Starting phenix.real_space_refine on Thu Mar 5 13:39:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jp5_9866/03_2026/6jp5_9866.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jp5_9866/03_2026/6jp5_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 { model { file = "/net/cci-nas-00/data/ceres_data/6jp5_9866/03_2026/6jp5_9866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jp5_9866/03_2026/6jp5_9866.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6jp5_9866/03_2026/6jp5_9866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jp5_9866/03_2026/6jp5_9866.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'TRP:plan': 1} 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, 'HIS:plan': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1} 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: {'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} 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-2': 1, '3PE:plan-1': 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: 6.32, per 1000 atoms: 0.29 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: 1.75 Conformation dependent library (CDL) restraints added in 1.2 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: 0.81 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: 4.05 Time building geometry restraints manager: 2.42 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: 2.300 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.540 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.460 ------------------------------------------------------------------------------- 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 : 28.95 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.027 0.002 ARG A 594 TYR 0.093 0.005 TYR A 627 PHE 0.059 0.005 PHE A1289 TRP 0.044 0.005 TRP E 32 HIS 0.026 0.004 HIS A 992 Details of bonding type rmsd covalent geometry : bond 0.01627 (22540) covalent geometry : angle 1.54349 (30516) SS BOND : bond 0.29054 ( 13) SS BOND : angle 17.17287 ( 26) hydrogen bonds : bond 0.29005 ( 900) hydrogen bonds : angle 9.75425 ( 2567) Misc. bond : bond 0.58158 ( 1) link_BETA1-3 : bond 0.00268 ( 3) link_BETA1-3 : angle 11.53199 ( 9) link_BETA1-4 : bond 0.09231 ( 7) link_BETA1-4 : angle 15.07335 ( 21) link_NAG-ASN : bond 0.22548 ( 14) link_NAG-ASN : angle 15.21183 ( 42) *********************** 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 : 0.718 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: 0.4991 time to fit residues: 284.2183 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 : 0.554 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.0070 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 40.0000 chunk 183 optimal weight: 0.5980 chunk 111 optimal weight: 0.8980 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 A1383 ASN A1464 ASN E 38 HIS E 50 HIS E 160 GLN F 56 GLN F 108 GLN F 228 ASN F 297 ASN F 299 ASN F 308 HIS F 357 ASN F 395 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 F1065 ASN ** F1066 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.210344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.137905 restraints weight = 33991.944| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 3.69 r_work: 0.3338 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 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 = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22578 Z= 0.171 Angle : 0.883 17.640 30614 Z= 0.423 Chirality : 0.050 0.554 3486 Planarity : 0.006 0.062 3811 Dihedral : 13.653 105.399 3775 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.70 % Favored : 95.22 % Rotamer: Outliers : 4.33 % Allowed : 13.90 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.15), residues: 2659 helix: -1.59 (0.13), residues: 1332 sheet: -0.93 (0.31), residues: 279 loop : -1.96 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 158 TYR 0.032 0.002 TYR F 629 PHE 0.023 0.002 PHE E 146 TRP 0.024 0.002 TRP F 723 HIS 0.012 0.001 HIS F 867 Details of bonding type rmsd covalent geometry : bond 0.00361 (22540) covalent geometry : angle 0.83191 (30516) SS BOND : bond 0.01432 ( 13) SS BOND : angle 1.39462 ( 26) hydrogen bonds : bond 0.05405 ( 900) hydrogen bonds : angle 5.29789 ( 2567) Misc. bond : bond 0.02669 ( 1) link_BETA1-3 : bond 0.01002 ( 3) link_BETA1-3 : angle 3.86327 ( 9) link_BETA1-4 : bond 0.01526 ( 7) link_BETA1-4 : angle 4.40817 ( 21) link_NAG-ASN : bond 0.00905 ( 14) link_NAG-ASN : angle 7.18519 ( 42) *********************** 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 363 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 263 time to evaluate : 0.607 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: 0.7249 (tm) cc_final: 0.7004 (tt) REVERT: A 165 ARG cc_start: 0.6900 (ttm-80) cc_final: 0.6440 (mtp-110) REVERT: A 222 MET cc_start: 0.8935 (mtp) cc_final: 0.8667 (mtp) REVERT: A 257 ASN cc_start: 0.7214 (OUTLIER) cc_final: 0.6852 (t0) REVERT: A 273 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8905 (p) REVERT: A 367 MET cc_start: 0.1135 (ttt) cc_final: 0.0463 (tmm) REVERT: A 537 LYS cc_start: 0.6589 (mtpp) cc_final: 0.6349 (tmtm) REVERT: A 686 MET cc_start: 0.2379 (ttp) cc_final: 0.0689 (mmt) REVERT: A 807 LEU cc_start: 0.7693 (mp) cc_final: 0.7307 (mt) REVERT: A 912 LYS cc_start: 0.6514 (tmtt) cc_final: 0.6016 (pptt) REVERT: A 922 PHE cc_start: 0.2553 (OUTLIER) cc_final: 0.2303 (t80) REVERT: A 928 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8271 (tp) REVERT: A 1243 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8196 (mp) REVERT: A 1287 GLN cc_start: 0.8948 (tp-100) cc_final: 0.8676 (tt0) REVERT: A 1314 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9089 (tp) REVERT: A 1329 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8927 (tt) REVERT: E 55 ARG cc_start: 0.2978 (OUTLIER) cc_final: 0.2391 (mtm180) REVERT: E 216 MET cc_start: 0.4265 (tpt) cc_final: 0.3862 (ttm) REVERT: F 34 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6932 (tttt) REVERT: F 40 MET cc_start: 0.8070 (ptt) cc_final: 0.7774 (ptt) REVERT: F 197 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8424 (ttmm) REVERT: F 237 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8668 (mp) REVERT: F 315 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8217 (tpt90) REVERT: F 361 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8274 (mtt) REVERT: F 379 ASN cc_start: 0.8004 (p0) cc_final: 0.7280 (p0) REVERT: F 457 GLU cc_start: 0.7585 (mp0) cc_final: 0.7183 (mm-30) REVERT: F 497 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8446 (mp0) REVERT: F 530 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.6949 (mp-120) REVERT: F 722 TYR cc_start: 0.7985 (t80) cc_final: 0.7758 (t80) REVERT: F 782 TYR cc_start: 0.8526 (m-80) cc_final: 0.8188 (m-80) outliers start: 100 outliers final: 33 residues processed: 332 average time/residue: 0.4711 time to fit residues: 185.6082 Evaluate side-chains 250 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 203 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 273 THR Chi-restraints excluded: chain A residue 275 PHE 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 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 1065 ILE Chi-restraints excluded: chain A residue 1243 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 1338 CYS Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 106 SER 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 197 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 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 892 ILE 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 195 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 196 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 194 optimal weight: 7.9990 chunk 257 optimal weight: 0.9980 chunk 4 optimal weight: 0.0570 overall best weight: 0.7898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 996 HIS ** A1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 GLN F 597 GLN F 679 ASN F1065 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 = 0.4419 r_free = 0.4419 target = 0.207913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.136084 restraints weight = 33856.355| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 3.79 r_work: 0.3282 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22578 Z= 0.145 Angle : 0.739 17.264 30614 Z= 0.359 Chirality : 0.047 0.478 3486 Planarity : 0.005 0.052 3811 Dihedral : 11.702 107.873 3748 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.82 % Favored : 95.11 % Rotamer: Outliers : 4.24 % Allowed : 15.24 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.15), residues: 2659 helix: -0.85 (0.13), residues: 1357 sheet: -0.66 (0.33), residues: 244 loop : -1.75 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 158 TYR 0.028 0.002 TYR F 629 PHE 0.028 0.001 PHE E 146 TRP 0.021 0.002 TRP A1258 HIS 0.008 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00319 (22540) covalent geometry : angle 0.70258 (30516) SS BOND : bond 0.00355 ( 13) SS BOND : angle 1.96686 ( 26) hydrogen bonds : bond 0.04326 ( 900) hydrogen bonds : angle 4.67950 ( 2567) Misc. bond : bond 0.01052 ( 1) link_BETA1-3 : bond 0.00961 ( 3) link_BETA1-3 : angle 3.40347 ( 9) link_BETA1-4 : bond 0.01197 ( 7) link_BETA1-4 : angle 3.25179 ( 21) link_NAG-ASN : bond 0.00830 ( 14) link_NAG-ASN : angle 5.44713 ( 42) *********************** 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 333 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 235 time to evaluate : 0.857 Fit side-chains 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 94 LEU cc_start: 0.7481 (tm) cc_final: 0.7238 (tt) REVERT: A 165 ARG cc_start: 0.6982 (ttm-80) cc_final: 0.6494 (mtp-110) REVERT: A 222 MET cc_start: 0.9006 (mtp) cc_final: 0.8708 (mtp) REVERT: A 273 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.8971 (p) REVERT: A 330 LEU cc_start: 0.8031 (tp) cc_final: 0.7791 (mt) REVERT: A 367 MET cc_start: 0.1032 (ttt) cc_final: 0.0400 (tmt) REVERT: A 686 MET cc_start: 0.2340 (ttp) cc_final: 0.0687 (mmt) REVERT: A 806 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.5908 (pp) REVERT: A 851 MET cc_start: 0.3143 (tpt) cc_final: 0.2188 (mtp) REVERT: A 912 LYS cc_start: 0.6465 (tmtt) cc_final: 0.5980 (pptt) REVERT: A 922 PHE cc_start: 0.2463 (OUTLIER) cc_final: 0.1593 (t80) REVERT: A 984 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8441 (pt0) REVERT: A 1243 LEU cc_start: 0.8445 (tt) cc_final: 0.8190 (OUTLIER) REVERT: A 1246 LEU cc_start: 0.7664 (mm) cc_final: 0.7424 (mp) REVERT: A 1314 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9126 (tp) REVERT: E 142 MET cc_start: 0.5039 (OUTLIER) cc_final: 0.4788 (mmt) REVERT: F 34 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7094 (tttt) REVERT: F 315 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8272 (tpt90) REVERT: F 361 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8231 (mtt) REVERT: F 379 ASN cc_start: 0.8101 (p0) cc_final: 0.7400 (p0) REVERT: F 391 VAL cc_start: 0.9127 (m) cc_final: 0.8857 (t) REVERT: F 457 GLU cc_start: 0.7832 (mp0) cc_final: 0.7395 (mm-30) REVERT: F 497 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8771 (mp0) REVERT: F 544 ARG cc_start: 0.8003 (mmm160) cc_final: 0.7754 (mtp85) REVERT: F 722 TYR cc_start: 0.8181 (t80) cc_final: 0.7939 (t80) REVERT: F 858 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7597 (p0) REVERT: F 1024 LYS cc_start: 0.7849 (ttmt) cc_final: 0.6989 (tttt) outliers start: 98 outliers final: 30 residues processed: 301 average time/residue: 0.4953 time to fit residues: 176.1413 Evaluate side-chains 229 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 190 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 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 806 LEU Chi-restraints excluded: chain A residue 922 PHE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1067 THR Chi-restraints excluded: chain A residue 1276 MET 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 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 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 F residue 1065 ASN 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 5 optimal weight: 0.2980 chunk 142 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 80 optimal weight: 0.0770 chunk 191 optimal weight: 2.9990 chunk 213 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 A1069 GLN ** A1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1383 ASN C 458 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.208038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.151289 restraints weight = 49380.948| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 3.07 r_work: 0.3270 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22578 Z= 0.122 Angle : 0.684 17.423 30614 Z= 0.330 Chirality : 0.045 0.402 3486 Planarity : 0.004 0.055 3811 Dihedral : 10.504 105.143 3727 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.59 % Favored : 95.37 % Rotamer: Outliers : 3.46 % Allowed : 16.85 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.16), residues: 2659 helix: -0.28 (0.14), residues: 1359 sheet: -0.66 (0.32), residues: 255 loop : -1.59 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 158 TYR 0.026 0.001 TYR F 629 PHE 0.024 0.001 PHE E 146 TRP 0.014 0.001 TRP A1258 HIS 0.005 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00261 (22540) covalent geometry : angle 0.65186 (30516) SS BOND : bond 0.00186 ( 13) SS BOND : angle 1.53466 ( 26) hydrogen bonds : bond 0.03693 ( 900) hydrogen bonds : angle 4.42475 ( 2567) Misc. bond : bond 0.00059 ( 1) link_BETA1-3 : bond 0.01002 ( 3) link_BETA1-3 : angle 3.17145 ( 9) link_BETA1-4 : bond 0.01000 ( 7) link_BETA1-4 : angle 3.03330 ( 21) link_NAG-ASN : bond 0.00635 ( 14) link_NAG-ASN : angle 4.94060 ( 42) *********************** 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 289 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 209 time to evaluate : 0.768 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 165 ARG cc_start: 0.6953 (ttm-80) cc_final: 0.6610 (mtp-110) REVERT: A 367 MET cc_start: 0.1677 (ttt) cc_final: 0.0740 (tmt) REVERT: A 493 MET cc_start: 0.3773 (mmm) cc_final: 0.3354 (mmp) REVERT: A 686 MET cc_start: 0.2166 (ttp) cc_final: 0.0213 (mmt) REVERT: A 806 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6240 (pp) REVERT: A 851 MET cc_start: 0.3573 (tpt) cc_final: 0.2635 (mtp) REVERT: A 912 LYS cc_start: 0.6399 (tmtt) cc_final: 0.5898 (pptt) REVERT: A 928 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8386 (tp) REVERT: A 1170 LEU cc_start: 0.6860 (mt) cc_final: 0.6557 (mm) REVERT: A 1246 LEU cc_start: 0.7714 (mm) cc_final: 0.7500 (mp) REVERT: A 1249 ARG cc_start: 0.5922 (OUTLIER) cc_final: 0.4693 (ptm160) REVERT: A 1314 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9114 (tp) REVERT: E 55 ARG cc_start: 0.2967 (OUTLIER) cc_final: 0.2252 (mtm180) REVERT: E 106 SER cc_start: 0.4187 (OUTLIER) cc_final: 0.3923 (t) REVERT: E 131 LYS cc_start: 0.5258 (OUTLIER) cc_final: 0.5045 (mtpp) REVERT: E 142 MET cc_start: 0.5430 (OUTLIER) cc_final: 0.5076 (mpt) REVERT: F 34 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7268 (tttt) REVERT: F 361 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8048 (mtt) REVERT: F 379 ASN cc_start: 0.7921 (p0) cc_final: 0.7268 (p0) REVERT: F 391 VAL cc_start: 0.9057 (m) cc_final: 0.8834 (t) REVERT: F 457 GLU cc_start: 0.7777 (mp0) cc_final: 0.7408 (mm-30) REVERT: F 490 MET cc_start: 0.8934 (tpp) cc_final: 0.8716 (mmt) REVERT: F 497 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8650 (mp0) REVERT: F 530 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7453 (mt0) REVERT: F 674 LYS cc_start: 0.8017 (mtmm) cc_final: 0.7644 (mmtm) REVERT: F 858 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7527 (p0) REVERT: F 1024 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.6968 (tttt) REVERT: F 1071 TYR cc_start: 0.7928 (p90) cc_final: 0.7667 (p90) outliers start: 80 outliers final: 29 residues processed: 263 average time/residue: 0.4700 time to fit residues: 146.2323 Evaluate side-chains 227 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 185 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 245 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 928 ILE 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 1068 PHE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1249 ARG Chi-restraints excluded: chain A residue 1263 SER Chi-restraints excluded: chain A residue 1276 MET Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 55 ARG Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 131 LYS 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 361 MET Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 451 VAL 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 853 CYS Chi-restraints excluded: chain F residue 858 ASP Chi-restraints excluded: chain F residue 1024 LYS 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 ************** Weight determination summary: number of chunks: 267 random chunks: chunk 96 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 242 optimal weight: 0.0770 chunk 176 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 143 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 213 optimal weight: 0.6980 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN ** A1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 ASN A1383 ASN F 297 ASN F 679 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.205157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.129691 restraints weight = 32977.214| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.49 r_work: 0.3221 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22578 Z= 0.145 Angle : 0.671 13.092 30614 Z= 0.330 Chirality : 0.045 0.380 3486 Planarity : 0.005 0.070 3811 Dihedral : 9.839 107.259 3722 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.00 % Favored : 94.96 % Rotamer: Outliers : 3.46 % Allowed : 16.80 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.16), residues: 2659 helix: 0.02 (0.14), residues: 1374 sheet: -0.41 (0.34), residues: 247 loop : -1.61 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 544 TYR 0.022 0.002 TYR F 629 PHE 0.025 0.001 PHE E 146 TRP 0.014 0.001 TRP A1258 HIS 0.007 0.001 HIS A 992 Details of bonding type rmsd covalent geometry : bond 0.00336 (22540) covalent geometry : angle 0.65316 (30516) SS BOND : bond 0.00216 ( 13) SS BOND : angle 1.53988 ( 26) hydrogen bonds : bond 0.03779 ( 900) hydrogen bonds : angle 4.28591 ( 2567) Misc. bond : bond 0.00084 ( 1) link_BETA1-3 : bond 0.00891 ( 3) link_BETA1-3 : angle 3.20979 ( 9) link_BETA1-4 : bond 0.00967 ( 7) link_BETA1-4 : angle 2.89587 ( 21) link_NAG-ASN : bond 0.00458 ( 14) link_NAG-ASN : angle 3.22398 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 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 277 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 197 time to evaluate : 0.726 Fit side-chains 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: 0.7051 (ttm-80) cc_final: 0.6750 (mtp-110) REVERT: A 367 MET cc_start: 0.0958 (ttt) cc_final: 0.0464 (tmt) REVERT: A 493 MET cc_start: 0.3452 (mmm) cc_final: 0.3149 (mmp) REVERT: A 686 MET cc_start: 0.2572 (ttp) cc_final: 0.1002 (mmt) REVERT: A 806 LEU cc_start: 0.6593 (OUTLIER) cc_final: 0.6020 (pp) REVERT: A 851 MET cc_start: 0.3345 (tpt) cc_final: 0.2571 (mtp) REVERT: A 912 LYS cc_start: 0.6444 (tmtt) cc_final: 0.5946 (pptt) REVERT: A 928 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8312 (tp) REVERT: A 984 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8542 (pt0) REVERT: A 1057 MET cc_start: 0.8021 (mtt) cc_final: 0.7659 (mtt) REVERT: A 1104 LYS cc_start: 0.5289 (OUTLIER) cc_final: 0.4783 (tppt) REVERT: A 1170 LEU cc_start: 0.6836 (mt) cc_final: 0.6563 (mm) REVERT: A 1246 LEU cc_start: 0.7422 (mm) cc_final: 0.7210 (mp) REVERT: A 1249 ARG cc_start: 0.5715 (ptm160) cc_final: 0.4551 (ptm160) REVERT: A 1314 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9152 (tp) REVERT: A 1329 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8973 (tt) REVERT: A 1350 TYR cc_start: 0.8867 (m-80) cc_final: 0.8422 (m-80) REVERT: A 1385 ASP cc_start: 0.7080 (m-30) cc_final: 0.6713 (p0) REVERT: E 1 MET cc_start: 0.3464 (tpt) cc_final: 0.3041 (tpp) REVERT: E 106 SER cc_start: 0.4376 (OUTLIER) cc_final: 0.4138 (t) REVERT: E 129 PHE cc_start: 0.5219 (OUTLIER) cc_final: 0.5006 (t80) REVERT: F 34 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7229 (tttt) REVERT: F 59 ASP cc_start: 0.8252 (t70) cc_final: 0.8023 (m-30) REVERT: F 361 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8222 (mtt) REVERT: F 379 ASN cc_start: 0.8226 (p0) cc_final: 0.7833 (p0) REVERT: F 391 VAL cc_start: 0.9133 (m) cc_final: 0.8885 (t) REVERT: F 457 GLU cc_start: 0.7943 (mp0) cc_final: 0.7472 (mm-30) REVERT: F 497 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8617 (mp0) REVERT: F 505 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7741 (ppt-90) REVERT: F 593 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8463 (pp) REVERT: F 648 SER cc_start: 0.7958 (t) cc_final: 0.7698 (p) REVERT: F 782 TYR cc_start: 0.8352 (m-80) cc_final: 0.7898 (m-80) REVERT: F 858 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7776 (p0) REVERT: F 1024 LYS cc_start: 0.7946 (ttmt) cc_final: 0.6869 (tttt) outliers start: 80 outliers final: 34 residues processed: 255 average time/residue: 0.4807 time to fit residues: 143.9943 Evaluate side-chains 226 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 273 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1067 THR Chi-restraints excluded: chain A residue 1068 PHE Chi-restraints excluded: chain A residue 1104 LYS Chi-restraints excluded: chain A residue 1146 MET 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 A residue 1384 PHE Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 215 CYS 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 270 THR Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 505 ARG Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 684 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 37 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 chunk 250 optimal weight: 0.0670 chunk 6 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 171 optimal weight: 0.8980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1383 ASN F 297 ASN F 679 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.205135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.143446 restraints weight = 34679.356| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.09 r_work: 0.3285 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22578 Z= 0.126 Angle : 0.637 13.638 30614 Z= 0.313 Chirality : 0.044 0.357 3486 Planarity : 0.004 0.052 3811 Dihedral : 9.494 106.821 3720 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.51 % Favored : 95.45 % Rotamer: Outliers : 2.90 % Allowed : 17.45 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.16), residues: 2659 helix: 0.38 (0.14), residues: 1360 sheet: -0.09 (0.34), residues: 238 loop : -1.61 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 158 TYR 0.018 0.001 TYR A 117 PHE 0.023 0.001 PHE E 146 TRP 0.010 0.001 TRP A1258 HIS 0.004 0.001 HIS A 992 Details of bonding type rmsd covalent geometry : bond 0.00286 (22540) covalent geometry : angle 0.62136 (30516) SS BOND : bond 0.00202 ( 13) SS BOND : angle 1.45285 ( 26) hydrogen bonds : bond 0.03463 ( 900) hydrogen bonds : angle 4.16064 ( 2567) Misc. bond : bond 0.00042 ( 1) link_BETA1-3 : bond 0.00836 ( 3) link_BETA1-3 : angle 3.25496 ( 9) link_BETA1-4 : bond 0.00897 ( 7) link_BETA1-4 : angle 2.67330 ( 21) link_NAG-ASN : bond 0.00473 ( 14) link_NAG-ASN : angle 2.86605 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 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 263 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 196 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash REVERT: A 165 ARG cc_start: 0.6996 (ttm-80) cc_final: 0.6716 (mtp-110) REVERT: A 367 MET cc_start: 0.1251 (ttt) cc_final: 0.0618 (tmt) REVERT: A 479 MET cc_start: 0.4798 (ppp) cc_final: 0.4474 (ppp) REVERT: A 664 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7864 (tp) REVERT: A 686 MET cc_start: 0.2499 (ttp) cc_final: 0.0719 (mmt) REVERT: A 806 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6303 (pp) REVERT: A 851 MET cc_start: 0.3356 (tpt) cc_final: 0.2738 (mtp) REVERT: A 928 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8454 (tp) REVERT: A 983 MET cc_start: 0.9385 (pmm) cc_final: 0.9041 (ptp) REVERT: A 984 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8446 (pt0) REVERT: A 1170 LEU cc_start: 0.7036 (mt) cc_final: 0.6755 (mm) REVERT: A 1191 ILE cc_start: 0.7233 (OUTLIER) cc_final: 0.6960 (tt) REVERT: A 1246 LEU cc_start: 0.7655 (mm) cc_final: 0.7449 (mp) REVERT: A 1249 ARG cc_start: 0.5855 (ptm160) cc_final: 0.4526 (ptm160) REVERT: A 1329 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8896 (tt) REVERT: A 1350 TYR cc_start: 0.8903 (m-80) cc_final: 0.8418 (m-80) REVERT: A 1385 ASP cc_start: 0.7147 (m-30) cc_final: 0.6839 (p0) REVERT: A 1453 MET cc_start: 0.3481 (tpp) cc_final: 0.1427 (pp-130) REVERT: E 1 MET cc_start: 0.3308 (tpt) cc_final: 0.2934 (tpp) REVERT: E 106 SER cc_start: 0.4562 (OUTLIER) cc_final: 0.4345 (t) REVERT: E 129 PHE cc_start: 0.5369 (OUTLIER) cc_final: 0.4338 (t80) REVERT: E 142 MET cc_start: 0.5191 (mmt) cc_final: 0.4857 (mmt) REVERT: F 34 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.7333 (tttt) REVERT: F 361 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8187 (mtt) REVERT: F 379 ASN cc_start: 0.8099 (p0) cc_final: 0.7602 (p0) REVERT: F 391 VAL cc_start: 0.9117 (m) cc_final: 0.8895 (t) REVERT: F 457 GLU cc_start: 0.7972 (mp0) cc_final: 0.7530 (mm-30) REVERT: F 490 MET cc_start: 0.9169 (tpp) cc_final: 0.8925 (mmt) REVERT: F 497 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8580 (mp0) REVERT: F 505 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7704 (ppt-90) REVERT: F 530 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7378 (mp10) REVERT: F 749 LYS cc_start: 0.8209 (mppt) cc_final: 0.7347 (mtmp) REVERT: F 782 TYR cc_start: 0.8305 (m-80) cc_final: 0.7880 (m-80) REVERT: F 858 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7794 (p0) REVERT: F 1024 LYS cc_start: 0.8056 (ttmt) cc_final: 0.7087 (tttt) REVERT: F 1042 ASP cc_start: 0.8055 (p0) cc_final: 0.7549 (p0) outliers start: 67 outliers final: 32 residues processed: 242 average time/residue: 0.4873 time to fit residues: 138.8977 Evaluate side-chains 229 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 245 CYS 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 806 LEU Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1067 THR Chi-restraints excluded: chain A residue 1068 PHE Chi-restraints excluded: chain A residue 1146 MET Chi-restraints excluded: chain A residue 1191 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1263 SER Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 165 MET Chi-restraints excluded: chain E residue 215 CYS 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 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 530 GLN Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 858 ASP Chi-restraints excluded: chain F residue 997 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 223 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 0.1980 chunk 47 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 254 optimal weight: 0.2980 chunk 3 optimal weight: 3.9990 chunk 112 optimal weight: 0.1980 chunk 66 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 226 optimal weight: 0.9980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 GLN A1383 ASN F 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.205844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.136051 restraints weight = 41689.346| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 4.45 r_work: 0.3224 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22578 Z= 0.111 Angle : 0.621 14.281 30614 Z= 0.302 Chirality : 0.043 0.339 3486 Planarity : 0.004 0.055 3811 Dihedral : 9.043 105.423 3715 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.67 % Favored : 95.30 % Rotamer: Outliers : 2.38 % Allowed : 18.36 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.16), residues: 2659 helix: 0.74 (0.14), residues: 1349 sheet: -0.05 (0.34), residues: 248 loop : -1.50 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 158 TYR 0.016 0.001 TYR A 117 PHE 0.022 0.001 PHE E 146 TRP 0.019 0.001 TRP A 309 HIS 0.005 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00243 (22540) covalent geometry : angle 0.60574 (30516) SS BOND : bond 0.00159 ( 13) SS BOND : angle 1.34816 ( 26) hydrogen bonds : bond 0.03203 ( 900) hydrogen bonds : angle 4.03148 ( 2567) Misc. bond : bond 0.00013 ( 1) link_BETA1-3 : bond 0.00790 ( 3) link_BETA1-3 : angle 3.21596 ( 9) link_BETA1-4 : bond 0.00869 ( 7) link_BETA1-4 : angle 2.53724 ( 21) link_NAG-ASN : bond 0.00508 ( 14) link_NAG-ASN : angle 2.82336 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 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 245 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 190 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash REVERT: A 165 ARG cc_start: 0.7126 (ttm-80) cc_final: 0.6915 (mtp-110) REVERT: A 367 MET cc_start: 0.1175 (ttt) cc_final: 0.0456 (tmt) REVERT: A 479 MET cc_start: 0.4590 (ppp) cc_final: 0.4301 (ppp) REVERT: A 537 LYS cc_start: 0.6173 (mtpp) cc_final: 0.5954 (tptt) REVERT: A 686 MET cc_start: 0.2346 (ttp) cc_final: 0.0751 (mmt) REVERT: A 806 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6212 (pp) REVERT: A 851 MET cc_start: 0.3337 (tpt) cc_final: 0.2793 (mtp) REVERT: A 928 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8450 (tp) REVERT: A 1170 LEU cc_start: 0.6845 (mt) cc_final: 0.6573 (mm) REVERT: A 1246 LEU cc_start: 0.7550 (mm) cc_final: 0.7325 (mp) REVERT: A 1249 ARG cc_start: 0.5611 (ptm160) cc_final: 0.4472 (ptm160) REVERT: A 1350 TYR cc_start: 0.8773 (m-80) cc_final: 0.8296 (m-80) REVERT: A 1385 ASP cc_start: 0.7093 (m-30) cc_final: 0.6801 (p0) REVERT: A 1453 MET cc_start: 0.3582 (tpp) cc_final: 0.1509 (pp-130) REVERT: E 1 MET cc_start: 0.3577 (tpt) cc_final: 0.3248 (tpp) REVERT: E 129 PHE cc_start: 0.5398 (OUTLIER) cc_final: 0.4385 (t80) REVERT: E 142 MET cc_start: 0.4892 (mmt) cc_final: 0.4421 (mmt) REVERT: E 152 PHE cc_start: 0.5068 (t80) cc_final: 0.4846 (t80) REVERT: F 361 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8039 (mtt) REVERT: F 379 ASN cc_start: 0.7886 (p0) cc_final: 0.7381 (p0) REVERT: F 457 GLU cc_start: 0.7866 (mp0) cc_final: 0.7571 (mm-30) REVERT: F 490 MET cc_start: 0.8997 (tpp) cc_final: 0.8771 (mmt) REVERT: F 497 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8500 (mp0) REVERT: F 505 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7659 (ppt-90) REVERT: F 587 GLU cc_start: 0.8202 (tt0) cc_final: 0.7980 (tt0) REVERT: F 749 LYS cc_start: 0.7961 (mppt) cc_final: 0.7174 (mtmp) REVERT: F 782 TYR cc_start: 0.8209 (m-80) cc_final: 0.7764 (m-80) REVERT: F 1024 LYS cc_start: 0.8013 (ttmt) cc_final: 0.7090 (tttt) REVERT: F 1042 ASP cc_start: 0.7862 (p0) cc_final: 0.7418 (p0) outliers start: 55 outliers final: 33 residues processed: 229 average time/residue: 0.5344 time to fit residues: 142.7662 Evaluate side-chains 213 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 962 LYS 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 1067 THR Chi-restraints excluded: chain A residue 1068 PHE Chi-restraints excluded: chain A residue 1146 MET Chi-restraints excluded: chain A residue 1263 SER Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 215 CYS 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 297 ASN Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 505 ARG Chi-restraints excluded: chain F residue 517 ILE Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 997 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 251 optimal weight: 30.0000 chunk 195 optimal weight: 4.9990 chunk 114 optimal weight: 0.0770 chunk 194 optimal weight: 9.9990 chunk 221 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 157 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 198 HIS A 454 HIS ** A1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 GLN A1383 ASN F 297 ASN F 372 GLN F 395 ASN F 570 ASN F 728 ASN ** F 867 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.199457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.135883 restraints weight = 42584.114| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.80 r_work: 0.3121 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 22578 Z= 0.313 Angle : 0.816 13.356 30614 Z= 0.403 Chirality : 0.052 0.414 3486 Planarity : 0.005 0.047 3811 Dihedral : 9.911 112.703 3715 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.38 % Favored : 94.58 % Rotamer: Outliers : 3.20 % Allowed : 18.02 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.16), residues: 2659 helix: 0.33 (0.14), residues: 1365 sheet: -0.08 (0.32), residues: 262 loop : -1.77 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 594 TYR 0.025 0.003 TYR F 762 PHE 0.036 0.003 PHE F 469 TRP 0.018 0.002 TRP A1406 HIS 0.013 0.002 HIS A 992 Details of bonding type rmsd covalent geometry : bond 0.00762 (22540) covalent geometry : angle 0.79826 (30516) SS BOND : bond 0.00467 ( 13) SS BOND : angle 2.05044 ( 26) hydrogen bonds : bond 0.04941 ( 900) hydrogen bonds : angle 4.49315 ( 2567) Misc. bond : bond 0.00235 ( 1) link_BETA1-3 : bond 0.01039 ( 3) link_BETA1-3 : angle 3.11566 ( 9) link_BETA1-4 : bond 0.00892 ( 7) link_BETA1-4 : angle 2.85854 ( 21) link_NAG-ASN : bond 0.00499 ( 14) link_NAG-ASN : angle 3.66311 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 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 260 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 186 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash REVERT: A 118 LEU cc_start: 0.4550 (OUTLIER) cc_final: 0.4334 (tp) REVERT: A 165 ARG cc_start: 0.7136 (ttm-80) cc_final: 0.6869 (mtp-110) REVERT: A 367 MET cc_start: 0.1329 (ttt) cc_final: 0.0573 (tmt) REVERT: A 479 MET cc_start: 0.4747 (ppp) cc_final: 0.4534 (ppp) REVERT: A 493 MET cc_start: 0.3258 (mmm) cc_final: 0.2823 (mmp) REVERT: A 537 LYS cc_start: 0.6423 (mtpp) cc_final: 0.6202 (tptt) REVERT: A 686 MET cc_start: 0.2235 (ttp) cc_final: 0.0413 (mmt) REVERT: A 806 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6122 (pp) REVERT: A 851 MET cc_start: 0.3303 (tpt) cc_final: 0.2644 (mtp) REVERT: A 928 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8460 (tp) REVERT: A 965 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8326 (tt0) REVERT: A 983 MET cc_start: 0.9444 (pmm) cc_final: 0.9116 (ptp) REVERT: A 1068 PHE cc_start: 0.6755 (OUTLIER) cc_final: 0.6273 (t80) REVERT: A 1170 LEU cc_start: 0.6799 (mt) cc_final: 0.6541 (mm) REVERT: A 1350 TYR cc_start: 0.8791 (m-80) cc_final: 0.8296 (m-80) REVERT: A 1385 ASP cc_start: 0.7154 (m-30) cc_final: 0.6879 (p0) REVERT: E 1 MET cc_start: 0.3477 (tpt) cc_final: 0.3086 (tpp) REVERT: E 129 PHE cc_start: 0.5438 (OUTLIER) cc_final: 0.4531 (t80) REVERT: F 283 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8375 (mt-10) REVERT: F 457 GLU cc_start: 0.8111 (mp0) cc_final: 0.7752 (mm-30) REVERT: F 497 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8445 (mp0) REVERT: F 505 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8180 (ppt-90) REVERT: F 530 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7585 (mp10) REVERT: F 587 GLU cc_start: 0.8254 (tt0) cc_final: 0.8050 (tt0) REVERT: F 749 LYS cc_start: 0.8089 (mppt) cc_final: 0.7608 (mtmp) REVERT: F 782 TYR cc_start: 0.8417 (m-80) cc_final: 0.7957 (m-80) REVERT: F 830 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7697 (ptmm) REVERT: F 1024 LYS cc_start: 0.8086 (ttmt) cc_final: 0.7075 (tptt) REVERT: F 1042 ASP cc_start: 0.8081 (p0) cc_final: 0.7536 (p0) outliers start: 74 outliers final: 36 residues processed: 243 average time/residue: 0.5327 time to fit residues: 150.6394 Evaluate side-chains 221 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 118 LEU 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 206 MET Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 962 LYS 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 1067 THR Chi-restraints excluded: chain A residue 1068 PHE Chi-restraints excluded: chain A residue 1146 MET Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR 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 517 ILE Chi-restraints excluded: chain F residue 530 GLN Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 684 LEU Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 830 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 235 optimal weight: 3.9990 chunk 153 optimal weight: 0.0970 chunk 119 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 266 optimal weight: 10.0000 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 GLN A1383 ASN F 108 GLN F 145 GLN F 975 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.201707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.120998 restraints weight = 34735.238| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.08 r_work: 0.3108 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 22578 Z= 0.154 Angle : 0.681 12.672 30614 Z= 0.332 Chirality : 0.045 0.376 3486 Planarity : 0.004 0.048 3811 Dihedral : 9.435 111.104 3712 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.44 % Favored : 95.52 % Rotamer: Outliers : 2.21 % Allowed : 19.36 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.16), residues: 2659 helix: 0.62 (0.14), residues: 1355 sheet: 0.06 (0.32), residues: 252 loop : -1.61 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 158 TYR 0.017 0.002 TYR F 514 PHE 0.026 0.002 PHE E 146 TRP 0.015 0.001 TRP A 309 HIS 0.006 0.001 HIS A 992 Details of bonding type rmsd covalent geometry : bond 0.00365 (22540) covalent geometry : angle 0.66012 (30516) SS BOND : bond 0.00191 ( 13) SS BOND : angle 2.43797 ( 26) hydrogen bonds : bond 0.03745 ( 900) hydrogen bonds : angle 4.23740 ( 2567) Misc. bond : bond 0.00074 ( 1) link_BETA1-3 : bond 0.00784 ( 3) link_BETA1-3 : angle 3.11807 ( 9) link_BETA1-4 : bond 0.00832 ( 7) link_BETA1-4 : angle 2.67427 ( 21) link_NAG-ASN : bond 0.00480 ( 14) link_NAG-ASN : angle 3.53532 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 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 239 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 188 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping REVERT: A 59 LEU cc_start: 0.8298 (mm) cc_final: 0.8002 (mt) REVERT: A 118 LEU cc_start: 0.4760 (OUTLIER) cc_final: 0.4559 (tp) REVERT: A 165 ARG cc_start: 0.7136 (ttm-80) cc_final: 0.6893 (mtp-110) REVERT: A 269 ASN cc_start: 0.8566 (OUTLIER) cc_final: 0.8354 (m-40) REVERT: A 367 MET cc_start: 0.1034 (ttt) cc_final: 0.0398 (tmt) REVERT: A 493 MET cc_start: 0.3400 (mmm) cc_final: 0.3044 (mmp) REVERT: A 686 MET cc_start: 0.2210 (ttp) cc_final: 0.0579 (mmt) REVERT: A 806 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6224 (pp) REVERT: A 851 MET cc_start: 0.3280 (tpt) cc_final: 0.2646 (mtp) REVERT: A 928 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8473 (tp) REVERT: A 983 MET cc_start: 0.9381 (pmm) cc_final: 0.8954 (ptp) REVERT: A 1170 LEU cc_start: 0.6770 (mt) cc_final: 0.6532 (mm) REVERT: A 1175 ARG cc_start: 0.5993 (ttt90) cc_final: 0.5639 (mtp-110) REVERT: A 1350 TYR cc_start: 0.8757 (m-80) cc_final: 0.8220 (m-80) REVERT: E 1 MET cc_start: 0.3727 (tpt) cc_final: 0.3329 (tpp) REVERT: E 129 PHE cc_start: 0.5511 (OUTLIER) cc_final: 0.4511 (t80) REVERT: F 283 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8438 (mt-10) REVERT: F 379 ASN cc_start: 0.8197 (p0) cc_final: 0.7754 (p0) REVERT: F 457 GLU cc_start: 0.8207 (mp0) cc_final: 0.7753 (mm-30) REVERT: F 497 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8585 (mp0) REVERT: F 505 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7953 (ppt-90) REVERT: F 649 GLU cc_start: 0.7604 (pm20) cc_final: 0.7289 (pm20) REVERT: F 749 LYS cc_start: 0.7990 (mppt) cc_final: 0.7551 (mtmp) REVERT: F 782 TYR cc_start: 0.8456 (m-80) cc_final: 0.8039 (m-80) REVERT: F 1024 LYS cc_start: 0.8136 (ttmt) cc_final: 0.7296 (tptt) REVERT: F 1042 ASP cc_start: 0.8046 (p0) cc_final: 0.7570 (p0) REVERT: C 292 MET cc_start: 0.1545 (tmm) cc_final: 0.1099 (tmm) outliers start: 51 outliers final: 31 residues processed: 226 average time/residue: 0.5175 time to fit residues: 136.7870 Evaluate side-chains 210 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 962 LYS 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 1067 THR Chi-restraints excluded: chain A residue 1146 MET Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 215 CYS 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 269 LEU Chi-restraints excluded: chain F residue 270 THR 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 594 VAL Chi-restraints excluded: chain F residue 670 CYS Chi-restraints excluded: chain F residue 684 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 22 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 219 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 chunk 169 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 chunk 243 optimal weight: 9.9990 chunk 113 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 GLN A1383 ASN F 145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.202362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.127536 restraints weight = 32383.984| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 4.33 r_work: 0.3167 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22578 Z= 0.135 Angle : 0.683 20.950 30614 Z= 0.329 Chirality : 0.044 0.365 3486 Planarity : 0.004 0.052 3811 Dihedral : 9.231 109.591 3712 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.93 % Favored : 95.03 % Rotamer: Outliers : 1.86 % Allowed : 19.71 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.16), residues: 2659 helix: 0.76 (0.14), residues: 1351 sheet: 0.11 (0.32), residues: 254 loop : -1.52 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 158 TYR 0.015 0.001 TYR F 514 PHE 0.035 0.001 PHE E 189 TRP 0.016 0.001 TRP A 309 HIS 0.005 0.001 HIS A 992 Details of bonding type rmsd covalent geometry : bond 0.00314 (22540) covalent geometry : angle 0.65413 (30516) SS BOND : bond 0.00166 ( 13) SS BOND : angle 2.16728 ( 26) hydrogen bonds : bond 0.03563 ( 900) hydrogen bonds : angle 4.18670 ( 2567) Misc. bond : bond 0.00075 ( 1) link_BETA1-3 : bond 0.00779 ( 3) link_BETA1-3 : angle 3.00348 ( 9) link_BETA1-4 : bond 0.00851 ( 7) link_BETA1-4 : angle 2.63568 ( 21) link_NAG-ASN : bond 0.00508 ( 14) link_NAG-ASN : angle 4.56703 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 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 223 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash REVERT: A 77 ASP cc_start: 0.8339 (m-30) cc_final: 0.7938 (t0) REVERT: A 165 ARG cc_start: 0.7200 (ttm-80) cc_final: 0.6944 (mtp-110) REVERT: A 367 MET cc_start: 0.0922 (ttt) cc_final: 0.0189 (tmt) REVERT: A 479 MET cc_start: 0.4350 (ppp) cc_final: 0.4058 (ppp) REVERT: A 493 MET cc_start: 0.3289 (mmm) cc_final: 0.2952 (mmp) REVERT: A 686 MET cc_start: 0.2350 (ttp) cc_final: 0.0893 (mmt) REVERT: A 806 LEU cc_start: 0.6737 (OUTLIER) cc_final: 0.6160 (pp) REVERT: A 851 MET cc_start: 0.3392 (tpt) cc_final: 0.2753 (mtp) REVERT: A 912 LYS cc_start: 0.6375 (tptp) cc_final: 0.5934 (pptt) REVERT: A 928 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8425 (tp) REVERT: A 983 MET cc_start: 0.9447 (pmm) cc_final: 0.9046 (ptp) REVERT: A 1170 LEU cc_start: 0.6771 (mt) cc_final: 0.6539 (mm) REVERT: A 1175 ARG cc_start: 0.6019 (ttt90) cc_final: 0.5457 (mmt180) REVERT: A 1243 LEU cc_start: 0.8663 (tt) cc_final: 0.8168 (mt) REVERT: A 1350 TYR cc_start: 0.8858 (m-80) cc_final: 0.8338 (m-80) REVERT: A 1453 MET cc_start: 0.3274 (tpp) cc_final: 0.1514 (pp-130) REVERT: E 1 MET cc_start: 0.3906 (tpt) cc_final: 0.3452 (tpp) REVERT: E 129 PHE cc_start: 0.5549 (OUTLIER) cc_final: 0.4564 (t80) REVERT: F 283 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8561 (mt-10) REVERT: F 379 ASN cc_start: 0.8346 (p0) cc_final: 0.7989 (p0) REVERT: F 457 GLU cc_start: 0.8248 (mp0) cc_final: 0.7744 (mm-30) REVERT: F 497 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8821 (mp0) REVERT: F 505 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8024 (ppt-90) REVERT: F 530 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7583 (mp10) REVERT: F 649 GLU cc_start: 0.7790 (pm20) cc_final: 0.7349 (pm20) REVERT: F 749 LYS cc_start: 0.8082 (mppt) cc_final: 0.7610 (mtmp) REVERT: F 782 TYR cc_start: 0.8513 (m-80) cc_final: 0.8102 (m-80) REVERT: F 1024 LYS cc_start: 0.8118 (ttmt) cc_final: 0.7172 (tttt) REVERT: F 1042 ASP cc_start: 0.8187 (p0) cc_final: 0.7719 (p0) REVERT: C 292 MET cc_start: 0.2046 (tmm) cc_final: 0.1786 (tmm) outliers start: 43 outliers final: 32 residues processed: 216 average time/residue: 0.5498 time to fit residues: 137.6729 Evaluate side-chains 207 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 206 MET Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 962 LYS 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 1067 THR Chi-restraints excluded: chain A residue 1146 MET Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 215 CYS 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 269 LEU Chi-restraints excluded: chain F residue 270 THR 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 530 GLN Chi-restraints excluded: chain F residue 670 CYS Chi-restraints excluded: chain F residue 684 LEU 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 881 ILE Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain B residue 156 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 136 optimal weight: 0.7980 chunk 221 optimal weight: 2.9990 chunk 210 optimal weight: 0.6980 chunk 106 optimal weight: 0.0010 chunk 178 optimal weight: 0.7980 chunk 255 optimal weight: 20.0000 chunk 199 optimal weight: 0.0670 chunk 167 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 147 optimal weight: 0.9980 chunk 217 optimal weight: 0.7980 overall best weight: 0.4524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** A1085 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 GLN A1383 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.204831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.132692 restraints weight = 35132.308| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 3.76 r_work: 0.3252 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 22578 Z= 0.110 Angle : 0.626 11.696 30614 Z= 0.304 Chirality : 0.042 0.322 3486 Planarity : 0.004 0.053 3811 Dihedral : 8.752 106.366 3712 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.78 % Favored : 95.18 % Rotamer: Outliers : 1.69 % Allowed : 20.05 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.16), residues: 2659 helix: 1.02 (0.14), residues: 1343 sheet: 0.25 (0.33), residues: 252 loop : -1.36 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 158 TYR 0.014 0.001 TYR A 117 PHE 0.029 0.001 PHE E 189 TRP 0.017 0.001 TRP F 187 HIS 0.005 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00240 (22540) covalent geometry : angle 0.61209 (30516) SS BOND : bond 0.00170 ( 13) SS BOND : angle 1.69770 ( 26) hydrogen bonds : bond 0.03053 ( 900) hydrogen bonds : angle 3.99149 ( 2567) Misc. bond : bond 0.00032 ( 1) link_BETA1-3 : bond 0.00785 ( 3) link_BETA1-3 : angle 2.85520 ( 9) link_BETA1-4 : bond 0.00873 ( 7) link_BETA1-4 : angle 2.43335 ( 21) link_NAG-ASN : bond 0.00667 ( 14) link_NAG-ASN : angle 2.71227 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11551.21 seconds wall clock time: 195 minutes 56.01 seconds (11756.01 seconds total)