084 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A1090 " --> pdb=" O ARG A1086 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TYR A1091 " --> pdb=" O GLN A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1116 removed outlier: 3.736A pdb=" N TYR A1109 " --> pdb=" O ASN A1105 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A1114 " --> pdb=" O GLN A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1125 removed outlier: 3.713A pdb=" N GLU A1121 " --> pdb=" O SER A1117 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A1123 " --> pdb=" O TYR A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1137 removed outlier: 3.678A pdb=" N ILE A1133 " --> pdb=" O MET A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1173 removed outlier: 3.566A pdb=" N ILE A1149 " --> pdb=" O GLU A1145 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A1150 " --> pdb=" O MET A1146 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP A1151 " --> pdb=" O ASN A1147 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A1158 " --> pdb=" O ASN A1154 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A1160 " --> pdb=" O ALA A1156 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET A1165 " --> pdb=" O PHE A1161 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A1167 " --> pdb=" O LEU A1163 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA A1171 " --> pdb=" O LEU A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1206 removed outlier: 3.574A pdb=" N VAL A1184 " --> pdb=" O ASP A1180 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP A1196 " --> pdb=" O GLY A1192 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP A1203 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR A1204 " --> pdb=" O SER A1200 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A1206 " --> pdb=" O ILE A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1239 Processing helix chain 'A' and resid 1240 through 1248 removed outlier: 3.508A pdb=" N ILE A1244 " --> pdb=" O MET A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1266 removed outlier: 3.660A pdb=" N ARG A1254 " --> pdb=" O ALA A1250 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A1256 " --> pdb=" O GLY A1252 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A1260 " --> pdb=" O LEU A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1289 removed outlier: 4.010A pdb=" N ALA A1271 " --> pdb=" O LEU A1267 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A1287 " --> pdb=" O VAL A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1322 Processing helix chain 'A' and resid 1324 through 1332 Processing helix chain 'A' and resid 1356 through 1381 removed outlier: 3.529A pdb=" N ILE A1373 " --> pdb=" O ALA A1369 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A1377 " --> pdb=" O ILE A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1388 Processing helix chain 'A' and resid 1395 through 1407 removed outlier: 3.996A pdb=" N LEU A1399 " --> pdb=" O GLY A1395 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A1401 " --> pdb=" O HIS A1397 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS A1403 " --> pdb=" O LEU A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1427 removed outlier: 3.559A pdb=" N ARG A1427 " --> pdb=" O VAL A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1451 removed outlier: 4.022A pdb=" N LEU A1448 " --> pdb=" O ALA A1444 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL A1449 " --> pdb=" O CYS A1445 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1475 removed outlier: 3.673A pdb=" N LEU A1467 " --> pdb=" O PHE A1463 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE A1468 " --> pdb=" O ASN A1464 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A1469 " --> pdb=" O ALA A1465 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA A1474 " --> pdb=" O LEU A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1482 through 1493 removed outlier: 3.617A pdb=" N ALA A1486 " --> pdb=" O ASN A1482 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN A1487 " --> pdb=" O PHE A1483 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A1492 " --> pdb=" O GLU A1488 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE A1493 " --> pdb=" O GLU A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1500 through 1506 removed outlier: 3.930A pdb=" N LYS A1504 " --> pdb=" O ARG A1500 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU A1506 " --> pdb=" O SER A1502 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 27 removed outlier: 3.948A pdb=" N THR E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL E 21 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET E 24 " --> pdb=" O ILE E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 128 removed outlier: 3.960A pdb=" N PHE E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 165 removed outlier: 3.695A pdb=" N ALA E 140 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER E 154 " --> pdb=" O CYS E 150 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN E 160 " --> pdb=" O GLU E 156 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER E 161 " --> pdb=" O VAL E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 202 removed outlier: 3.776A pdb=" N ALA E 185 " --> pdb=" O SER E 181 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL E 190 " --> pdb=" O CYS E 186 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE E 197 " --> pdb=" O PHE E 193 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU E 199 " --> pdb=" O GLY E 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 38 Processing helix chain 'F' and resid 41 through 53 removed outlier: 3.800A pdb=" N GLY F 53 " --> pdb=" O LYS F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 65 removed outlier: 3.652A pdb=" N TYR F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN F 65 " --> pdb=" O TYR F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 109 removed outlier: 3.725A pdb=" N SER F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 188 removed outlier: 3.919A pdb=" N GLU F 184 " --> pdb=" O ILE F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 202 removed outlier: 3.604A pdb=" N ARG F 199 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU F 201 " --> pdb=" O LYS F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 251 removed outlier: 3.862A pdb=" N GLY F 249 " --> pdb=" O TRP F 245 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA F 251 " --> pdb=" O ILE F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 268 through 284 removed outlier: 3.617A pdb=" N ARG F 275 " --> pdb=" O LEU F 271 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER F 279 " --> pdb=" O ARG F 275 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR F 284 " --> pdb=" O GLU F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 324 Processing helix chain 'F' and resid 334 through 347 Processing helix chain 'F' and resid 371 through 379 removed outlier: 3.827A pdb=" N PHE F 375 " --> pdb=" O ALA F 371 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS F 377 " --> pdb=" O GLU F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 408 Processing helix chain 'F' and resid 417 through 421 Processing helix chain 'F' and resid 428 through 433 Processing helix chain 'F' and resid 433 through 438 Processing helix chain 'F' and resid 439 through 444 removed outlier: 3.682A pdb=" N LYS F 442 " --> pdb=" O ALA F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 500 Processing helix chain 'F' and resid 542 through 546 removed outlier: 3.845A pdb=" N ARG F 546 " --> pdb=" O LEU F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 567 removed outlier: 3.502A pdb=" N GLU F 567 " --> pdb=" O PHE F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 580 Processing helix chain 'F' and resid 640 through 647 Processing helix chain 'F' and resid 652 through 656 removed outlier: 4.021A pdb=" N PHE F 656 " --> pdb=" O PRO F 653 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 693 removed outlier: 3.686A pdb=" N PHE F 689 " --> pdb=" O ASN F 685 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE F 690 " --> pdb=" O PHE F 686 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP F 691 " --> pdb=" O ASN F 687 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 713 removed outlier: 4.023A pdb=" N ILE F 705 " --> pdb=" O ASN F 701 " (cutoff:3.500A) Processing helix chain 'F' and resid 713 through 722 removed outlier: 3.839A pdb=" N GLU F 717 " --> pdb=" O GLY F 713 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU F 718 " --> pdb=" O PHE F 714 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL F 719 " --> pdb=" O THR F 715 " (cutoff:3.500A) Processing helix chain 'F' and resid 750 through 754 removed outlier: 3.519A pdb=" N GLU F 753 " --> pdb=" O GLU F 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 764 through 773 removed outlier: 3.650A pdb=" N LYS F 768 " --> pdb=" O ASP F 764 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU F 771 " --> pdb=" O TYR F 767 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP F 772 " --> pdb=" O LYS F 768 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN F 773 " --> pdb=" O ARG F 769 " (cutoff:3.500A) Processing helix chain 'F' and resid 820 through 830 removed outlier: 3.506A pdb=" N GLU F 826 " --> pdb=" O ASN F 822 " (cutoff:3.500A) Processing helix chain 'F' and resid 877 through 881 Processing helix chain 'F' and resid 882 through 892 removed outlier: 3.619A pdb=" N MET F 886 " --> pdb=" O ASP F 882 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN F 891 " --> pdb=" O ARG F 887 " (cutoff:3.500A) Processing helix chain 'F' and resid 1024 through 1027 Processing helix chain 'F' and resid 1045 through 1050 removed outlier: 3.752A pdb=" N MET F1049 " --> pdb=" O ASP F1045 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 95 removed outlier: 3.601A pdb=" N ARG B 82 " --> pdb=" O HIS B 78 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS B 83 " --> pdb=" O MET B 79 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 171 removed outlier: 3.992A pdb=" N ARG B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU B 170 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 304 removed outlier: 3.534A pdb=" N ASP C 291 " --> pdb=" O TYR C 287 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET C 292 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU C 297 " --> pdb=" O MET C 293 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE C 300 " --> pdb=" O ALA C 296 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS C 303 " --> pdb=" O ASP C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 357 removed outlier: 3.723A pdb=" N VAL C 347 " --> pdb=" O SER C 343 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU C 350 " --> pdb=" O GLU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 378 removed outlier: 3.567A pdb=" N SER C 378 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 402 removed outlier: 4.026A pdb=" N LEU C 397 " --> pdb=" O SER C 393 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN C 398 " --> pdb=" O PRO C 394 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG C 399 " --> pdb=" O LYS C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 410 removed outlier: 3.761A pdb=" N LYS C 410 " --> pdb=" O SER C 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 407 through 410' Processing helix chain 'C' and resid 411 through 425 removed outlier: 4.041A pdb=" N GLN C 415 " --> pdb=" O HIS C 411 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE C 416 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 417 " --> pdb=" O ASN C 413 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA C 418 " --> pdb=" O VAL C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 430 Processing helix chain 'C' and resid 438 through 458 removed outlier: 3.550A pdb=" N ALA C 442 " --> pdb=" O GLN C 438 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS C 445 " --> pdb=" O ASP C 441 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU C 450 " --> pdb=" O LEU C 446 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 226 through 228 Processing sheet with id=AA2, first strand: chain 'A' and resid 971 through 975 Processing sheet with id=AA3, first strand: chain 'A' and resid 1416 through 1417 Processing sheet with id=AA4, first strand: chain 'E' and resid 48 through 50 removed outlier: 3.680A pdb=" N CYS E 57 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN E 79 " --> pdb=" O THR E 58 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 68 through 72 Processing sheet with id=AA6, first strand: chain 'F' and resid 124 through 125 removed outlier: 6.028A pdb=" N VAL F 124 " --> pdb=" O GLN F 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 127 through 128 removed outlier: 6.993A pdb=" N TYR F 127 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY F 488 " --> pdb=" O VAL F 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 127 through 128 removed outlier: 6.993A pdb=" N TYR F 127 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY F 488 " --> pdb=" O VAL F 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 300 through 302 removed outlier: 5.987A pdb=" N LYS F 254 " --> pdb=" O PHE F 290 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ASN F 292 " --> pdb=" O LYS F 254 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N MET F 256 " --> pdb=" O ASN F 292 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ALA F 294 " --> pdb=" O MET F 256 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ILE F 258 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE F 296 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL F 260 " --> pdb=" O PHE F 296 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE F 359 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS F 358 " --> pdb=" O ARG F 385 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N PHE F 387 " --> pdb=" O LYS F 358 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE F 360 " --> pdb=" O PHE F 387 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N PHE F 389 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU F 362 " --> pdb=" O PHE F 389 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL F 391 " --> pdb=" O LEU F 362 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR F 364 " --> pdb=" O VAL F 391 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL F 386 " --> pdb=" O TYR F 411 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N TYR F 413 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR F 388 " --> pdb=" O TYR F 413 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE F 415 " --> pdb=" O THR F 388 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N SER F 390 " --> pdb=" O ILE F 415 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 523 through 525 removed outlier: 3.660A pdb=" N LEU F 525 " --> pdb=" O ALA F 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 661 through 662 Processing sheet with id=AB3, first strand: chain 'F' and resid 732 through 734 removed outlier: 3.564A pdb=" N ALA F 734 " --> pdb=" O LYS F 818 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 732 through 734 removed outlier: 3.564A pdb=" N ALA F 734 " --> pdb=" O LYS F 818 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 803 through 804 Processing sheet with id=AB6, first strand: chain 'F' and resid 862 through 865 removed outlier: 3.624A pdb=" N MET F 864 " --> pdb=" O ILE F 855 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 896 through 907 removed outlier: 3.619A pdb=" N GLN F 983 " --> pdb=" O ASN F 898 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLN F 904 " --> pdb=" O CYS F 977 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N CYS F 977 " --> pdb=" O GLN F 904 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL F 906 " --> pdb=" O GLN F 975 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLN F 975 " --> pdb=" O VAL F 906 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 997 through 998 Processing sheet with id=AB9, first strand: chain 'B' and resid 156 through 160 removed outlier: 6.459A pdb=" N ARG B 148 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ILE B 136 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE B 103 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA B 104 " --> pdb=" O VAL C 271 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 309 through 313 removed outlier: 6.375A pdb=" N SER C 310 " --> pdb=" O ALA C 365 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ASP C 367 " --> pdb=" O SER C 310 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N THR C 312 " --> pdb=" O ASP C 367 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU C 279 " --> pdb=" O LEU C 366 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL C 387 " --> pdb=" O PRO C 276 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE C 278 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ILE C 389 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL C 280 " --> pdb=" O ILE C 389 " (cutoff:3.500A) 920 hydrogen bonds defined for protein. 2567 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: 8.71 Time building geometry restraints manager: 7.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3603 1.31 - 1.44: 6228 1.44 - 1.57: 12495 1.57 - 1.70: 20 1.70 - 1.84: 194 Bond restraints: 22540 Sorted by residual: bond pdb=" N21 C5U A1911 " pdb=" O22 C5U A1911 " ideal model delta sigma weight residual 1.205 1.397 -0.192 2.00e-02 2.50e+03 9.21e+01 bond pdb=" C05 C5U A1911 " pdb=" C06 C5U A1911 " ideal model delta sigma weight residual 1.355 1.524 -0.169 2.00e-02 2.50e+03 7.13e+01 bond pdb=" C08 C5U A1911 " pdb=" C09 C5U A1911 " ideal model delta sigma weight residual 1.357 1.523 -0.166 2.00e-02 2.50e+03 6.87e+01 bond pdb=" C21 3PE A1913 " pdb=" O21 3PE A1913 " ideal model delta sigma weight residual 1.316 1.458 -0.142 2.00e-02 2.50e+03 5.07e+01 bond pdb=" C21 3PE A1905 " pdb=" O21 3PE A1905 " ideal model delta sigma weight residual 1.316 1.458 -0.142 2.00e-02 2.50e+03 5.06e+01 ... (remaining 22535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 28749 3.05 - 6.10: 1503 6.10 - 9.16: 214 9.16 - 12.21: 34 12.21 - 15.26: 16 Bond angle restraints: 30516 Sorted by residual: angle pdb=" N LYS F 478 " pdb=" CA LYS F 478 " pdb=" C LYS F 478 " ideal model delta sigma weight residual 111.28 121.89 -10.61 1.09e+00 8.42e-01 9.47e+01 angle pdb=" N MET A 493 " pdb=" CA MET A 493 " pdb=" C MET A 493 " ideal model delta sigma weight residual 111.28 121.17 -9.89 1.09e+00 8.42e-01 8.23e+01 angle pdb=" N ASP F 869 " pdb=" CA ASP F 869 " pdb=" C ASP F 869 " ideal model delta sigma weight residual 113.28 103.40 9.88 1.22e+00 6.72e-01 6.56e+01 angle pdb=" N LYS F 991 " pdb=" CA LYS F 991 " pdb=" C LYS F 991 " ideal model delta sigma weight residual 111.28 120.02 -8.74 1.09e+00 8.42e-01 6.43e+01 angle pdb=" N ASN F 325 " pdb=" CA ASN F 325 " pdb=" C ASN F 325 " ideal model delta sigma weight residual 111.71 120.85 -9.14 1.15e+00 7.56e-01 6.31e+01 ... (remaining 30511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.40: 13168 27.40 - 54.79: 598 54.79 - 82.19: 77 82.19 - 109.59: 27 109.59 - 136.98: 14 Dihedral angle restraints: 13884 sinusoidal: 5985 harmonic: 7899 Sorted by residual: dihedral pdb=" CB CYS F 406 " pdb=" SG CYS F 406 " pdb=" SG CYS F1074 " pdb=" CB CYS F1074 " ideal model delta sinusoidal sigma weight residual -86.00 0.08 -86.08 1 1.00e+01 1.00e-02 8.94e+01 dihedral pdb=" CB CYS F 907 " pdb=" SG CYS F 907 " pdb=" SG CYS F 977 " pdb=" CB CYS F 977 " ideal model delta sinusoidal sigma weight residual 93.00 174.04 -81.04 1 1.00e+01 1.00e-02 8.11e+01 dihedral pdb=" CB CYS A 245 " pdb=" SG CYS A 245 " pdb=" SG CYS A 261 " pdb=" CB CYS A 261 " ideal model delta sinusoidal sigma weight residual 93.00 20.47 72.53 1 1.00e+01 1.00e-02 6.72e+01 ... (remaining 13881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.765: 3482 0.765 - 1.530: 2 1.530 - 2.295: 0 2.295 - 3.060: 1 3.060 - 3.825: 1 Chirality restraints: 3486 Sorted by residual: chirality pdb=" C1 NAG L 2 " pdb=" O3 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.75 -0.65 2.00e-02 2.50e+03 1.05e+03 chirality pdb=" C1 NAG F1120 " pdb=" ND2 ASN F 784 " pdb=" C2 NAG F1120 " pdb=" O5 NAG F1120 " both_signs ideal model delta sigma weight residual False -2.40 1.42 -3.82 2.00e-01 2.50e+01 3.66e+02 chirality pdb=" C1 NAG L 1 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " pdb=" O4 NAG F1125 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.29 2.00e-02 2.50e+03 2.15e+02 ... (remaining 3483 not shown) Planarity restraints: 3825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F1125 " 0.347 2.00e-02 2.50e+03 3.00e-01 1.12e+03 pdb=" C7 NAG F1125 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG F1125 " 0.103 2.00e-02 2.50e+03 pdb=" N2 NAG F1125 " -0.534 2.00e-02 2.50e+03 pdb=" O7 NAG F1125 " 0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.344 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG D 1 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.116 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.532 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.153 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F1104 " -0.315 2.00e-02 2.50e+03 2.67e-01 8.88e+02 pdb=" C7 NAG F1104 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG F1104 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG F1104 " 0.462 2.00e-02 2.50e+03 pdb=" O7 NAG F1104 " -0.042 2.00e-02 2.50e+03 ... (remaining 3822 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 153 2.52 - 3.11: 16190 3.11 - 3.71: 32716 3.71 - 4.30: 47451 4.30 - 4.90: 78309 Nonbonded interactions: 174819 Sorted by model distance: nonbonded pdb=" O ASN F 480 " pdb=" ND2 ASN F 480 " model vdw 1.921 3.120 nonbonded pdb=" O3 NAG A1901 " pdb=" O7 NAG A1901 " model vdw 1.949 3.040 nonbonded pdb=" O GLY F 521 " pdb=" OD1 ASP F 562 " model vdw 2.209 3.040 nonbonded pdb=" N GLU F 792 " pdb=" OE1 GLU F 792 " model vdw 2.215 3.120 nonbonded pdb=" CD2 TYR A 117 " pdb=" OD1 ASN A 123 " model vdw 2.221 3.340 ... (remaining 174814 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 'D' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'H' selection = chain 'I' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 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: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 57.030 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.130 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:14.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6025 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 : 0.019 0.739 22578 Z= 0.957 Angle : 1.771 55.809 30614 Z= 0.962 Chirality : 0.125 3.825 3486 Planarity : 0.014 0.300 3811 Dihedral : 16.262 136.983 8735 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 28.83 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.71 % Favored : 91.69 % Rotamer: Outliers : 6.11 % Allowed : 8.27 % Favored : 85.62 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.14), residues: 2659 helix: -2.61 (0.12), residues: 1309 sheet: -1.12 (0.35), residues: 221 loop : -2.29 (0.16), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.005 TRP E 32 HIS 0.026 0.004 HIS A 992 PHE 0.059 0.005 PHE A1289 TYR 0.093 0.005 TYR A 627 ARG 0.027 0.002 ARG A 594 Details of bonding type rmsd link_NAG-ASN : bond 0.22548 ( 14) link_NAG-ASN : angle 15.21183 ( 42) link_BETA1-4 : bond 0.09231 ( 7) link_BETA1-4 : angle 15.07335 ( 21) hydrogen bonds : bond 0.29005 ( 900) hydrogen bonds : angle 9.75425 ( 2567) SS BOND : bond 0.29054 ( 13) SS BOND : angle 17.17287 ( 26) link_BETA1-3 : bond 0.00268 ( 3) link_BETA1-3 : angle 11.53199 ( 9) covalent geometry : bond 0.01627 (22540) covalent geometry : angle 1.54349 (30516) Misc. bond : bond 0.58158 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 386 time to evaluate : 2.415 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 Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.2932 (OUTLIER) cc_final: 0.2115 (tm) REVERT: A 328 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8094 (mp) REVERT: A 1056 MET cc_start: 0.7883 (tpp) cc_final: 0.7674 (tpt) REVERT: A 1329 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8694 (tt) REVERT: E 82 TYR cc_start: 0.3128 (OUTLIER) cc_final: 0.0647 (p90) REVERT: F 133 LEU cc_start: 0.5338 (OUTLIER) cc_final: 0.4857 (mm) REVERT: F 197 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7995 (ttmm) REVERT: F 237 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8579 (mp) REVERT: F 315 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7376 (tpt90) REVERT: F 373 GLU cc_start: 0.6617 (tp30) cc_final: 0.6405 (tp30) REVERT: F 457 GLU cc_start: 0.7409 (mp0) cc_final: 0.7145 (mm-30) REVERT: F 480 ASN cc_start: 0.3673 (OUTLIER) cc_final: 0.3354 (t0) REVERT: F 490 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7847 (mtt) REVERT: F 497 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7496 (mp0) REVERT: F 530 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7394 (mt0) REVERT: F 782 TYR cc_start: 0.8085 (m-80) cc_final: 0.7818 (m-80) outliers start: 141 outliers final: 24 residues processed: 487 average time/residue: 1.0953 time to fit residues: 625.6441 Evaluate side-chains 271 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1276 MET Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1338 CYS Chi-restraints excluded: chain E residue 82 TYR Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 197 LYS Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 315 ARG Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 480 ASN Chi-restraints excluded: chain F residue 490 MET Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 530 GLN Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 853 CYS Chi-restraints excluded: chain F residue 864 MET Chi-restraints excluded: chain F residue 892 ILE Chi-restraints excluded: chain F residue 1062 CYS Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain B residue 156 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 225 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 209 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 127 optimal weight: 0.2980 chunk 155 optimal weight: 4.9990 chunk 242 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 143 ASN A 269 ASN A 327 ASN A 426 HIS A 982 GLN ** A 996 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1037 ASN ** A1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 GLN A1141 HIS A1383 ASN A1464 ASN E 38 HIS E 50 HIS F 56 GLN F 108 GLN F 228 ASN F 299 ASN F 308 HIS F 357 ASN F 426 GLN F 450 ASN F 511 ASN F 520 ASN F 542 ASN F 687 ASN ** F 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 773 ASN F1039 GLN ** F1066 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.210028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.137008 restraints weight = 33894.329| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.53 r_work: 0.3322 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22578 Z= 0.174 Angle : 0.883 17.740 30614 Z= 0.423 Chirality : 0.050 0.525 3486 Planarity : 0.006 0.061 3811 Dihedral : 13.542 110.003 3775 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.59 % Favored : 95.33 % Rotamer: Outliers : 4.37 % Allowed : 13.77 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.65 (0.15), residues: 2659 helix: -1.60 (0.13), residues: 1335 sheet: -1.11 (0.31), residues: 282 loop : -1.95 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 723 HIS 0.012 0.001 HIS F 867 PHE 0.024 0.002 PHE F 689 TYR 0.033 0.002 TYR F 629 ARG 0.007 0.001 ARG F 158 Details of bonding type rmsd link_NAG-ASN : bond 0.01207 ( 14) link_NAG-ASN : angle 6.87806 ( 42) link_BETA1-4 : bond 0.01418 ( 7) link_BETA1-4 : angle 4.43185 ( 21) hydrogen bonds : bond 0.05226 ( 900) hydrogen bonds : angle 5.24090 ( 2567) SS BOND : bond 0.00592 ( 13) SS BOND : angle 1.53061 ( 26) link_BETA1-3 : bond 0.01617 ( 3) link_BETA1-3 : angle 3.98731 ( 9) covalent geometry : bond 0.00371 (22540) covalent geometry : angle 0.83526 (30516) Misc. bond : bond 0.02550 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 267 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash REVERT: A 94 LEU cc_start: 0.7332 (tm) cc_final: 0.7091 (tt) REVERT: A 165 ARG cc_start: 0.6942 (ttm-80) cc_final: 0.6451 (mtp-110) REVERT: A 222 MET cc_start: 0.8868 (mtp) cc_final: 0.8604 (mtp) REVERT: A 257 ASN cc_start: 0.7189 (OUTLIER) cc_final: 0.6847 (t0) REVERT: A 367 MET cc_start: 0.1221 (ttt) cc_final: 0.0493 (tmm) REVERT: A 537 LYS cc_start: 0.6569 (mtpp) cc_final: 0.6259 (tptt) REVERT: A 686 MET cc_start: 0.2452 (ttp) cc_final: 0.0656 (mmt) REVERT: A 806 LEU cc_start: 0.6596 (OUTLIER) cc_final: 0.5867 (pp) REVERT: A 807 LEU cc_start: 0.7798 (mp) cc_final: 0.7539 (mt) REVERT: A 912 LYS cc_start: 0.6515 (tmtt) cc_final: 0.6013 (pptt) REVERT: A 922 PHE cc_start: 0.2350 (OUTLIER) cc_final: 0.1375 (t80) REVERT: A 928 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8299 (tp) REVERT: A 1243 LEU cc_start: 0.8504 (tt) cc_final: 0.8246 (mp) REVERT: A 1314 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9064 (tp) REVERT: A 1329 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8896 (tt) REVERT: A 1366 MET cc_start: 0.9135 (mtp) cc_final: 0.8891 (mtp) REVERT: E 142 MET cc_start: 0.5022 (OUTLIER) cc_final: 0.4728 (mpt) REVERT: E 216 MET cc_start: 0.4489 (tpt) cc_final: 0.4189 (ttm) REVERT: F 34 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6916 (tttt) REVERT: F 40 MET cc_start: 0.8082 (ptt) cc_final: 0.7783 (ptt) REVERT: F 237 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8709 (mp) REVERT: F 315 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8269 (tpt90) REVERT: F 361 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8327 (mtt) REVERT: F 379 ASN cc_start: 0.8109 (p0) cc_final: 0.7303 (p0) REVERT: F 391 VAL cc_start: 0.9095 (m) cc_final: 0.8832 (t) REVERT: F 457 GLU cc_start: 0.7679 (mp0) cc_final: 0.7243 (mm-30) REVERT: F 497 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8606 (mp0) REVERT: F 530 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7408 (mt0) REVERT: F 544 ARG cc_start: 0.7961 (mmm160) cc_final: 0.7737 (mtp85) REVERT: F 722 TYR cc_start: 0.8066 (t80) cc_final: 0.7750 (t80) REVERT: F 782 TYR cc_start: 0.8529 (m-80) cc_final: 0.8180 (m-80) outliers start: 101 outliers final: 30 residues processed: 337 average time/residue: 1.0444 time to fit residues: 418.5099 Evaluate side-chains 238 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 922 PHE Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1373 ILE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 315 ARG Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 530 GLN Chi-restraints excluded: chain F residue 571 ASP Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 853 CYS Chi-restraints excluded: chain F residue 864 MET Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain B residue 156 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 218 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 164 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 240 optimal weight: 0.0170 chunk 232 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 254 optimal weight: 0.7980 chunk 187 optimal weight: 2.9990 chunk 122 optimal weight: 0.0020 overall best weight: 0.7228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 649 ASN A 996 HIS ** A1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 GLN F 597 GLN F 679 ASN F1066 ASN C 294 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.208163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.135330 restraints weight = 33197.570| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.70 r_work: 0.3302 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22578 Z= 0.140 Angle : 0.728 17.196 30614 Z= 0.354 Chirality : 0.046 0.478 3486 Planarity : 0.005 0.054 3811 Dihedral : 11.506 106.947 3740 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.00 % Favored : 94.92 % Rotamer: Outliers : 4.03 % Allowed : 15.37 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.15), residues: 2659 helix: -0.83 (0.13), residues: 1360 sheet: -0.65 (0.33), residues: 238 loop : -1.76 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1258 HIS 0.008 0.001 HIS E 31 PHE 0.029 0.001 PHE E 146 TYR 0.029 0.001 TYR F 629 ARG 0.006 0.001 ARG F 158 Details of bonding type rmsd link_NAG-ASN : bond 0.00805 ( 14) link_NAG-ASN : angle 5.30389 ( 42) link_BETA1-4 : bond 0.01195 ( 7) link_BETA1-4 : angle 3.13509 ( 21) hydrogen bonds : bond 0.04290 ( 900) hydrogen bonds : angle 4.63077 ( 2567) SS BOND : bond 0.00689 ( 13) SS BOND : angle 1.63870 ( 26) link_BETA1-3 : bond 0.01132 ( 3) link_BETA1-3 : angle 3.31572 ( 9) covalent geometry : bond 0.00304 (22540) covalent geometry : angle 0.69371 (30516) Misc. bond : bond 0.01503 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 233 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.7511 (tm) cc_final: 0.7298 (tt) REVERT: A 165 ARG cc_start: 0.6993 (ttm-80) cc_final: 0.6548 (mtp-110) REVERT: A 222 MET cc_start: 0.9039 (mtp) cc_final: 0.8812 (mtp) REVERT: A 330 LEU cc_start: 0.7986 (tp) cc_final: 0.7751 (mt) REVERT: A 367 MET cc_start: 0.0999 (ttt) cc_final: 0.0466 (ttp) REVERT: A 686 MET cc_start: 0.2351 (ttp) cc_final: 0.0699 (mmt) REVERT: A 851 MET cc_start: 0.3114 (tpt) cc_final: 0.2200 (mtp) REVERT: A 912 LYS cc_start: 0.6471 (tmtt) cc_final: 0.5983 (pptt) REVERT: A 1170 LEU cc_start: 0.6718 (mt) cc_final: 0.6421 (mm) REVERT: A 1243 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8247 (OUTLIER) REVERT: A 1246 LEU cc_start: 0.7713 (mm) cc_final: 0.7421 (mp) REVERT: A 1314 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9134 (tp) REVERT: E 106 SER cc_start: 0.4093 (OUTLIER) cc_final: 0.3813 (t) REVERT: E 142 MET cc_start: 0.4764 (OUTLIER) cc_final: 0.4417 (mpt) REVERT: F 34 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7095 (tttt) REVERT: F 315 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8218 (tpt90) REVERT: F 361 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8243 (mtt) REVERT: F 379 ASN cc_start: 0.8166 (p0) cc_final: 0.7420 (p0) REVERT: F 391 VAL cc_start: 0.9131 (m) cc_final: 0.8865 (t) REVERT: F 457 GLU cc_start: 0.7856 (mp0) cc_final: 0.7356 (mm-30) REVERT: F 497 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8813 (mp0) REVERT: F 544 ARG cc_start: 0.7982 (mmm160) cc_final: 0.7747 (mtp85) REVERT: F 722 TYR cc_start: 0.8177 (t80) cc_final: 0.7881 (t80) REVERT: F 858 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7543 (p0) REVERT: F 1024 LYS cc_start: 0.7861 (ttmt) cc_final: 0.7008 (tptt) outliers start: 93 outliers final: 29 residues processed: 295 average time/residue: 1.1006 time to fit residues: 385.7653 Evaluate side-chains 226 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1067 THR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 315 ARG Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 853 CYS Chi-restraints excluded: chain F residue 858 ASP Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 293 MET Chi-restraints excluded: chain C residue 433 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 103 optimal weight: 0.0980 chunk 74 optimal weight: 2.9990 chunk 253 optimal weight: 9.9990 chunk 144 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 243 optimal weight: 1.9990 chunk 260 optimal weight: 20.0000 chunk 209 optimal weight: 0.9990 chunk 247 optimal weight: 50.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 269 ASN A1069 GLN ** A1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.207125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.148565 restraints weight = 37159.202| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.25 r_work: 0.3286 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22578 Z= 0.129 Angle : 0.682 17.108 30614 Z= 0.330 Chirality : 0.045 0.394 3486 Planarity : 0.004 0.074 3811 Dihedral : 10.341 106.521 3726 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.55 % Favored : 95.41 % Rotamer: Outliers : 3.46 % Allowed : 16.20 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.16), residues: 2659 helix: -0.27 (0.14), residues: 1359 sheet: -0.36 (0.34), residues: 223 loop : -1.65 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1258 HIS 0.008 0.001 HIS E 31 PHE 0.025 0.001 PHE E 146 TYR 0.026 0.001 TYR F 629 ARG 0.006 0.000 ARG A1389 Details of bonding type rmsd link_NAG-ASN : bond 0.00623 ( 14) link_NAG-ASN : angle 4.82002 ( 42) link_BETA1-4 : bond 0.00989 ( 7) link_BETA1-4 : angle 2.97551 ( 21) hydrogen bonds : bond 0.03773 ( 900) hydrogen bonds : angle 4.39126 ( 2567) SS BOND : bond 0.00200 ( 13) SS BOND : angle 1.51386 ( 26) link_BETA1-3 : bond 0.01043 ( 3) link_BETA1-3 : angle 3.19993 ( 9) covalent geometry : bond 0.00285 (22540) covalent geometry : angle 0.65096 (30516) Misc. bond : bond 0.00493 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 210 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash REVERT: A 165 ARG cc_start: 0.7020 (ttm-80) cc_final: 0.6647 (mtp-110) REVERT: A 367 MET cc_start: 0.1244 (ttt) cc_final: 0.0575 (ttp) REVERT: A 376 MET cc_start: 0.0016 (tpt) cc_final: -0.0210 (tpt) REVERT: A 493 MET cc_start: 0.3667 (mmm) cc_final: 0.3305 (mmp) REVERT: A 686 MET cc_start: 0.2329 (ttp) cc_final: 0.0573 (mmt) REVERT: A 806 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6207 (pp) REVERT: A 851 MET cc_start: 0.3649 (tpt) cc_final: 0.2621 (mtp) REVERT: A 912 LYS cc_start: 0.6449 (tmtt) cc_final: 0.5905 (pptt) REVERT: A 1170 LEU cc_start: 0.6874 (mt) cc_final: 0.6576 (mm) REVERT: A 1243 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8296 (OUTLIER) REVERT: A 1246 LEU cc_start: 0.7756 (mm) cc_final: 0.7500 (mp) REVERT: A 1314 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9118 (tp) REVERT: A 1329 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8902 (tt) REVERT: E 106 SER cc_start: 0.4314 (OUTLIER) cc_final: 0.4039 (t) REVERT: E 142 MET cc_start: 0.5049 (OUTLIER) cc_final: 0.4753 (mpt) REVERT: F 34 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7232 (tttt) REVERT: F 361 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8143 (mtt) REVERT: F 379 ASN cc_start: 0.8151 (p0) cc_final: 0.7469 (p0) REVERT: F 391 VAL cc_start: 0.9102 (m) cc_final: 0.8863 (t) REVERT: F 457 GLU cc_start: 0.7908 (mp0) cc_final: 0.7465 (mm-30) REVERT: F 497 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8660 (mp0) REVERT: F 505 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7479 (ppt-90) REVERT: F 530 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7577 (mt0) REVERT: F 674 LYS cc_start: 0.8091 (mtmm) cc_final: 0.7687 (mmtm) REVERT: F 858 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7657 (p0) REVERT: F 1024 LYS cc_start: 0.7957 (ttmt) cc_final: 0.7006 (tttt) outliers start: 80 outliers final: 33 residues processed: 268 average time/residue: 1.1136 time to fit residues: 354.3111 Evaluate side-chains 223 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1067 THR Chi-restraints excluded: chain A residue 1068 PHE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1263 SER Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 142 MET Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 505 ARG Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 530 GLN Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 743 ILE Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 853 CYS Chi-restraints excluded: chain F residue 858 ASP Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain C residue 433 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.1606 > 50: distance: 55 - 96: 21.441 distance: 84 - 88: 22.988 distance: 88 - 89: 33.404 distance: 89 - 90: 41.246 distance: 89 - 92: 35.834 distance: 90 - 96: 48.355 distance: 92 - 93: 31.923 distance: 93 - 95: 38.602 distance: 96 - 97: 24.837 distance: 97 - 98: 41.130 distance: 97 - 100: 36.772 distance: 98 - 99: 4.394 distance: 98 - 104: 3.054 distance: 100 - 101: 35.854 distance: 101 - 102: 25.387 distance: 101 - 103: 26.618 distance: 104 - 105: 41.014 distance: 105 - 106: 69.161 distance: 105 - 108: 33.970 distance: 106 - 107: 25.267 distance: 106 - 112: 62.408 distance: 108 - 109: 42.931 distance: 109 - 110: 3.108 distance: 109 - 111: 8.336 distance: 112 - 113: 42.755 distance: 113 - 114: 20.562 distance: 113 - 116: 13.399 distance: 114 - 115: 38.486 distance: 114 - 121: 30.028 distance: 116 - 117: 48.869 distance: 117 - 118: 42.555 distance: 118 - 119: 21.557 distance: 118 - 120: 21.885 distance: 121 - 122: 36.690 distance: 122 - 123: 37.066 distance: 122 - 125: 33.935 distance: 123 - 124: 38.841 distance: 123 - 129: 36.833 distance: 125 - 126: 35.826 distance: 126 - 127: 31.852 distance: 126 - 128: 32.844 distance: 130 - 131: 27.903 distance: 130 - 133: 55.067 distance: 131 - 132: 27.486 distance: 131 - 138: 47.938 distance: 133 - 134: 55.835 distance: 134 - 135: 41.095 distance: 135 - 136: 26.272 distance: 135 - 137: 58.757 distance: 138 - 139: 39.788 distance: 139 - 140: 35.667 distance: 139 - 142: 32.885 distance: 140 - 141: 28.693 distance: 140 - 146: 16.595 distance: 141 - 168: 28.421 distance: 142 - 143: 10.972 distance: 143 - 144: 44.794 distance: 143 - 145: 57.677 distance: 146 - 147: 19.157 distance: 147 - 148: 14.103 distance: 147 - 150: 38.855 distance: 148 - 149: 18.545 distance: 148 - 155: 28.498 distance: 149 - 174: 23.053 distance: 150 - 151: 55.978 distance: 151 - 152: 32.677 distance: 152 - 153: 46.731 distance: 152 - 154: 42.272 distance: 155 - 156: 11.284 distance: 156 - 157: 3.670 distance: 156 - 159: 15.550 distance: 157 - 158: 8.757 distance: 157 - 163: 26.058 distance: 159 - 160: 4.285 distance: 160 - 161: 27.695 distance: 160 - 162: 20.925 distance: 163 - 164: 16.014 distance: 164 - 165: 20.403 distance: 164 - 167: 32.833 distance: 165 - 166: 19.373 distance: 165 - 168: 9.705 distance: 166 - 189: 19.248