Starting phenix.real_space_refine on Mon Oct 26 23:38:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6jpb_9869/10_2026/6jpb_9869.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jpb_9869/10_2026/6jpb_9869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6jpb_9869/10_2026/6jpb_9869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jpb_9869/10_2026/6jpb_9869.map" model { file = "/net/cci-nas-00/data/ceres_data/6jpb_9869/10_2026/6jpb_9869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jpb_9869/10_2026/6jpb_9869.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6jpb_9869/10_2026/6jpb_9869.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6jpb_9869/10_2026/6jpb_9869.cif" } 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 5 5.49 5 S 127 5.16 5 C 14226 2.51 5 N 3592 2.21 5 O 4036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21989 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: "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: 74 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: "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: "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 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 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 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 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 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 chiralities: 2 Chain: "L" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 228 Unusual residues: {' CA': 2, '3PE': 4, 'C9F': 1, 'NAG': 1, 'PC1': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 103 Unusual residues: {' CA': 1, 'ETA': 1, 'NAG': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.60, per 1000 atoms: 0.25 Number of scatterers: 21989 At special positions: 0 Unit cell: (171.287, 183.288, 165.832, 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 127 16.00 P 5 15.00 O 4036 8.00 N 3592 7.00 C 14226 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=1.35 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=2.98 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=1.92 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=1.57 Simple disulfide: pdb=" SG CYS F 907 " - pdb=" SG CYS F 977 " distance=2.03 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 "HETATM21903 O5 NAG F1105 .*. O " rejected from bonding due to valence issues. Atom "HETATM21931 O5 NAG F1115 .*. 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 2 " - " NAG L 3 " 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 L 2 " NAG-ASN " NAG A1901 " - " ASN A 257 " " NAG F1105 " - " ASN F 326 " " NAG F1108 " - " ASN F 891 " " NAG F1115 " - " ASN F 92 " " NAG F1116 " - " ASN F 606 " " NAG F1121 " - " ASN F 784 " " NAG F1122 " - " ASN F1001 " " NAG F1123 " - " ASN F 988 " " 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 " " NAG L 1 " - " ASN F 827 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 1.3 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: 120 helices and 19 sheets defined 52.6% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 39 through 44 removed outlier: 3.511A pdb=" N ALA A 43 " --> pdb=" O PRO A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.502A pdb=" N GLU A 49 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 70 removed outlier: 4.144A pdb=" N THR A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 57 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 removed outlier: 3.510A pdb=" N LEU A 84 " --> pdb=" O ASN A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 101 removed outlier: 3.580A pdb=" N TYR A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 120 removed outlier: 3.596A pdb=" N LEU A 118 " --> pdb=" O GLN A 114 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 143 removed outlier: 3.845A pdb=" N LEU A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP A 126 " --> pdb=" O TRP A 122 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU A 140 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 171 removed outlier: 3.762A pdb=" N ALA A 166 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE A 167 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG A 168 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL A 169 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG A 171 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 removed outlier: 3.580A pdb=" N SER A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 179' Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 188 through 193 removed outlier: 4.390A pdb=" N LYS A 191 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET A 193 " --> pdb=" O PHE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 208 removed outlier: 3.924A pdb=" N LEU A 202 " --> pdb=" O HIS A 198 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 219 Processing helix chain 'A' and resid 277 through 290 removed outlier: 3.598A pdb=" N THR A 284 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 4.020A pdb=" N VAL A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 322 removed outlier: 3.924A pdb=" N PHE A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 337 removed outlier: 4.383A pdb=" N SER A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 346 Processing helix chain 'A' and resid 351 through 372 removed outlier: 3.602A pdb=" N LYS A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP A 369 " --> pdb=" O GLY A 365 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A 370 " --> pdb=" O TYR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 430 removed outlier: 3.900A pdb=" N CYS A 425 " --> pdb=" O PHE A 421 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N HIS A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 429 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 450 removed outlier: 3.514A pdb=" N ALA A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 485 removed outlier: 3.637A pdb=" N ASP A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 466 " --> pdb=" O HIS A 462 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 473 " --> pdb=" O ARG A 469 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 494 removed outlier: 3.657A pdb=" N TYR A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 3.677A 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: 3.531A pdb=" N ASP A 500 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 511 " --> pdb=" O GLY A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 removed outlier: 4.019A pdb=" N ARG A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 542 removed outlier: 3.519A pdb=" N LEU A 535 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 538 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A 540 " --> pdb=" O LYS A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 554 removed outlier: 3.617A pdb=" N LEU A 553 " --> pdb=" O VAL A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 564 through 581 removed outlier: 3.698A pdb=" N ILE A 571 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 573 " --> pdb=" O PHE A 569 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 577 " --> pdb=" O PHE A 573 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 612 Processing helix chain 'A' and resid 615 through 627 removed outlier: 3.759A pdb=" N VAL A 619 " --> pdb=" O ASP A 615 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 623 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR A 627 " --> pdb=" O GLY A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 638 removed outlier: 3.570A pdb=" N LEU A 636 " --> pdb=" O PRO A 633 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 637 " --> pdb=" O GLY A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 650 removed outlier: 3.594A pdb=" N ILE A 643 " --> pdb=" O ILE A 639 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE A 645 " --> pdb=" O PHE A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 687 removed outlier: 3.623A pdb=" N GLU A 666 " --> pdb=" O ASP A 662 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR A 671 " --> pdb=" O ALA A 667 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 676 " --> pdb=" O SER A 672 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 680 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG A 681 " --> pdb=" O LYS A 677 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG A 684 " --> pdb=" O GLU A 680 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 685 " --> pdb=" O ARG A 681 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 686 " --> pdb=" O LYS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 796 removed outlier: 4.055A pdb=" N ARG A 794 " --> pdb=" O VAL A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 807 removed outlier: 3.646A pdb=" N THR A 802 " --> pdb=" O ALA A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 818 removed outlier: 3.819A pdb=" N LEU A 816 " --> pdb=" O SER A 812 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 840 removed outlier: 4.288A pdb=" N PHE A 835 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP A 836 " --> pdb=" O LEU A 832 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 837 " --> pdb=" O GLY A 833 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 854 removed outlier: 4.312A pdb=" N ILE A 847 " --> pdb=" O PHE A 843 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 848 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A 852 " --> pdb=" O VAL A 848 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR A 854 " --> pdb=" O LYS A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 882 removed outlier: 3.787A pdb=" N ASP A 872 " --> pdb=" O PHE A 868 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 873 " --> pdb=" O ASN A 869 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL A 876 " --> pdb=" O ASP A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 899 removed outlier: 3.865A pdb=" N VAL A 898 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU A 899 " --> pdb=" O ILE A 895 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 894 through 899' Processing helix chain 'A' and resid 900 through 903 removed outlier: 3.784A pdb=" N ARG A 903 " --> pdb=" O ARG A 900 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 900 through 903' Processing helix chain 'A' and resid 904 through 908 removed outlier: 3.643A pdb=" N ILE A 908 " --> pdb=" O LEU A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 927 removed outlier: 3.564A pdb=" N LYS A 915 " --> pdb=" O ALA A 911 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS A 916 " --> pdb=" O LYS A 912 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 917 " --> pdb=" O GLY A 913 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 926 " --> pdb=" O PHE A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 950 removed outlier: 3.678A pdb=" N PHE A 940 " --> pdb=" O THR A 936 " (cutoff:3.500A) removed outlier: 3.582A 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 1013 removed outlier: 3.741A pdb=" N THR A1009 " --> pdb=" O MET A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1025 removed outlier: 3.686A pdb=" N ARG A1022 " --> pdb=" O GLN A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1042 removed outlier: 3.772A pdb=" N ALA A1042 " --> pdb=" O VAL A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1052 removed outlier: 3.640A pdb=" N ILE A1049 " --> pdb=" O PHE A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1068 removed outlier: 3.639A pdb=" N VAL A1061 " --> pdb=" O MET A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1094 Processing helix chain 'A' and resid 1105 through 1116 removed outlier: 3.508A pdb=" N TYR A1109 " --> pdb=" O ASN A1105 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A1111 " --> pdb=" O TYR A1107 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL A1114 " --> pdb=" O GLN A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1137 removed outlier: 4.056A pdb=" N LEU A1123 " --> pdb=" O TYR A1119 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N MET A1129 " --> pdb=" O PHE A1125 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE A1133 " --> pdb=" O MET A1129 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A1135 " --> pdb=" O ASN A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1171 removed outlier: 4.032A pdb=" N ILE A1149 " --> pdb=" O GLU A1145 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR A1158 " --> pdb=" O ASN A1154 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A1160 " --> pdb=" O ALA A1156 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET A1165 " --> pdb=" O PHE A1161 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A1167 " --> pdb=" O LEU A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1179 removed outlier: 3.774A pdb=" N GLY A1179 " --> pdb=" O GLY A1176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1176 through 1179' Processing helix chain 'A' and resid 1180 through 1205 removed outlier: 3.579A pdb=" N PHE A1185 " --> pdb=" O PRO A1181 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP A1203 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR A1204 " --> pdb=" O SER A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1239 removed outlier: 3.683A pdb=" N PHE A1235 " --> pdb=" O SER A1232 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A1238 " --> pdb=" O PHE A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1249 removed outlier: 3.519A pdb=" N ILE A1244 " --> pdb=" O MET A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1266 removed outlier: 3.512A pdb=" N THR A1255 " --> pdb=" O GLU A1251 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A1256 " --> pdb=" O GLY A1252 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A1260 " --> pdb=" O LEU A1256 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER A1263 " --> pdb=" O THR A1259 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A1264 " --> pdb=" O PHE A1260 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A1265 " --> pdb=" O ILE A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1289 removed outlier: 3.683A pdb=" N ILE A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A1275 " --> pdb=" O ALA A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1322 Processing helix chain 'A' and resid 1324 through 1330 Processing helix chain 'A' and resid 1331 through 1333 No H-bonds generated for 'chain 'A' and resid 1331 through 1333' Processing helix chain 'A' and resid 1356 through 1381 removed outlier: 3.655A pdb=" N LEU A1375 " --> pdb=" O LEU A1371 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A1379 " --> pdb=" O LEU A1375 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1410 removed outlier: 4.039A pdb=" N GLU A1401 " --> pdb=" O HIS A1397 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A1402 " --> pdb=" O HIS A1398 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS A1403 " --> pdb=" O LEU A1399 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR A1409 " --> pdb=" O ILE A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1427 removed outlier: 3.911A pdb=" N VAL A1422 " --> pdb=" O LYS A1418 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A1423 " --> pdb=" O HIS A1419 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR A1424 " --> pdb=" O LEU A1420 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A1426 " --> pdb=" O VAL A1422 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG A1427 " --> pdb=" O VAL A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1451 removed outlier: 4.410A pdb=" N VAL A1449 " --> pdb=" O CYS A1445 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET A1451 " --> pdb=" O ARG A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1475 removed outlier: 3.512A pdb=" N VAL A1471 " --> pdb=" O LEU A1467 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A1473 " --> pdb=" O ALA A1469 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A1474 " --> pdb=" O LEU A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1493 removed outlier: 3.669A pdb=" N ILE A1493 " --> pdb=" O GLU A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1499 through 1504 removed outlier: 3.663A pdb=" N SER A1502 " --> pdb=" O LYS A1499 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 27 removed outlier: 3.546A pdb=" N THR E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY E 19 " --> pdb=" O CYS E 15 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL E 21 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU E 22 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA E 23 " --> pdb=" O GLY E 19 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET E 24 " --> pdb=" O ILE E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 128 removed outlier: 3.519A pdb=" N ALA E 109 " --> pdb=" O ILE E 105 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER E 111 " --> pdb=" O ALA E 107 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N CYS E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 164 removed outlier: 3.603A pdb=" N ALA E 140 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER E 141 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET E 142 " --> pdb=" O ARG E 138 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL E 162 " --> pdb=" O MET E 158 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG E 164 " --> pdb=" O GLN E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 202 removed outlier: 3.730A pdb=" N ALA E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL E 190 " --> pdb=" O CYS E 186 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU E 194 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE E 197 " --> pdb=" O PHE E 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 95 removed outlier: 3.511A pdb=" N ARG B 82 " --> pdb=" O HIS B 78 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 174 removed outlier: 3.541A pdb=" N LEU B 170 " --> pdb=" O ASP B 166 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.658A pdb=" N ASP C 291 " --> pdb=" O TYR C 287 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET C 292 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 304 removed outlier: 4.132A pdb=" N HIS C 303 " --> pdb=" O ASP C 299 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 304 " --> pdb=" O PHE C 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 299 through 304' Processing helix chain 'C' and resid 343 through 358 removed outlier: 3.629A pdb=" N VAL C 347 " --> pdb=" O SER C 343 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU C 350 " --> pdb=" O GLU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 378 removed outlier: 3.572A pdb=" N SER C 378 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 402 removed outlier: 3.843A pdb=" N LEU C 397 " --> pdb=" O SER C 393 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN C 398 " --> pdb=" O PRO C 394 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG C 399 " --> pdb=" O LYS C 395 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS C 402 " --> pdb=" O GLN C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 410 removed outlier: 4.062A 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 419 removed outlier: 4.103A pdb=" N GLN C 415 " --> pdb=" O HIS C 411 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE C 416 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA C 418 " --> pdb=" O VAL C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 425 Processing helix chain 'C' and resid 426 through 430 Processing helix chain 'C' and resid 438 through 458 removed outlier: 3.951A pdb=" N HIS C 445 " --> pdb=" O ASP C 441 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU C 450 " --> pdb=" O LEU C 446 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 456 " --> pdb=" O ALA C 452 " (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: 4.008A 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: 3.920A 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: 3.685A 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: 3.826A pdb=" N PHE F 375 " --> pdb=" O ALA F 371 " (cutoff:3.500A) removed outlier: 3.939A 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: 3.844A 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: 4.022A 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: 3.637A 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: 4.022A 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: 3.725A pdb=" N LEU F 718 " --> pdb=" O PHE F 714 " (cutoff:3.500A) removed outlier: 4.105A 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: 3.683A 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 sheet with id=AA1, first strand: chain 'A' and resid 225 through 228 Processing sheet with id=AA2, first strand: chain 'A' and resid 955 through 956 Processing sheet with id=AA3, first strand: chain 'A' and resid 971 through 975 Processing sheet with id=AA4, first strand: chain 'E' and resid 48 through 51 Processing sheet with id=AA5, first strand: chain 'B' and resid 156 through 160 removed outlier: 6.528A pdb=" N ARG B 148 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 5.060A 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: 3.656A pdb=" N ALA B 104 " --> pdb=" O VAL C 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 309 through 313 removed outlier: 6.320A pdb=" N SER C 310 " --> pdb=" O ALA C 365 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ASP C 367 " --> pdb=" O SER C 310 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N THR C 312 " --> pdb=" O ASP C 367 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU C 279 " --> pdb=" O LEU C 366 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL C 387 " --> pdb=" O PRO C 276 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE C 278 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE C 389 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL C 280 " --> pdb=" O ILE C 389 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 68 through 72 Processing sheet with id=AA8, 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=AA8 Processing sheet with id=AA9, 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=AB1, 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=AB2, 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: 7.801A 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: 3.514A 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: 7.921A pdb=" N PHE F 389 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU F 362 " --> pdb=" O PHE F 389 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL F 391 " --> pdb=" O LEU F 362 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR F 364 " --> pdb=" O VAL F 391 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL F 386 " --> pdb=" O TYR F 411 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N TYR F 413 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 6.504A 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: 6.374A pdb=" N SER F 390 " --> pdb=" O ILE F 415 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 523 through 525 removed outlier: 3.659A pdb=" N LEU F 525 " --> pdb=" O ALA F 516 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 661 through 662 Processing sheet with id=AB5, 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=AB6, 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=AB7, first strand: chain 'F' and resid 803 through 804 Processing sheet with id=AB8, first strand: chain 'F' and resid 862 through 865 removed outlier: 3.618A pdb=" N MET F 864 " --> pdb=" O ILE F 855 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 896 through 907 removed outlier: 3.618A pdb=" N GLN F 983 " --> pdb=" O ASN F 898 " (cutoff:3.500A) removed outlier: 4.487A 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=AC1, first strand: chain 'F' and resid 997 through 998 863 hydrogen bonds defined for protein. 2393 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: 4.23 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3540 1.30 - 1.43: 6083 1.43 - 1.56: 12635 1.56 - 1.69: 12 1.69 - 1.82: 196 Bond restraints: 22466 Sorted by residual: bond pdb=" C21 3PE A1904 " pdb=" O21 3PE A1904 " ideal model delta sigma weight residual 1.316 1.453 -0.137 2.00e-02 2.50e+03 4.68e+01 bond pdb=" C02 C9F A1909 " pdb=" N03 C9F A1909 " ideal model delta sigma weight residual 1.358 1.483 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C31 3PE A1904 " pdb=" O31 3PE A1904 " ideal model delta sigma weight residual 1.331 1.455 -0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" C04 C9F A1909 " pdb=" N03 C9F A1909 " ideal model delta sigma weight residual 1.414 1.531 -0.117 2.00e-02 2.50e+03 3.42e+01 bond pdb=" C ALA F 665 " pdb=" N PRO F 666 " ideal model delta sigma weight residual 1.334 1.207 0.127 2.34e-02 1.83e+03 2.95e+01 ... (remaining 22461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 28910 3.04 - 6.09: 1267 6.09 - 9.13: 208 9.13 - 12.18: 27 12.18 - 15.22: 15 Bond angle restraints: 30427 Sorted by residual: angle pdb=" N HIS F 867 " pdb=" CA HIS F 867 " pdb=" C HIS F 867 " ideal model delta sigma weight residual 111.28 122.20 -10.92 1.09e+00 8.42e-01 1.00e+02 angle pdb=" N LYS F 478 " pdb=" CA LYS F 478 " pdb=" C LYS F 478 " ideal model delta sigma weight residual 111.28 121.92 -10.64 1.09e+00 8.42e-01 9.53e+01 angle pdb=" N SER E 181 " pdb=" CA SER E 181 " pdb=" C SER E 181 " ideal model delta sigma weight residual 111.28 121.14 -9.86 1.09e+00 8.42e-01 8.18e+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 6.42e+01 angle pdb=" N ASN F 325 " pdb=" CA ASN F 325 " pdb=" C ASN F 325 " ideal model delta sigma weight residual 111.71 120.82 -9.11 1.15e+00 7.56e-01 6.28e+01 ... (remaining 30422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.64: 12454 22.64 - 45.28: 638 45.28 - 67.92: 98 67.92 - 90.56: 21 90.56 - 113.20: 1 Dihedral angle restraints: 13212 sinusoidal: 5313 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 0.15 -86.15 1 1.00e+01 1.00e-02 8.96e+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 93.00 174.00 -81.00 1 1.00e+01 1.00e-02 8.10e+01 dihedral pdb=" CB CYS F 844 " pdb=" SG CYS F 844 " pdb=" SG CYS F 853 " pdb=" CB CYS F 853 " ideal model delta sinusoidal sigma weight residual -86.00 -162.03 76.03 1 1.00e+01 1.00e-02 7.28e+01 ... (remaining 13209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.765: 3480 0.765 - 1.530: 3 1.530 - 2.295: 0 2.295 - 3.059: 1 3.059 - 3.824: 1 Chirality restraints: 3485 Sorted by residual: chirality pdb=" C1 NAG L 3 " pdb=" O3 NAG L 2 " pdb=" C2 NAG L 3 " pdb=" O5 NAG L 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-02 2.50e+03 1.04e+03 chirality pdb=" C1 NAG F1121 " pdb=" ND2 ASN F 784 " pdb=" C2 NAG F1121 " pdb=" O5 NAG F1121 " 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 D 2 " pdb=" O3 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.91e+02 ... (remaining 3482 not shown) Planarity restraints: 3819 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " 0.347 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG L 1 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " 0.104 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " -0.534 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " 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 2.99e-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 " 0.533 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 F1105 " -0.315 2.00e-02 2.50e+03 2.66e-01 8.87e+02 pdb=" C7 NAG F1105 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG F1105 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG F1105 " 0.461 2.00e-02 2.50e+03 pdb=" O7 NAG F1105 " -0.042 2.00e-02 2.50e+03 ... (remaining 3816 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 57 2.37 - 3.00: 11637 3.00 - 3.64: 31611 3.64 - 4.27: 49353 4.27 - 4.90: 80924 Nonbonded interactions: 173582 Sorted by model distance: nonbonded pdb=" SG CYS A1079 " pdb=" CD1 LEU A1081 " model vdw 1.739 3.820 nonbonded pdb=" ND2 ASN A 38 " pdb=" CD PRO A 39 " model vdw 1.865 3.520 nonbonded pdb=" O ASN F 480 " pdb=" ND2 ASN F 480 " model vdw 1.921 3.120 nonbonded pdb=" O TYR A1334 " pdb=" O CYS A1352 " model vdw 2.033 3.040 nonbonded pdb=" OD1 ASN F 891 " pdb=" O5 NAG F1108 " model vdw 2.082 3.040 ... (remaining 173577 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' } ncs_group { reference = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) } 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: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 22.430 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:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 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 0.953 22504 Z= 0.972 Angle : 1.721 58.030 30525 Z= 0.908 Chirality : 0.121 3.824 3485 Planarity : 0.014 0.300 3805 Dihedral : 13.696 113.203 8063 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 21.17 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.50 % Favored : 91.08 % Rotamer: Outliers : 4.38 % Allowed : 7.41 % Favored : 88.21 % Cbeta Deviations : 0.12 % 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: -4.25 (0.14), residues: 2659 helix: -3.32 (0.11), residues: 1269 sheet: -1.70 (0.32), residues: 237 loop : -2.27 (0.17), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG F 275 TYR 0.060 0.005 TYR F 762 PHE 0.043 0.004 PHE F 663 TRP 0.045 0.005 TRP A 265 HIS 0.023 0.003 HIS A 274 Details of bonding type rmsd/Z covalent geometry : bond 0.01493 / 0.68 (22466) covalent geometry : angle 1.48056 / 0.84 (30427) SS BOND : bond 0.41204 / 24.38 ( 13) SS BOND : angle 17.33121 / 9.28 ( 26) hydrogen bonds : bond 0.29625 / 19.15 ( 843) hydrogen bonds : angle 10.19656 / 7.08 ( 2393) Misc. bond : bond 0.58154 / 30.61 ( 1) link_BETA1-3 : bond 0.00280 / 0.14 ( 3) link_BETA1-3 : angle 11.52175 / 6.08 ( 9) link_BETA1-4 : bond 0.04641 / 3.46 ( 7) link_BETA1-4 : angle 15.31455 / 8.24 ( 21) link_NAG-ASN : bond 0.23044 / 14.79 ( 14) link_NAG-ASN : angle 15.22733 / 11.33 ( 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 592 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 491 time to evaluate : 0.828 Fit side-chains revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.5112 (OUTLIER) cc_final: 0.3212 (tpm170) REVERT: A 59 LEU cc_start: 0.8314 (mm) cc_final: 0.8020 (mt) REVERT: A 111 LEU cc_start: 0.4910 (mm) cc_final: 0.4488 (tt) REVERT: A 190 PHE cc_start: 0.7007 (t80) cc_final: 0.6784 (t80) REVERT: A 339 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7578 (ttpt) REVERT: A 345 LYS cc_start: 0.5517 (tttp) cc_final: 0.5232 (ttpp) REVERT: A 557 ARG cc_start: 0.6118 (mpt90) cc_final: 0.5653 (ttt-90) REVERT: A 791 LEU cc_start: 0.4890 (OUTLIER) cc_final: 0.4230 (tm) REVERT: A 819 GLU cc_start: 0.7442 (tt0) cc_final: 0.7146 (tp30) REVERT: A 851 MET cc_start: 0.5663 (ptm) cc_final: 0.5408 (tmt) REVERT: A 919 GLN cc_start: 0.6580 (mt0) cc_final: 0.6027 (mt0) REVERT: A 988 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7809 (ptt-90) REVERT: A 1005 MET cc_start: 0.8906 (tpt) cc_final: 0.8604 (tpt) REVERT: A 1057 MET cc_start: 0.6184 (tmm) cc_final: 0.5978 (mmt) REVERT: A 1113 TYR cc_start: 0.6648 (t80) cc_final: 0.6311 (t80) REVERT: A 1321 THR cc_start: 0.8290 (m) cc_final: 0.7649 (p) REVERT: E 151 LEU cc_start: 0.7866 (mt) cc_final: 0.7406 (tp) REVERT: E 216 MET cc_start: 0.3328 (ptt) cc_final: 0.1825 (tmm) REVERT: C 292 MET cc_start: 0.3475 (mtt) cc_final: 0.2930 (ttm) REVERT: C 293 MET cc_start: 0.2774 (mtp) cc_final: 0.2306 (tmm) REVERT: C 384 PRO cc_start: 0.1501 (Cg_endo) cc_final: 0.1206 (Cg_exo) REVERT: F 361 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8134 (ptp) REVERT: F 404 MET cc_start: 0.8725 (mtt) cc_final: 0.8395 (mtm) REVERT: F 650 THR cc_start: 0.8199 (m) cc_final: 0.7882 (p) outliers start: 101 outliers final: 20 residues processed: 559 average time/residue: 0.5263 time to fit residues: 342.1559 Evaluate side-chains 297 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 272 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 252 ARG Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 339 LYS Chi-restraints excluded: chain A residue 791 LEU Chi-restraints excluded: chain A residue 988 ARG Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1339 ASP Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain F residue 133 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 271 LEU Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 853 CYS Chi-restraints excluded: chain F residue 868 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 111] chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.0470 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 ASN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN A 143 ASN A 269 ASN A 274 HIS A 277 ASN A 307 ASN A 327 ASN A 599 ASN A 654 ASN A 663 ASN A1355 ASN A1383 ASN ** A1398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1456 ASN A1464 ASN F 56 GLN F 108 GLN F 228 ASN F 357 ASN F 450 ASN F 480 ASN F 511 ASN F 520 ASN F 570 ASN F 687 ASN F 773 ASN F 847 ASN F1066 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.200834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.132566 restraints weight = 43432.930| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 3.39 r_work: 0.3389 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22504 Z= 0.173 Angle : 0.881 17.191 30525 Z= 0.427 Chirality : 0.050 0.620 3485 Planarity : 0.006 0.067 3805 Dihedral : 9.732 89.287 3086 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.04 % Favored : 94.81 % Rotamer: Outliers : 4.51 % Allowed : 15.34 % Favored : 80.16 % 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: -3.13 (0.14), residues: 2659 helix: -2.13 (0.12), residues: 1303 sheet: -1.34 (0.29), residues: 285 loop : -2.00 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 646 TYR 0.027 0.002 TYR F 629 PHE 0.027 0.002 PHE A1402 TRP 0.028 0.002 TRP E 32 HIS 0.009 0.001 HIS F 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (22466) covalent geometry : angle 0.84177 / 0.42 (30427) SS BOND : bond 0.00409 / 0.29 ( 13) SS BOND : angle 2.08790 / 1.13 ( 26) hydrogen bonds : bond 0.05594 / 3.60 ( 843) hydrogen bonds : angle 5.41123 / 3.76 ( 2393) Misc. bond : bond 0.00051 / 0.03 ( 1) link_BETA1-3 : bond 0.01861 / 0.93 ( 3) link_BETA1-3 : angle 2.56690 / 1.45 ( 9) link_BETA1-4 : bond 0.02016 / 1.49 ( 7) link_BETA1-4 : angle 3.40258 / 1.77 ( 21) link_NAG-ASN : bond 0.00948 / 0.65 ( 14) link_NAG-ASN : angle 6.36420 / 3.89 ( 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 401 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 297 time to evaluate : 0.746 Fit side-chains Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.5712 (OUTLIER) cc_final: 0.5487 (tmm-80) REVERT: A 87 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7954 (mt-10) REVERT: A 111 LEU cc_start: 0.5064 (mm) cc_final: 0.4542 (tt) REVERT: A 114 GLN cc_start: 0.5680 (OUTLIER) cc_final: 0.5312 (pp30) REVERT: A 190 PHE cc_start: 0.7475 (t80) cc_final: 0.7176 (t80) REVERT: A 273 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8668 (m) REVERT: A 455 ASN cc_start: 0.7732 (OUTLIER) cc_final: 0.7426 (m110) REVERT: A 557 ARG cc_start: 0.6641 (mpt90) cc_final: 0.5635 (ttt-90) REVERT: A 653 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8626 (mp) REVERT: A 819 GLU cc_start: 0.8213 (tt0) cc_final: 0.7374 (tp30) REVERT: A 820 ASP cc_start: 0.7977 (t0) cc_final: 0.7613 (t0) REVERT: A 919 GLN cc_start: 0.5768 (mt0) cc_final: 0.5311 (mt0) REVERT: A 938 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8377 (tp) REVERT: A 988 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7771 (ptp-170) REVERT: A 1005 MET cc_start: 0.9195 (tpt) cc_final: 0.8940 (tpt) REVERT: A 1057 MET cc_start: 0.7294 (tmm) cc_final: 0.6190 (mmt) REVERT: A 1093 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6562 (mt) REVERT: A 1105 ASN cc_start: 0.4456 (t0) cc_final: 0.4006 (t0) REVERT: A 1110 GLN cc_start: 0.5754 (tt0) cc_final: 0.5538 (mm110) REVERT: A 1137 MET cc_start: 0.8470 (mmt) cc_final: 0.8163 (mpp) REVERT: A 1163 LEU cc_start: 0.7860 (mt) cc_final: 0.7658 (mt) REVERT: A 1288 MET cc_start: 0.7917 (ptp) cc_final: 0.7593 (ptp) REVERT: E 17 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7613 (tm) REVERT: E 151 LEU cc_start: 0.8042 (mt) cc_final: 0.7442 (tp) REVERT: E 156 GLU cc_start: 0.6118 (mm-30) cc_final: 0.5837 (mt-10) REVERT: E 216 MET cc_start: 0.2604 (ptt) cc_final: 0.1993 (tmm) REVERT: C 292 MET cc_start: 0.3323 (mtt) cc_final: 0.2364 (tpp) REVERT: C 293 MET cc_start: 0.2907 (mtp) cc_final: 0.2408 (tmm) REVERT: F 39 LYS cc_start: 0.7813 (tptp) cc_final: 0.7468 (tptp) REVERT: F 43 ASP cc_start: 0.7206 (m-30) cc_final: 0.7004 (m-30) REVERT: F 330 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7989 (tttm) REVERT: F 355 ASN cc_start: 0.7552 (t0) cc_final: 0.7310 (t0) REVERT: F 361 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8076 (mtt) REVERT: F 404 MET cc_start: 0.9079 (mtt) cc_final: 0.8784 (mtm) REVERT: F 659 SER cc_start: 0.8642 (t) cc_final: 0.8434 (m) REVERT: F 674 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7932 (mptt) REVERT: F 689 PHE cc_start: 0.7024 (OUTLIER) cc_final: 0.6628 (m-80) REVERT: F 761 THR cc_start: 0.8368 (t) cc_final: 0.7991 (p) REVERT: F 867 HIS cc_start: 0.7540 (t-170) cc_final: 0.7041 (t-170) REVERT: F 991 LYS cc_start: 0.7226 (mtpp) cc_final: 0.6824 (mttm) REVERT: F 1019 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8476 (pp) REVERT: F 1020 MET cc_start: 0.8018 (ttt) cc_final: 0.7441 (ttp) outliers start: 104 outliers final: 22 residues processed: 367 average time/residue: 0.4917 time to fit residues: 211.8864 Evaluate side-chains 273 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 236 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 988 ARG Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1236 ARG Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 197 LYS Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 330 LYS Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 648 SER Chi-restraints excluded: chain F residue 674 LYS Chi-restraints excluded: chain F residue 689 PHE 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 900 SER Chi-restraints excluded: chain F residue 1019 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: [266, 164, 194, 10, 263, 23, 142, 215, 3, 109, 77] chunk 266 optimal weight: 0.1980 chunk 164 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 263 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 142 optimal weight: 7.9990 chunk 215 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 ASN A1148 HIS ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 679 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.198238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.134169 restraints weight = 50105.575| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.54 r_work: 0.3361 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 22504 Z= 0.151 Angle : 0.750 17.109 30525 Z= 0.364 Chirality : 0.047 0.441 3485 Planarity : 0.005 0.057 3805 Dihedral : 8.532 79.165 3058 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.23 % Favored : 94.70 % Rotamer: Outliers : 4.59 % Allowed : 16.81 % Favored : 78.60 % 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: -2.25 (0.15), residues: 2659 helix: -1.26 (0.13), residues: 1305 sheet: -0.97 (0.30), residues: 268 loop : -1.76 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 168 TYR 0.026 0.001 TYR F 629 PHE 0.021 0.001 PHE F 469 TRP 0.025 0.002 TRP E 32 HIS 0.011 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (22466) covalent geometry : angle 0.72125 / 0.36 (30427) SS BOND : bond 0.00565 / 0.35 ( 13) SS BOND : angle 1.73966 / 0.94 ( 26) hydrogen bonds : bond 0.04439 / 2.88 ( 843) hydrogen bonds : angle 4.75773 / 3.33 ( 2393) Misc. bond : bond 0.00117 / 0.06 ( 1) link_BETA1-3 : bond 0.00934 / 0.47 ( 3) link_BETA1-3 : angle 1.51358 / 0.85 ( 9) link_BETA1-4 : bond 0.00887 / 0.64 ( 7) link_BETA1-4 : angle 2.44120 / 1.31 ( 21) link_NAG-ASN : bond 0.01028 / 0.70 ( 14) link_NAG-ASN : angle 5.15230 / 3.09 ( 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 362 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 256 time to evaluate : 0.715 Fit side-chains Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8002 (mt-10) REVERT: A 96 VAL cc_start: 0.7506 (t) cc_final: 0.7214 (p) REVERT: A 111 LEU cc_start: 0.5428 (mm) cc_final: 0.5116 (tt) REVERT: A 190 PHE cc_start: 0.7613 (t80) cc_final: 0.7316 (t80) REVERT: A 205 PHE cc_start: 0.8233 (m-10) cc_final: 0.7532 (t80) REVERT: A 273 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8700 (m) REVERT: A 455 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7529 (m110) REVERT: A 557 ARG cc_start: 0.6800 (mpt90) cc_final: 0.5742 (ttt-90) REVERT: A 819 GLU cc_start: 0.8341 (tt0) cc_final: 0.7273 (tp30) REVERT: A 820 ASP cc_start: 0.8093 (t0) cc_final: 0.7593 (t0) REVERT: A 988 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7701 (ptt180) REVERT: A 1057 MET cc_start: 0.7293 (tmm) cc_final: 0.6175 (mmt) REVERT: A 1093 LEU cc_start: 0.6832 (OUTLIER) cc_final: 0.6600 (mt) REVERT: A 1110 GLN cc_start: 0.5833 (tt0) cc_final: 0.5570 (mm110) REVERT: A 1163 LEU cc_start: 0.7852 (mt) cc_final: 0.7517 (mt) REVERT: A 1167 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7928 (mt) REVERT: E 151 LEU cc_start: 0.8116 (mt) cc_final: 0.7548 (tp) REVERT: E 156 GLU cc_start: 0.6579 (mm-30) cc_final: 0.6290 (mm-30) REVERT: E 216 MET cc_start: 0.2320 (ptt) cc_final: 0.1690 (tmm) REVERT: C 292 MET cc_start: 0.3327 (mtt) cc_final: 0.2678 (tpp) REVERT: C 293 MET cc_start: 0.2924 (mtp) cc_final: 0.2467 (tmm) REVERT: C 400 LEU cc_start: -0.0017 (OUTLIER) cc_final: -0.0418 (tt) REVERT: F 39 LYS cc_start: 0.8184 (tptp) cc_final: 0.7656 (tptp) REVERT: F 43 ASP cc_start: 0.7448 (m-30) cc_final: 0.7164 (m-30) REVERT: F 132 ASP cc_start: 0.7870 (m-30) cc_final: 0.7497 (t0) REVERT: F 237 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8476 (mp) REVERT: F 355 ASN cc_start: 0.7625 (t0) cc_final: 0.7389 (t0) REVERT: F 361 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8420 (mtt) REVERT: F 508 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7582 (mt) REVERT: F 644 GLN cc_start: 0.8358 (mt0) cc_final: 0.7681 (mp10) REVERT: F 688 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7324 (mt-10) REVERT: F 689 PHE cc_start: 0.7111 (OUTLIER) cc_final: 0.6707 (m-80) REVERT: F 806 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7283 (mp10) outliers start: 106 outliers final: 32 residues processed: 331 average time/residue: 0.4771 time to fit residues: 187.3499 Evaluate side-chains 267 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 223 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 988 ARG Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1152 ILE Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1236 ARG Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 534 ILE Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 668 ASP Chi-restraints excluded: chain F residue 689 PHE Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 806 GLN Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 988 ASN Chi-restraints excluded: chain F residue 1035 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: [136, 252, 240, 248, 95, 247, 104, 144, 48, 151, 139] chunk 136 optimal weight: 4.9990 chunk 252 optimal weight: 0.9980 chunk 240 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 247 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 151 optimal weight: 7.9990 chunk 139 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 GLN F 395 ASN F 866 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.197517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.131346 restraints weight = 38002.651| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.43 r_work: 0.3408 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22504 Z= 0.134 Angle : 0.705 16.115 30525 Z= 0.339 Chirality : 0.046 0.433 3485 Planarity : 0.005 0.057 3805 Dihedral : 7.908 76.830 3053 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.97 % Favored : 95.00 % Rotamer: Outliers : 4.07 % Allowed : 18.46 % Favored : 77.47 % 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: -1.67 (0.16), residues: 2659 helix: -0.68 (0.14), residues: 1309 sheet: -0.69 (0.30), residues: 266 loop : -1.63 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 897 TYR 0.022 0.001 TYR F 629 PHE 0.025 0.001 PHE E 113 TRP 0.021 0.001 TRP E 32 HIS 0.006 0.001 HIS A 992 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (22466) covalent geometry : angle 0.68304 / 0.33 (30427) SS BOND : bond 0.00285 / 0.19 ( 13) SS BOND : angle 1.68742 / 0.87 ( 26) hydrogen bonds : bond 0.03773 / 2.45 ( 843) hydrogen bonds : angle 4.41804 / 3.10 ( 2393) Misc. bond : bond 0.00026 / 0.01 ( 1) link_BETA1-3 : bond 0.00975 / 0.48 ( 3) link_BETA1-3 : angle 1.46568 / 0.83 ( 9) link_BETA1-4 : bond 0.00979 / 0.71 ( 7) link_BETA1-4 : angle 2.38385 / 1.28 ( 21) link_NAG-ASN : bond 0.00821 / 0.60 ( 14) link_NAG-ASN : angle 4.31495 / 2.59 ( 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 343 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 249 time to evaluate : 0.525 Fit side-chains Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 VAL cc_start: 0.7187 (t) cc_final: 0.6960 (p) REVERT: A 111 LEU cc_start: 0.5465 (mm) cc_final: 0.5190 (tt) REVERT: A 190 PHE cc_start: 0.7468 (t80) cc_final: 0.7161 (t80) REVERT: A 205 PHE cc_start: 0.8009 (m-10) cc_final: 0.7273 (t80) REVERT: A 273 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8721 (m) REVERT: A 455 ASN cc_start: 0.7730 (OUTLIER) cc_final: 0.7435 (m110) REVERT: A 537 LYS cc_start: 0.6822 (mtpp) cc_final: 0.6616 (mtmm) REVERT: A 594 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8589 (mmm160) REVERT: A 819 GLU cc_start: 0.8175 (tt0) cc_final: 0.7236 (tp30) REVERT: A 820 ASP cc_start: 0.8124 (t0) cc_final: 0.7620 (t0) REVERT: A 925 ILE cc_start: 0.7449 (OUTLIER) cc_final: 0.7238 (mm) REVERT: A 988 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7743 (ptt180) REVERT: A 1041 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7971 (mmm) REVERT: A 1057 MET cc_start: 0.7315 (tmm) cc_final: 0.6131 (mmt) REVERT: A 1093 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6571 (mt) REVERT: A 1137 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7941 (mtm) REVERT: A 1163 LEU cc_start: 0.7613 (mt) cc_final: 0.7291 (mt) REVERT: A 1167 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7663 (mt) REVERT: A 1199 LEU cc_start: 0.8581 (tt) cc_final: 0.8128 (mp) REVERT: A 1236 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7079 (mpp-170) REVERT: A 1451 MET cc_start: 0.5342 (mpt) cc_final: 0.5098 (mpt) REVERT: E 127 MET cc_start: 0.6953 (tmm) cc_final: 0.6745 (ttp) REVERT: E 133 ARG cc_start: 0.4137 (OUTLIER) cc_final: 0.3550 (mmt180) REVERT: E 151 LEU cc_start: 0.8105 (mt) cc_final: 0.7542 (tp) REVERT: E 207 MET cc_start: 0.8125 (mmp) cc_final: 0.7846 (mmt) REVERT: E 216 MET cc_start: 0.2390 (ptt) cc_final: 0.2156 (pp-130) REVERT: C 292 MET cc_start: 0.3417 (mtt) cc_final: 0.2814 (tpp) REVERT: C 293 MET cc_start: 0.3013 (mtp) cc_final: 0.2510 (tmm) REVERT: C 400 LEU cc_start: -0.0160 (OUTLIER) cc_final: -0.0435 (tt) REVERT: F 39 LYS cc_start: 0.8279 (tptp) cc_final: 0.7799 (tptp) REVERT: F 43 ASP cc_start: 0.7069 (m-30) cc_final: 0.6796 (m-30) REVERT: F 132 ASP cc_start: 0.7825 (m-30) cc_final: 0.7417 (t0) REVERT: F 283 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8310 (mt-10) REVERT: F 355 ASN cc_start: 0.7660 (t0) cc_final: 0.7448 (t0) REVERT: F 361 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8402 (mtt) REVERT: F 508 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7831 (mt) REVERT: F 688 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7217 (mt-10) REVERT: F 689 PHE cc_start: 0.6688 (OUTLIER) cc_final: 0.6387 (m-80) REVERT: F 1019 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8536 (pp) REVERT: F 1024 LYS cc_start: 0.7348 (tttt) cc_final: 0.6765 (tttp) outliers start: 94 outliers final: 33 residues processed: 315 average time/residue: 0.4672 time to fit residues: 175.7622 Evaluate side-chains 273 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 224 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 988 ARG Chi-restraints excluded: chain A residue 1041 MET Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1236 ARG Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1352 CYS Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 517 ILE Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 668 ASP Chi-restraints excluded: chain F residue 689 PHE Chi-restraints excluded: chain F residue 728 ASN Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 853 CYS Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1035 ILE Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: [0, 139, 156, 19, 241, 101, 244, 85, 34, 215, 190] chunk 0 optimal weight: 30.0000 chunk 139 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 19 optimal weight: 0.0570 chunk 241 optimal weight: 0.4980 chunk 101 optimal weight: 0.8980 chunk 244 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 190 optimal weight: 0.0980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 294 GLN F 644 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.198500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.129884 restraints weight = 45148.669| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 3.64 r_work: 0.3359 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22504 Z= 0.113 Angle : 0.659 15.642 30525 Z= 0.316 Chirality : 0.044 0.463 3485 Planarity : 0.004 0.052 3805 Dihedral : 7.421 72.171 3049 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.25 % Allowed : 18.93 % Favored : 76.82 % 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: -1.21 (0.16), residues: 2659 helix: -0.24 (0.14), residues: 1306 sheet: -0.43 (0.30), residues: 263 loop : -1.51 (0.19), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 897 TYR 0.018 0.001 TYR F 629 PHE 0.019 0.001 PHE F 993 TRP 0.020 0.001 TRP E 32 HIS 0.003 0.001 HIS A 992 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (22466) covalent geometry : angle 0.63857 / 0.31 (30427) SS BOND : bond 0.00638 / 0.50 ( 13) SS BOND : angle 1.56124 / 0.85 ( 26) hydrogen bonds : bond 0.03344 / 2.17 ( 843) hydrogen bonds : angle 4.22917 / 2.97 ( 2393) Misc. bond : bond 0.00008 / 0.00 ( 1) link_BETA1-3 : bond 0.01012 / 0.50 ( 3) link_BETA1-3 : angle 1.39354 / 0.78 ( 9) link_BETA1-4 : bond 0.00880 / 0.64 ( 7) link_BETA1-4 : angle 2.24792 / 1.21 ( 21) link_NAG-ASN : bond 0.00805 / 0.60 ( 14) link_NAG-ASN : angle 4.00221 / 2.39 ( 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 337 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 239 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7551 (mt-10) REVERT: A 190 PHE cc_start: 0.7326 (t80) cc_final: 0.7040 (t80) REVERT: A 205 PHE cc_start: 0.7938 (m-10) cc_final: 0.7259 (t80) REVERT: A 273 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8721 (m) REVERT: A 819 GLU cc_start: 0.8026 (tt0) cc_final: 0.7343 (mm-30) REVERT: A 820 ASP cc_start: 0.8099 (t0) cc_final: 0.7692 (t0) REVERT: A 851 MET cc_start: 0.4601 (OUTLIER) cc_final: 0.4272 (tmm) REVERT: A 925 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7368 (mm) REVERT: A 988 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7772 (ptt180) REVERT: A 1057 MET cc_start: 0.7089 (tmm) cc_final: 0.5900 (mmt) REVERT: A 1090 GLN cc_start: 0.6817 (OUTLIER) cc_final: 0.6369 (tp-100) REVERT: A 1093 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6419 (mt) REVERT: A 1163 LEU cc_start: 0.7436 (mt) cc_final: 0.7120 (mt) REVERT: A 1167 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7595 (mt) REVERT: A 1199 LEU cc_start: 0.8566 (tt) cc_final: 0.8111 (mp) REVERT: A 1337 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7779 (tp) REVERT: A 1374 ASN cc_start: 0.8696 (t0) cc_final: 0.8339 (t0) REVERT: E 119 ILE cc_start: 0.8529 (mt) cc_final: 0.8219 (mp) REVERT: E 127 MET cc_start: 0.6913 (tmm) cc_final: 0.6605 (ttt) REVERT: E 133 ARG cc_start: 0.3771 (OUTLIER) cc_final: 0.3468 (mmt180) REVERT: E 207 MET cc_start: 0.8117 (mmp) cc_final: 0.7833 (mmt) REVERT: E 216 MET cc_start: 0.2415 (ptt) cc_final: 0.2204 (pp-130) REVERT: C 292 MET cc_start: 0.3207 (mtt) cc_final: 0.2668 (tpp) REVERT: C 293 MET cc_start: 0.3309 (mtp) cc_final: 0.2677 (tmm) REVERT: C 400 LEU cc_start: 0.0071 (OUTLIER) cc_final: -0.0195 (tt) REVERT: F 39 LYS cc_start: 0.8342 (tptp) cc_final: 0.7932 (tptp) REVERT: F 43 ASP cc_start: 0.7045 (m-30) cc_final: 0.6795 (m-30) REVERT: F 132 ASP cc_start: 0.7820 (m-30) cc_final: 0.7427 (t0) REVERT: F 283 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8149 (mt-10) REVERT: F 355 ASN cc_start: 0.7566 (t0) cc_final: 0.7316 (t0) REVERT: F 361 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8382 (mtt) REVERT: F 404 MET cc_start: 0.9089 (mtt) cc_final: 0.8784 (mtm) REVERT: F 508 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7756 (mt) REVERT: F 546 ARG cc_start: 0.7585 (tmt170) cc_final: 0.7384 (tpt170) REVERT: F 688 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7254 (mt-10) REVERT: F 689 PHE cc_start: 0.6859 (OUTLIER) cc_final: 0.6499 (m-80) REVERT: F 829 THR cc_start: 0.6200 (m) cc_final: 0.5569 (p) REVERT: F 1019 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8471 (pp) REVERT: F 1024 LYS cc_start: 0.7540 (tttt) cc_final: 0.6987 (tttp) outliers start: 98 outliers final: 33 residues processed: 314 average time/residue: 0.4757 time to fit residues: 176.5631 Evaluate side-chains 272 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 224 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 988 ARG Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1236 ARG Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1352 CYS Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 528 ASN Chi-restraints excluded: chain F residue 534 ILE Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 674 LYS Chi-restraints excluded: chain F residue 689 PHE Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain F residue 826 GLU Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: [42, 34, 219, 238, 62, 191, 197, 256, 65, 44, 46] chunk 42 optimal weight: 4.9990 chunk 34 optimal weight: 0.4980 chunk 219 optimal weight: 0.8980 chunk 238 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 197 optimal weight: 0.1980 chunk 256 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 454 HIS A1311 GLN A1355 ASN F 644 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.197469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.136331 restraints weight = 55113.540| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 4.03 r_work: 0.3343 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22504 Z= 0.118 Angle : 0.660 15.184 30525 Z= 0.315 Chirality : 0.045 0.471 3485 Planarity : 0.004 0.052 3805 Dihedral : 7.215 67.102 3049 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.60 % Allowed : 19.89 % Favored : 76.52 % 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: -0.91 (0.16), residues: 2659 helix: 0.07 (0.14), residues: 1307 sheet: -0.25 (0.30), residues: 261 loop : -1.47 (0.19), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 646 TYR 0.013 0.001 TYR F 629 PHE 0.020 0.001 PHE A1063 TRP 0.020 0.001 TRP E 32 HIS 0.006 0.001 HIS A1148 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (22466) covalent geometry : angle 0.64065 / 0.31 (30427) SS BOND : bond 0.00321 / 0.24 ( 13) SS BOND : angle 1.53443 / 0.80 ( 26) hydrogen bonds : bond 0.03363 / 2.17 ( 843) hydrogen bonds : angle 4.16209 / 2.92 ( 2393) Misc. bond : bond 0.00011 / 0.01 ( 1) link_BETA1-3 : bond 0.00998 / 0.50 ( 3) link_BETA1-3 : angle 1.36284 / 0.77 ( 9) link_BETA1-4 : bond 0.00864 / 0.63 ( 7) link_BETA1-4 : angle 2.21962 / 1.21 ( 21) link_NAG-ASN : bond 0.00778 / 0.58 ( 14) link_NAG-ASN : angle 3.86509 / 2.31 ( 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 320 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 237 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.6792 (OUTLIER) cc_final: 0.6555 (tmmt) REVERT: A 87 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7540 (mt-10) REVERT: A 190 PHE cc_start: 0.7430 (t80) cc_final: 0.7158 (t80) REVERT: A 205 PHE cc_start: 0.7961 (m-10) cc_final: 0.7352 (t80) REVERT: A 273 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8679 (m) REVERT: A 594 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8297 (mmm-85) REVERT: A 653 LEU cc_start: 0.8791 (mp) cc_final: 0.8589 (mm) REVERT: A 819 GLU cc_start: 0.8081 (tt0) cc_final: 0.7057 (pp20) REVERT: A 820 ASP cc_start: 0.7996 (t0) cc_final: 0.7619 (t0) REVERT: A 851 MET cc_start: 0.4752 (OUTLIER) cc_final: 0.4442 (tmm) REVERT: A 925 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7476 (mm) REVERT: A 988 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7998 (ptp90) REVERT: A 1057 MET cc_start: 0.7236 (tmm) cc_final: 0.6097 (mmt) REVERT: A 1090 GLN cc_start: 0.6834 (OUTLIER) cc_final: 0.6368 (tp-100) REVERT: A 1093 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6497 (mt) REVERT: A 1163 LEU cc_start: 0.7543 (mt) cc_final: 0.7250 (mt) REVERT: A 1167 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7675 (mt) REVERT: A 1199 LEU cc_start: 0.8629 (tt) cc_final: 0.8154 (mp) REVERT: A 1267 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8033 (mp) REVERT: A 1334 TYR cc_start: 0.6859 (t80) cc_final: 0.6648 (t80) REVERT: A 1374 ASN cc_start: 0.8800 (t0) cc_final: 0.8482 (t0) REVERT: A 1451 MET cc_start: 0.5512 (mpt) cc_final: 0.5257 (mpt) REVERT: E 111 SER cc_start: 0.8551 (t) cc_final: 0.8201 (p) REVERT: E 126 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6671 (pp) REVERT: E 127 MET cc_start: 0.7095 (tmm) cc_final: 0.6850 (ttt) REVERT: E 133 ARG cc_start: 0.3984 (OUTLIER) cc_final: 0.3613 (mmt180) REVERT: E 151 LEU cc_start: 0.7902 (mt) cc_final: 0.7196 (pp) REVERT: E 207 MET cc_start: 0.8220 (mmp) cc_final: 0.7891 (mmt) REVERT: E 216 MET cc_start: 0.2562 (ptt) cc_final: 0.2245 (ppp) REVERT: C 292 MET cc_start: 0.3092 (mtt) cc_final: 0.2614 (tpp) REVERT: C 293 MET cc_start: 0.3254 (mtp) cc_final: 0.2664 (tmm) REVERT: C 400 LEU cc_start: 0.0152 (OUTLIER) cc_final: -0.0093 (tt) REVERT: F 39 LYS cc_start: 0.8462 (tptp) cc_final: 0.8125 (tptp) REVERT: F 132 ASP cc_start: 0.7821 (m-30) cc_final: 0.7429 (t0) REVERT: F 355 ASN cc_start: 0.7574 (t0) cc_final: 0.7339 (t0) REVERT: F 361 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8255 (mtt) REVERT: F 508 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7942 (mt) REVERT: F 593 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8374 (mt) REVERT: F 689 PHE cc_start: 0.6886 (OUTLIER) cc_final: 0.6545 (m-80) REVERT: F 829 THR cc_start: 0.6493 (m) cc_final: 0.5899 (p) REVERT: F 1019 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8544 (pp) REVERT: F 1024 LYS cc_start: 0.7694 (tttt) cc_final: 0.7187 (tttp) outliers start: 83 outliers final: 41 residues processed: 298 average time/residue: 0.4667 time to fit residues: 165.7388 Evaluate side-chains 286 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 226 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 988 ARG Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1236 ARG Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1352 CYS Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 205 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 271 LEU Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 517 ILE Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 528 ASN Chi-restraints excluded: chain F residue 534 ILE Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 674 LYS Chi-restraints excluded: chain F residue 689 PHE Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain F residue 826 GLU Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: [25, 150, 77, 83, 155, 0, 14, 147, 206, 142, 80] chunk 25 optimal weight: 0.9980 chunk 150 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 14 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 455 ASN A1398 HIS C 303 HIS F 308 HIS F 644 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.194805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.123815 restraints weight = 43910.562| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 3.17 r_work: 0.3267 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22504 Z= 0.152 Angle : 0.692 14.570 30525 Z= 0.331 Chirality : 0.046 0.479 3485 Planarity : 0.005 0.051 3805 Dihedral : 7.272 59.956 3049 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.90 % Allowed : 19.71 % Favored : 76.39 % 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: -0.76 (0.16), residues: 2659 helix: 0.23 (0.14), residues: 1315 sheet: -0.18 (0.31), residues: 261 loop : -1.44 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 199 TYR 0.016 0.001 TYR A1021 PHE 0.020 0.002 PHE A1063 TRP 0.018 0.001 TRP E 32 HIS 0.007 0.001 HIS A 992 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (22466) covalent geometry : angle 0.67365 / 0.33 (30427) SS BOND : bond 0.00367 / 0.27 ( 13) SS BOND : angle 1.69701 / 0.88 ( 26) hydrogen bonds : bond 0.03711 / 2.41 ( 843) hydrogen bonds : angle 4.17853 / 2.93 ( 2393) Misc. bond : bond 0.00057 / 0.03 ( 1) link_BETA1-3 : bond 0.01129 / 0.56 ( 3) link_BETA1-3 : angle 1.34531 / 0.78 ( 9) link_BETA1-4 : bond 0.00845 / 0.61 ( 7) link_BETA1-4 : angle 2.21311 / 1.21 ( 21) link_NAG-ASN : bond 0.00748 / 0.55 ( 14) link_NAG-ASN : angle 3.83489 / 2.29 ( 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 331 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 241 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.6790 (OUTLIER) cc_final: 0.6444 (tmmt) REVERT: A 87 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7898 (mt-10) REVERT: A 96 VAL cc_start: 0.7409 (t) cc_final: 0.7103 (p) REVERT: A 139 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6582 (tt) REVERT: A 190 PHE cc_start: 0.7445 (t80) cc_final: 0.7150 (t80) REVERT: A 205 PHE cc_start: 0.8168 (m-10) cc_final: 0.7416 (t80) REVERT: A 273 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8866 (m) REVERT: A 594 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8534 (mmm160) REVERT: A 653 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8617 (mm) REVERT: A 819 GLU cc_start: 0.8213 (tt0) cc_final: 0.6858 (pp20) REVERT: A 820 ASP cc_start: 0.8164 (t0) cc_final: 0.7597 (t0) REVERT: A 851 MET cc_start: 0.4807 (OUTLIER) cc_final: 0.4520 (tmm) REVERT: A 988 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8029 (ptp-170) REVERT: A 1057 MET cc_start: 0.7587 (tmm) cc_final: 0.6274 (mmt) REVERT: A 1090 GLN cc_start: 0.6737 (OUTLIER) cc_final: 0.6321 (tp-100) REVERT: A 1093 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6454 (mt) REVERT: A 1154 ASN cc_start: 0.8553 (t0) cc_final: 0.8146 (t0) REVERT: A 1163 LEU cc_start: 0.7525 (mt) cc_final: 0.7228 (mt) REVERT: A 1167 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7536 (mt) REVERT: A 1199 LEU cc_start: 0.8738 (tt) cc_final: 0.8287 (mp) REVERT: A 1337 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8169 (tp) REVERT: A 1374 ASN cc_start: 0.8888 (t0) cc_final: 0.8540 (t0) REVERT: E 2 SER cc_start: 0.7212 (p) cc_final: 0.6999 (t) REVERT: E 126 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6636 (pp) REVERT: E 133 ARG cc_start: 0.4120 (OUTLIER) cc_final: 0.3664 (mmt180) REVERT: E 207 MET cc_start: 0.8214 (mmp) cc_final: 0.7869 (mmt) REVERT: E 216 MET cc_start: 0.2433 (ptt) cc_final: 0.2046 (ppp) REVERT: C 273 SER cc_start: 0.0582 (m) cc_final: 0.0080 (t) REVERT: C 293 MET cc_start: 0.3179 (mtp) cc_final: 0.2583 (tmm) REVERT: C 400 LEU cc_start: 0.0147 (OUTLIER) cc_final: -0.0107 (tt) REVERT: F 39 LYS cc_start: 0.8427 (tptp) cc_final: 0.8192 (tptp) REVERT: F 55 HIS cc_start: 0.8200 (m170) cc_final: 0.7994 (m90) REVERT: F 59 ASP cc_start: 0.8530 (m-30) cc_final: 0.8142 (m-30) REVERT: F 132 ASP cc_start: 0.7918 (m-30) cc_final: 0.7438 (t0) REVERT: F 508 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8002 (mt) REVERT: F 593 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8377 (mt) REVERT: F 689 PHE cc_start: 0.6643 (t80) cc_final: 0.6352 (m-80) REVERT: F 829 THR cc_start: 0.6312 (m) cc_final: 0.5677 (p) REVERT: F 874 ILE cc_start: 0.6652 (OUTLIER) cc_final: 0.6428 (mm) REVERT: F 1019 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8480 (pp) REVERT: F 1024 LYS cc_start: 0.7703 (tttt) cc_final: 0.7127 (tttp) outliers start: 90 outliers final: 41 residues processed: 306 average time/residue: 0.4474 time to fit residues: 163.9834 Evaluate side-chains 276 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 216 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 988 ARG Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1236 ARG Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1352 CYS Chi-restraints excluded: chain A residue 1381 MET Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 152 ILE 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 271 LEU Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 517 ILE Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 534 ILE Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 674 LYS Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain F residue 826 GLU Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: [237, 248, 166, 241, 112, 85, 214, 115, 159, 143, 47] chunk 237 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 chunk 241 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 214 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 455 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.196169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.132956 restraints weight = 49754.603| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.46 r_work: 0.3347 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22504 Z= 0.119 Angle : 0.661 13.815 30525 Z= 0.313 Chirality : 0.045 0.470 3485 Planarity : 0.004 0.051 3805 Dihedral : 7.019 58.793 3046 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.38 % Allowed : 20.71 % Favored : 75.91 % 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: -0.54 (0.16), residues: 2659 helix: 0.46 (0.15), residues: 1318 sheet: -0.10 (0.30), residues: 265 loop : -1.40 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 646 TYR 0.012 0.001 TYR A1119 PHE 0.029 0.001 PHE E 113 TRP 0.021 0.001 TRP E 32 HIS 0.005 0.001 HIS A 992 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (22466) covalent geometry : angle 0.64442 / 0.31 (30427) SS BOND : bond 0.00333 / 0.25 ( 13) SS BOND : angle 1.51634 / 0.80 ( 26) hydrogen bonds : bond 0.03248 / 2.11 ( 843) hydrogen bonds : angle 4.08256 / 2.87 ( 2393) Misc. bond : bond 0.00022 / 0.01 ( 1) link_BETA1-3 : bond 0.01063 / 0.53 ( 3) link_BETA1-3 : angle 1.33450 / 0.77 ( 9) link_BETA1-4 : bond 0.00809 / 0.59 ( 7) link_BETA1-4 : angle 2.11156 / 1.15 ( 21) link_NAG-ASN : bond 0.00755 / 0.55 ( 14) link_NAG-ASN : angle 3.57314 / 2.13 ( 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 304 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 226 time to evaluate : 0.699 Fit side-chains revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.6766 (OUTLIER) cc_final: 0.6413 (tmmt) REVERT: A 96 VAL cc_start: 0.7523 (t) cc_final: 0.7187 (p) REVERT: A 139 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6706 (tt) REVERT: A 190 PHE cc_start: 0.7566 (t80) cc_final: 0.7208 (t80) REVERT: A 205 PHE cc_start: 0.8088 (m-10) cc_final: 0.7434 (t80) REVERT: A 273 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8802 (m) REVERT: A 276 ASP cc_start: 0.8354 (p0) cc_final: 0.8007 (m-30) REVERT: A 486 LEU cc_start: 0.4495 (OUTLIER) cc_final: 0.4266 (mm) REVERT: A 594 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8328 (mmm-85) REVERT: A 653 LEU cc_start: 0.8855 (mp) cc_final: 0.8652 (mm) REVERT: A 819 GLU cc_start: 0.8108 (tt0) cc_final: 0.6925 (pp20) REVERT: A 820 ASP cc_start: 0.8107 (t0) cc_final: 0.7644 (t0) REVERT: A 851 MET cc_start: 0.4936 (OUTLIER) cc_final: 0.4658 (tmm) REVERT: A 988 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7690 (ptp-170) REVERT: A 1057 MET cc_start: 0.7670 (tmm) cc_final: 0.6455 (mmt) REVERT: A 1090 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.6295 (tp-100) REVERT: A 1093 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6679 (mt) REVERT: A 1154 ASN cc_start: 0.8674 (t0) cc_final: 0.8293 (t0) REVERT: A 1163 LEU cc_start: 0.7629 (mt) cc_final: 0.7385 (mt) REVERT: A 1167 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7675 (mt) REVERT: A 1199 LEU cc_start: 0.8761 (tt) cc_final: 0.8298 (mp) REVERT: A 1267 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8083 (mp) REVERT: A 1334 TYR cc_start: 0.6792 (t80) cc_final: 0.6574 (t80) REVERT: A 1337 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8260 (tp) REVERT: A 1374 ASN cc_start: 0.8918 (t0) cc_final: 0.8622 (t0) REVERT: A 1451 MET cc_start: 0.5371 (mpt) cc_final: 0.5167 (mpt) REVERT: E 2 SER cc_start: 0.7124 (p) cc_final: 0.6893 (t) REVERT: E 111 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.8058 (p) REVERT: E 126 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6679 (pp) REVERT: E 133 ARG cc_start: 0.4336 (OUTLIER) cc_final: 0.3709 (mmt180) REVERT: E 207 MET cc_start: 0.8266 (mmp) cc_final: 0.7924 (mmt) REVERT: E 216 MET cc_start: 0.2471 (ptt) cc_final: 0.2125 (ppp) REVERT: C 293 MET cc_start: 0.3512 (mtp) cc_final: 0.2542 (tmm) REVERT: F 59 ASP cc_start: 0.8609 (m-30) cc_final: 0.8263 (m-30) REVERT: F 132 ASP cc_start: 0.7847 (m-30) cc_final: 0.7396 (t0) REVERT: F 593 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8492 (mt) REVERT: F 668 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8609 (m-30) REVERT: F 674 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8128 (mttt) REVERT: F 689 PHE cc_start: 0.6752 (t80) cc_final: 0.6446 (m-80) REVERT: F 726 GLN cc_start: 0.6693 (mm-40) cc_final: 0.5696 (mt0) REVERT: F 829 THR cc_start: 0.6379 (m) cc_final: 0.5725 (p) REVERT: F 1019 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8572 (pp) REVERT: F 1024 LYS cc_start: 0.7737 (tttt) cc_final: 0.7181 (tttp) outliers start: 78 outliers final: 35 residues processed: 283 average time/residue: 0.4784 time to fit residues: 160.8486 Evaluate side-chains 272 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 218 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 988 ARG Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1381 MET Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 205 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 271 LEU Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 517 ILE Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 534 ILE Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 668 ASP Chi-restraints excluded: chain F residue 674 LYS Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain F residue 826 GLU Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: [44, 226, 71, 46, 193, 65, 227, 6, 211, 165, 205] chunk 44 optimal weight: 5.9990 chunk 226 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 193 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 227 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 211 optimal weight: 0.7980 chunk 165 optimal weight: 8.9990 chunk 205 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 456 GLN F 655 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.195781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.128099 restraints weight = 35947.527| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.92 r_work: 0.3297 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22504 Z= 0.121 Angle : 0.666 13.281 30525 Z= 0.317 Chirality : 0.045 0.471 3485 Planarity : 0.004 0.052 3805 Dihedral : 6.864 57.201 3044 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.90 % Allowed : 21.62 % Favored : 75.48 % 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: -0.39 (0.16), residues: 2659 helix: 0.60 (0.15), residues: 1319 sheet: -0.04 (0.30), residues: 264 loop : -1.37 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 646 TYR 0.012 0.001 TYR F 629 PHE 0.021 0.001 PHE A1063 TRP 0.019 0.001 TRP E 32 HIS 0.006 0.001 HIS A 462 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (22466) covalent geometry : angle 0.65095 / 0.31 (30427) SS BOND : bond 0.00330 / 0.24 ( 13) SS BOND : angle 1.47652 / 0.78 ( 26) hydrogen bonds : bond 0.03250 / 2.13 ( 843) hydrogen bonds : angle 4.04151 / 2.83 ( 2393) Misc. bond : bond 0.00029 / 0.02 ( 1) link_BETA1-3 : bond 0.00936 / 0.47 ( 3) link_BETA1-3 : angle 1.31961 / 0.76 ( 9) link_BETA1-4 : bond 0.00779 / 0.57 ( 7) link_BETA1-4 : angle 2.03569 / 1.12 ( 21) link_NAG-ASN : bond 0.00725 / 0.53 ( 14) link_NAG-ASN : angle 3.44224 / 2.06 ( 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 291 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 224 time to evaluate : 0.821 Fit side-chains revert: symmetry clash Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.6867 (OUTLIER) cc_final: 0.6577 (ttpt) REVERT: A 96 VAL cc_start: 0.7343 (t) cc_final: 0.7031 (p) REVERT: A 190 PHE cc_start: 0.7316 (t80) cc_final: 0.6904 (t80) REVERT: A 193 MET cc_start: 0.7769 (ttp) cc_final: 0.7440 (ptp) REVERT: A 205 PHE cc_start: 0.8057 (m-10) cc_final: 0.7269 (t80) REVERT: A 276 ASP cc_start: 0.8264 (p0) cc_final: 0.8051 (m-30) REVERT: A 594 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8228 (mmm-85) REVERT: A 653 LEU cc_start: 0.8859 (mp) cc_final: 0.8625 (mm) REVERT: A 819 GLU cc_start: 0.8202 (tt0) cc_final: 0.6889 (pp20) REVERT: A 820 ASP cc_start: 0.8170 (t0) cc_final: 0.7632 (t0) REVERT: A 851 MET cc_start: 0.4980 (OUTLIER) cc_final: 0.4710 (tmm) REVERT: A 988 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7659 (ptt-90) REVERT: A 1057 MET cc_start: 0.7649 (tmm) cc_final: 0.6330 (mmt) REVERT: A 1090 GLN cc_start: 0.6657 (OUTLIER) cc_final: 0.6258 (tp-100) REVERT: A 1093 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6854 (mt) REVERT: A 1154 ASN cc_start: 0.8640 (t0) cc_final: 0.8329 (t0) REVERT: A 1163 LEU cc_start: 0.7480 (mt) cc_final: 0.7216 (mt) REVERT: A 1167 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7538 (mt) REVERT: A 1199 LEU cc_start: 0.8593 (tt) cc_final: 0.8138 (mp) REVERT: A 1267 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7905 (mp) REVERT: A 1334 TYR cc_start: 0.6735 (t80) cc_final: 0.6494 (t80) REVERT: A 1374 ASN cc_start: 0.8816 (t0) cc_final: 0.8474 (t0) REVERT: A 1451 MET cc_start: 0.5132 (mpt) cc_final: 0.4823 (mpt) REVERT: E 2 SER cc_start: 0.7123 (p) cc_final: 0.6874 (t) REVERT: E 111 SER cc_start: 0.8382 (OUTLIER) cc_final: 0.8034 (p) REVERT: E 126 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6678 (pp) REVERT: E 133 ARG cc_start: 0.3900 (OUTLIER) cc_final: 0.3485 (mmt180) REVERT: E 207 MET cc_start: 0.8153 (mmp) cc_final: 0.7862 (mmt) REVERT: E 216 MET cc_start: 0.2618 (ptt) cc_final: 0.2204 (ppp) REVERT: C 293 MET cc_start: 0.3587 (mtp) cc_final: 0.2534 (tmm) REVERT: F 59 ASP cc_start: 0.8563 (m-30) cc_final: 0.7956 (m-30) REVERT: F 132 ASP cc_start: 0.7864 (m-30) cc_final: 0.7401 (t0) REVERT: F 593 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8523 (mt) REVERT: F 646 ARG cc_start: 0.7709 (ttm-80) cc_final: 0.7445 (tmm-80) REVERT: F 657 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7210 (mt-10) REVERT: F 674 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8078 (mttt) REVERT: F 689 PHE cc_start: 0.6635 (t80) cc_final: 0.6367 (m-80) REVERT: F 729 ILE cc_start: 0.7313 (mm) cc_final: 0.6987 (mt) REVERT: F 1019 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8485 (pp) REVERT: F 1024 LYS cc_start: 0.7675 (tttt) cc_final: 0.7233 (tttp) outliers start: 67 outliers final: 35 residues processed: 271 average time/residue: 0.4585 time to fit residues: 148.6816 Evaluate side-chains 264 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 215 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 988 ARG Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1352 CYS Chi-restraints excluded: chain A residue 1381 MET Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 205 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 271 LEU Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 517 ILE Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 528 ASN Chi-restraints excluded: chain F residue 534 ILE Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 674 LYS Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain F residue 826 GLU Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: [149, 233, 218, 127, 90, 134, 24, 186, 47, 260, 38] chunk 149 optimal weight: 40.0000 chunk 233 optimal weight: 0.6980 chunk 218 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 24 optimal weight: 0.0060 chunk 186 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 260 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 456 GLN F 655 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.196132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.125754 restraints weight = 37936.220| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.98 r_work: 0.3293 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22504 Z= 0.115 Angle : 0.656 12.590 30525 Z= 0.311 Chirality : 0.044 0.466 3485 Planarity : 0.004 0.054 3805 Dihedral : 6.748 58.553 3044 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.34 % Allowed : 22.23 % Favored : 75.43 % 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: -0.26 (0.16), residues: 2659 helix: 0.73 (0.15), residues: 1321 sheet: 0.01 (0.31), residues: 263 loop : -1.33 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 646 TYR 0.012 0.001 TYR F 629 PHE 0.035 0.001 PHE E 113 TRP 0.021 0.001 TRP E 32 HIS 0.004 0.001 HIS A 992 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (22466) covalent geometry : angle 0.64179 / 0.31 (30427) SS BOND : bond 0.00326 / 0.24 ( 13) SS BOND : angle 1.43555 / 0.77 ( 26) hydrogen bonds : bond 0.03087 / 2.02 ( 843) hydrogen bonds : angle 3.97815 / 2.78 ( 2393) Misc. bond : bond 0.00020 / 0.01 ( 1) link_BETA1-3 : bond 0.00980 / 0.49 ( 3) link_BETA1-3 : angle 1.36098 / 0.78 ( 9) link_BETA1-4 : bond 0.00799 / 0.58 ( 7) link_BETA1-4 : angle 1.97431 / 1.10 ( 21) link_NAG-ASN : bond 0.00717 / 0.52 ( 14) link_NAG-ASN : angle 3.27282 / 1.97 ( 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 277 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 223 time to evaluate : 0.796 Fit side-chains Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.6957 (OUTLIER) cc_final: 0.6674 (ttpt) REVERT: A 190 PHE cc_start: 0.7316 (t80) cc_final: 0.7077 (t80) REVERT: A 205 PHE cc_start: 0.7765 (m-10) cc_final: 0.7131 (t80) REVERT: A 540 LYS cc_start: 0.7130 (tmmt) cc_final: 0.6630 (tppt) REVERT: A 594 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8144 (mtp180) REVERT: A 653 LEU cc_start: 0.8782 (mp) cc_final: 0.8578 (mm) REVERT: A 819 GLU cc_start: 0.8129 (tt0) cc_final: 0.6998 (pp20) REVERT: A 820 ASP cc_start: 0.8169 (t0) cc_final: 0.7673 (t0) REVERT: A 851 MET cc_start: 0.4843 (tmt) cc_final: 0.4619 (tmm) REVERT: A 894 LYS cc_start: 0.6155 (tptp) cc_final: 0.5764 (tmtm) REVERT: A 988 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7526 (ptt-90) REVERT: A 1057 MET cc_start: 0.7438 (tmm) cc_final: 0.6884 (tmt) REVERT: A 1090 GLN cc_start: 0.6491 (OUTLIER) cc_final: 0.6123 (tp-100) REVERT: A 1093 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6930 (mt) REVERT: A 1154 ASN cc_start: 0.8660 (t0) cc_final: 0.8356 (t0) REVERT: A 1163 LEU cc_start: 0.7450 (mt) cc_final: 0.7186 (mt) REVERT: A 1167 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7547 (mt) REVERT: A 1199 LEU cc_start: 0.8487 (tt) cc_final: 0.7962 (mp) REVERT: A 1267 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7859 (mp) REVERT: A 1334 TYR cc_start: 0.6666 (t80) cc_final: 0.6402 (t80) REVERT: A 1374 ASN cc_start: 0.8623 (t0) cc_final: 0.8291 (t0) REVERT: A 1451 MET cc_start: 0.5199 (mpt) cc_final: 0.4890 (mpt) REVERT: E 2 SER cc_start: 0.7058 (p) cc_final: 0.6829 (t) REVERT: E 111 SER cc_start: 0.8369 (OUTLIER) cc_final: 0.8013 (p) REVERT: E 119 ILE cc_start: 0.8563 (mt) cc_final: 0.8263 (mp) REVERT: E 126 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6684 (pp) REVERT: E 133 ARG cc_start: 0.3894 (OUTLIER) cc_final: 0.3440 (mmt180) REVERT: E 207 MET cc_start: 0.8126 (mmp) cc_final: 0.7796 (mmt) REVERT: C 293 MET cc_start: 0.3631 (mtp) cc_final: 0.2550 (tmm) REVERT: F 59 ASP cc_start: 0.8467 (m-30) cc_final: 0.7866 (m-30) REVERT: F 132 ASP cc_start: 0.7803 (m-30) cc_final: 0.7347 (t0) REVERT: F 646 ARG cc_start: 0.7656 (ttm-80) cc_final: 0.7426 (tmm-80) REVERT: F 657 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7084 (mt-10) REVERT: F 674 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8047 (mttt) REVERT: F 689 PHE cc_start: 0.6688 (t80) cc_final: 0.6405 (m-80) REVERT: F 726 GLN cc_start: 0.6581 (mm-40) cc_final: 0.5554 (mt0) REVERT: F 729 ILE cc_start: 0.7340 (mm) cc_final: 0.6917 (mt) REVERT: F 1019 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8431 (pp) REVERT: F 1024 LYS cc_start: 0.7686 (tttt) cc_final: 0.7157 (tttp) outliers start: 54 outliers final: 33 residues processed: 263 average time/residue: 0.4368 time to fit residues: 137.6497 Evaluate side-chains 260 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 215 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 659 ILE Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 905 LEU Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 988 ARG Chi-restraints excluded: chain A residue 1081 LEU Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1352 CYS Chi-restraints excluded: chain A residue 1381 MET Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 205 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 271 LEU Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 517 ILE Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 528 ASN Chi-restraints excluded: chain F residue 534 ILE Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 674 LYS Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1067 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: [184, 164, 107, 57, 222, 32, 191, 76, 178, 46, 30] chunk 184 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 222 optimal weight: 0.6980 chunk 32 optimal weight: 30.0000 chunk 191 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 178 optimal weight: 0.0270 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 455 ASN F 655 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.196367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.127805 restraints weight = 40369.515| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.79 r_work: 0.3308 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22504 Z= 0.114 Angle : 0.656 14.008 30525 Z= 0.311 Chirality : 0.044 0.465 3485 Planarity : 0.004 0.054 3805 Dihedral : 6.614 59.567 3042 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.25 % Allowed : 22.53 % Favored : 75.22 % 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: -0.13 (0.16), residues: 2659 helix: 0.83 (0.15), residues: 1319 sheet: 0.02 (0.30), residues: 281 loop : -1.26 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 646 TYR 0.012 0.001 TYR F 629 PHE 0.022 0.001 PHE A1063 TRP 0.019 0.001 TRP E 32 HIS 0.004 0.001 HIS A 992 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (22466) covalent geometry : angle 0.64293 / 0.31 (30427) SS BOND : bond 0.00323 / 0.24 ( 13) SS BOND : angle 1.42851 / 0.76 ( 26) hydrogen bonds : bond 0.03045 / 2.00 ( 843) hydrogen bonds : angle 3.94127 / 2.75 ( 2393) Misc. bond : bond 0.00023 / 0.01 ( 1) link_BETA1-3 : bond 0.00973 / 0.49 ( 3) link_BETA1-3 : angle 1.35922 / 0.79 ( 9) link_BETA1-4 : bond 0.00737 / 0.53 ( 7) link_BETA1-4 : angle 1.92089 / 1.07 ( 21) link_NAG-ASN : bond 0.00701 / 0.51 ( 14) link_NAG-ASN : angle 3.17032 / 1.91 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11294.39 seconds wall clock time: 191 minutes 46.84 seconds (11506.84 seconds total)