Starting phenix.real_space_refine on Sun Sep 29 16:00:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpb_9869/09_2024/6jpb_9869.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpb_9869/09_2024/6jpb_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpb_9869/09_2024/6jpb_9869.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpb_9869/09_2024/6jpb_9869.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpb_9869/09_2024/6jpb_9869.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpb_9869/09_2024/6jpb_9869.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 P 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLN:plan1': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 57 Chain: "E" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1326 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 4 Chain: "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, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1367 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 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 dihedrals: 9 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: 78 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 dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 15.42, per 1000 atoms: 0.70 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: 5.65 Conformation dependent library (CDL) restraints added in 3.6 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: 2.82 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: 8.33 Time building geometry restraints manager: 6.56 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 - 27.40: 13114 27.40 - 54.80: 572 54.80 - 82.20: 84 82.20 - 109.60: 26 109.60 - 136.99: 18 Dihedral angle restraints: 13814 sinusoidal: 5915 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 13811 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: 0.010 Normalize map: mean=0, sd=1: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 52.920 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 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 : 0.015 0.154 22466 Z= 0.968 Angle : 1.480 15.224 30427 Z= 0.844 Chirality : 0.121 3.824 3485 Planarity : 0.014 0.300 3805 Dihedral : 16.402 136.994 8665 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 21.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (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 TRP 0.045 0.005 TRP A 265 HIS 0.023 0.003 HIS A 274 PHE 0.043 0.004 PHE F 663 TYR 0.060 0.005 TYR F 762 ARG 0.021 0.002 ARG F 275 *********************** 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 fitting. rotamer outliers: 101 poor density : 491 time to evaluate : 2.368 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: 1.1401 time to fit residues: 737.4550 Evaluate side-chains 297 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 272 time to evaluate : 2.328 ------------------------------------------------------------------------------- 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: chunk 225 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 209 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 chunk 242 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 A 793 HIS ** A1148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1355 ASN A1383 ASN ** A1398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1456 ASN A1464 ASN C 303 HIS F 56 GLN F 108 GLN F 228 ASN F 357 ASN F 450 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: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22466 Z= 0.242 Angle : 0.859 15.187 30427 Z= 0.421 Chirality : 0.051 0.674 3485 Planarity : 0.006 0.064 3805 Dihedral : 14.718 106.695 3688 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.12 % Favored : 94.73 % Rotamer: Outliers : 4.55 % Allowed : 14.99 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.14), residues: 2659 helix: -2.13 (0.12), residues: 1302 sheet: -1.40 (0.29), residues: 271 loop : -2.01 (0.17), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 32 HIS 0.009 0.001 HIS F 888 PHE 0.029 0.002 PHE A1402 TYR 0.029 0.002 TYR F 629 ARG 0.008 0.001 ARG F 646 *********************** 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 403 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 298 time to evaluate : 2.436 Fit side-chains Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7296 (mt-10) REVERT: A 111 LEU cc_start: 0.5155 (mm) cc_final: 0.4660 (tt) REVERT: A 114 GLN cc_start: 0.5595 (OUTLIER) cc_final: 0.5172 (pp30) REVERT: A 190 PHE cc_start: 0.7265 (t80) cc_final: 0.7013 (t80) REVERT: A 273 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8572 (m) REVERT: A 455 ASN cc_start: 0.7480 (OUTLIER) cc_final: 0.7226 (m110) REVERT: A 557 ARG cc_start: 0.6526 (mpt90) cc_final: 0.5847 (ttt-90) REVERT: A 653 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8457 (mp) REVERT: A 819 GLU cc_start: 0.7394 (tt0) cc_final: 0.7085 (tp30) REVERT: A 919 GLN cc_start: 0.5890 (mt0) cc_final: 0.5445 (mt0) REVERT: A 988 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7796 (ptp-170) REVERT: A 1005 MET cc_start: 0.8783 (tpt) cc_final: 0.8515 (tpt) REVERT: A 1057 MET cc_start: 0.6504 (tmm) cc_final: 0.6216 (mmt) REVERT: A 1093 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6674 (mt) REVERT: A 1105 ASN cc_start: 0.4508 (t0) cc_final: 0.4041 (t0) REVERT: A 1110 GLN cc_start: 0.5747 (tt0) cc_final: 0.5521 (mm110) REVERT: A 1137 MET cc_start: 0.8233 (mmt) cc_final: 0.7932 (mpp) REVERT: A 1163 LEU cc_start: 0.7798 (mt) cc_final: 0.7591 (mt) REVERT: E 17 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7678 (tm) REVERT: E 142 MET cc_start: 0.5957 (OUTLIER) cc_final: 0.5745 (mtt) REVERT: E 151 LEU cc_start: 0.8036 (mt) cc_final: 0.7445 (tp) REVERT: E 156 GLU cc_start: 0.6252 (mm-30) cc_final: 0.5941 (mt-10) REVERT: E 216 MET cc_start: 0.2659 (ptt) cc_final: 0.2105 (tmm) REVERT: C 292 MET cc_start: 0.3327 (mtt) cc_final: 0.2300 (tpp) REVERT: C 293 MET cc_start: 0.2962 (mtp) cc_final: 0.2435 (tmm) REVERT: F 39 LYS cc_start: 0.7711 (tptp) cc_final: 0.7209 (tptp) REVERT: F 355 ASN cc_start: 0.7225 (t0) cc_final: 0.7004 (t0) REVERT: F 361 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7879 (mtt) REVERT: F 659 SER cc_start: 0.8606 (t) cc_final: 0.8363 (m) REVERT: F 689 PHE cc_start: 0.6943 (OUTLIER) cc_final: 0.6488 (m-80) REVERT: F 761 THR cc_start: 0.8310 (t) cc_final: 0.8002 (p) REVERT: F 867 HIS cc_start: 0.7424 (t-170) cc_final: 0.6929 (t-170) REVERT: F 991 LYS cc_start: 0.7144 (mtpp) cc_final: 0.6789 (mttm) REVERT: F 1019 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8397 (pp) REVERT: F 1020 MET cc_start: 0.7446 (ttt) cc_final: 0.6927 (ttp) outliers start: 105 outliers final: 27 residues processed: 371 average time/residue: 1.0424 time to fit residues: 455.6961 Evaluate side-chains 278 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 239 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 653 LEU Chi-restraints excluded: chain A residue 659 ILE 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 E residue 142 MET 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 271 LEU Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 328 THR 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 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 Chi-restraints excluded: chain F residue 1035 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 134 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 201 optimal weight: 0.8980 chunk 165 optimal weight: 8.9990 chunk 66 optimal weight: 20.0000 chunk 242 optimal weight: 0.0050 chunk 262 optimal weight: 0.1980 chunk 216 optimal weight: 4.9990 chunk 240 optimal weight: 0.0670 chunk 82 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 overall best weight: 0.4332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 654 ASN A1148 HIS ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 480 ASN ** F 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22466 Z= 0.176 Angle : 0.706 11.645 30427 Z= 0.348 Chirality : 0.046 0.462 3485 Planarity : 0.005 0.057 3805 Dihedral : 12.716 105.259 3660 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.08 % Favored : 94.88 % Rotamer: Outliers : 4.29 % Allowed : 16.90 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.15), residues: 2659 helix: -1.26 (0.13), residues: 1304 sheet: -1.03 (0.29), residues: 268 loop : -1.78 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 32 HIS 0.010 0.001 HIS A 113 PHE 0.016 0.001 PHE A1063 TYR 0.026 0.001 TYR F 629 ARG 0.005 0.000 ARG A 168 *********************** 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 358 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 259 time to evaluate : 2.281 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 57 ILE cc_start: 0.6896 (OUTLIER) cc_final: 0.6320 (mp) REVERT: A 87 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.7061 (mt-10) REVERT: A 111 LEU cc_start: 0.5747 (mm) cc_final: 0.5418 (tt) REVERT: A 190 PHE cc_start: 0.7225 (t80) cc_final: 0.7002 (t80) REVERT: A 273 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8558 (m) REVERT: A 455 ASN cc_start: 0.7511 (OUTLIER) cc_final: 0.7284 (m110) REVERT: A 557 ARG cc_start: 0.6572 (mpt90) cc_final: 0.5996 (ttt-90) REVERT: A 819 GLU cc_start: 0.7362 (tt0) cc_final: 0.7099 (tp30) REVERT: A 948 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7609 (mp10) REVERT: A 988 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7719 (ptp-170) REVERT: A 1057 MET cc_start: 0.6350 (tmm) cc_final: 0.6015 (mmt) REVERT: A 1093 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6648 (mt) REVERT: A 1163 LEU cc_start: 0.7734 (mt) cc_final: 0.7392 (mt) REVERT: A 1167 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7832 (mt) REVERT: A 1318 ARG cc_start: 0.8421 (ttt-90) cc_final: 0.8052 (ttt180) REVERT: E 118 LEU cc_start: 0.7507 (tp) cc_final: 0.7305 (tp) REVERT: E 151 LEU cc_start: 0.8157 (mt) cc_final: 0.7601 (tp) REVERT: E 156 GLU cc_start: 0.6780 (mm-30) cc_final: 0.6387 (mm-30) REVERT: E 216 MET cc_start: 0.2351 (ptt) cc_final: 0.1886 (tmm) REVERT: C 292 MET cc_start: 0.3275 (mtt) cc_final: 0.2654 (tpp) REVERT: C 293 MET cc_start: 0.2891 (mtp) cc_final: 0.2342 (tmm) REVERT: C 400 LEU cc_start: 0.0118 (OUTLIER) cc_final: -0.0291 (tt) REVERT: F 39 LYS cc_start: 0.7925 (tptp) cc_final: 0.7479 (tptp) REVERT: F 43 ASP cc_start: 0.6861 (m-30) cc_final: 0.6526 (m-30) REVERT: F 132 ASP cc_start: 0.7437 (m-30) cc_final: 0.7137 (t0) REVERT: F 355 ASN cc_start: 0.7052 (t0) cc_final: 0.6840 (t0) REVERT: F 404 MET cc_start: 0.8659 (mtt) cc_final: 0.8407 (mtm) REVERT: F 508 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7078 (mt) REVERT: F 591 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7633 (ttt90) REVERT: F 644 GLN cc_start: 0.8116 (mt0) cc_final: 0.7458 (mp10) REVERT: F 689 PHE cc_start: 0.6994 (OUTLIER) cc_final: 0.6550 (m-80) REVERT: F 806 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.6993 (mp10) REVERT: F 1019 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8475 (pp) outliers start: 99 outliers final: 26 residues processed: 326 average time/residue: 0.9985 time to fit residues: 385.7289 Evaluate side-chains 266 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 226 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE 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 273 THR Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 509 LEU 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 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 400 LEU Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 152 ILE 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 302 ASP Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain F residue 591 ARG 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 728 ASN Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 806 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 239 optimal weight: 0.9990 chunk 182 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 258 optimal weight: 0.9980 chunk 127 optimal weight: 8.9990 chunk 231 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 GLN F 395 ASN F 687 ASN F 866 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22466 Z= 0.203 Angle : 0.688 11.579 30427 Z= 0.335 Chirality : 0.046 0.404 3485 Planarity : 0.005 0.053 3805 Dihedral : 11.604 103.875 3653 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.33 % Allowed : 18.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.16), residues: 2659 helix: -0.66 (0.14), residues: 1303 sheet: -0.65 (0.30), residues: 266 loop : -1.62 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 32 HIS 0.006 0.001 HIS A 992 PHE 0.024 0.001 PHE E 113 TYR 0.021 0.001 TYR F 629 ARG 0.009 0.000 ARG F 646 *********************** 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 fitting. rotamer outliers: 100 poor density : 243 time to evaluate : 2.622 Fit side-chains Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash REVERT: A 57 ILE cc_start: 0.6990 (OUTLIER) cc_final: 0.6650 (mp) REVERT: A 111 LEU cc_start: 0.5784 (mm) cc_final: 0.5504 (tt) REVERT: A 273 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8614 (m) REVERT: A 988 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7698 (ptt180) REVERT: A 1057 MET cc_start: 0.6372 (tmm) cc_final: 0.6114 (mmt) REVERT: A 1093 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6715 (mt) REVERT: A 1137 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.6968 (mpp) REVERT: A 1163 LEU cc_start: 0.7557 (mt) cc_final: 0.7257 (mt) REVERT: A 1167 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7693 (mt) REVERT: A 1236 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7111 (mpp-170) REVERT: E 127 MET cc_start: 0.6744 (tmm) cc_final: 0.6370 (ttt) REVERT: E 133 ARG cc_start: 0.4000 (OUTLIER) cc_final: 0.3426 (mmt180) REVERT: E 151 LEU cc_start: 0.8150 (mt) cc_final: 0.7628 (tp) REVERT: E 207 MET cc_start: 0.8140 (mmp) cc_final: 0.7902 (mmt) REVERT: C 292 MET cc_start: 0.3297 (mtt) cc_final: 0.2753 (tpp) REVERT: C 293 MET cc_start: 0.3207 (mtp) cc_final: 0.2584 (tmm) REVERT: C 400 LEU cc_start: 0.0168 (OUTLIER) cc_final: -0.0138 (tt) REVERT: F 39 LYS cc_start: 0.8106 (tptp) cc_final: 0.7682 (tptp) REVERT: F 132 ASP cc_start: 0.7451 (m-30) cc_final: 0.7155 (t0) REVERT: F 404 MET cc_start: 0.8822 (mtt) cc_final: 0.8479 (mtm) REVERT: F 508 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7343 (mt) REVERT: F 644 GLN cc_start: 0.8066 (mt0) cc_final: 0.7478 (mp10) REVERT: F 688 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7378 (mt-10) REVERT: F 689 PHE cc_start: 0.6804 (OUTLIER) cc_final: 0.6466 (m-80) REVERT: F 845 LYS cc_start: 0.6521 (mppt) cc_final: 0.6262 (mtmt) REVERT: F 1019 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8524 (pp) REVERT: F 1024 LYS cc_start: 0.7461 (tttt) cc_final: 0.6940 (tttp) outliers start: 100 outliers final: 37 residues processed: 317 average time/residue: 0.9660 time to fit residues: 365.2753 Evaluate side-chains 271 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 222 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE 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 182 LEU Chi-restraints excluded: chain A residue 273 THR 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 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 205 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 369 GLU Chi-restraints excluded: chain F residue 406 CYS 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 668 ASP 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 793 SER Chi-restraints excluded: chain F residue 826 GLU 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 1067 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 214 optimal weight: 1.9990 chunk 146 optimal weight: 20.0000 chunk 3 optimal weight: 0.0050 chunk 192 optimal weight: 0.7980 chunk 106 optimal weight: 0.2980 chunk 220 optimal weight: 3.9990 chunk 178 optimal weight: 0.0670 chunk 0 optimal weight: 30.0000 chunk 131 optimal weight: 8.9990 chunk 231 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 overall best weight: 0.6334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1311 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 644 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22466 Z= 0.167 Angle : 0.650 11.101 30427 Z= 0.314 Chirality : 0.044 0.360 3485 Planarity : 0.004 0.052 3805 Dihedral : 10.973 108.046 3651 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.42 % Allowed : 18.46 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.16), residues: 2659 helix: -0.24 (0.14), residues: 1319 sheet: -0.41 (0.30), residues: 265 loop : -1.53 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 32 HIS 0.004 0.001 HIS A 992 PHE 0.018 0.001 PHE A1063 TYR 0.015 0.001 TYR F 629 ARG 0.005 0.000 ARG A 528 *********************** 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 341 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 239 time to evaluate : 2.491 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: 0.7078 (OUTLIER) cc_final: 0.6844 (mt-10) REVERT: A 273 THR cc_start: 0.8867 (OUTLIER) cc_final: 0.8636 (m) REVERT: A 851 MET cc_start: 0.4622 (OUTLIER) cc_final: 0.4234 (tmm) REVERT: A 988 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7706 (ptt180) REVERT: A 1057 MET cc_start: 0.6241 (tmm) cc_final: 0.6035 (mmt) REVERT: A 1090 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6532 (tp-100) REVERT: A 1093 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6633 (mt) REVERT: A 1163 LEU cc_start: 0.7499 (mt) cc_final: 0.7207 (mt) REVERT: A 1167 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7671 (mt) REVERT: A 1199 LEU cc_start: 0.8461 (tt) cc_final: 0.8076 (mp) REVERT: A 1374 ASN cc_start: 0.8437 (t0) cc_final: 0.8233 (t0) REVERT: A 1383 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.7986 (m-40) REVERT: E 119 ILE cc_start: 0.8668 (mt) cc_final: 0.8359 (mp) REVERT: E 133 ARG cc_start: 0.4045 (OUTLIER) cc_final: 0.3680 (mmt180) REVERT: E 207 MET cc_start: 0.8175 (mmp) cc_final: 0.7929 (mmt) REVERT: C 292 MET cc_start: 0.3229 (mtt) cc_final: 0.2765 (tpp) REVERT: C 293 MET cc_start: 0.3323 (mtp) cc_final: 0.2689 (tmm) REVERT: C 400 LEU cc_start: 0.0249 (OUTLIER) cc_final: -0.0028 (tt) REVERT: F 132 ASP cc_start: 0.7459 (m-30) cc_final: 0.7154 (t0) REVERT: F 404 MET cc_start: 0.8817 (mtt) cc_final: 0.8487 (mtm) REVERT: F 508 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7471 (mt) REVERT: F 674 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7844 (mttt) REVERT: F 689 PHE cc_start: 0.6775 (OUTLIER) cc_final: 0.6417 (m-80) REVERT: F 829 THR cc_start: 0.6259 (m) cc_final: 0.5764 (p) REVERT: F 1019 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8487 (pp) REVERT: F 1024 LYS cc_start: 0.7501 (tttt) cc_final: 0.6998 (tttp) outliers start: 102 outliers final: 39 residues processed: 317 average time/residue: 1.0037 time to fit residues: 378.4677 Evaluate side-chains 270 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 217 time to evaluate : 2.309 ------------------------------------------------------------------------------- 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 182 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 486 LEU 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 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 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 1383 ASN Chi-restraints excluded: chain E residue 9 VAL 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 152 ILE Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 406 CYS 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 668 ASP 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: chunk 86 optimal weight: 0.0770 chunk 232 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 258 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 135 optimal weight: 0.1980 overall best weight: 1.2542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 HIS ** A1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1398 HIS C 294 GLN F 308 HIS F 644 GLN F 847 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22466 Z= 0.225 Angle : 0.681 12.408 30427 Z= 0.330 Chirality : 0.045 0.364 3485 Planarity : 0.005 0.052 3805 Dihedral : 10.645 104.656 3650 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.94 % Allowed : 19.45 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.16), residues: 2659 helix: 0.06 (0.14), residues: 1306 sheet: -0.22 (0.30), residues: 264 loop : -1.49 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 32 HIS 0.007 0.001 HIS A 992 PHE 0.020 0.002 PHE E 152 TYR 0.016 0.001 TYR A 627 ARG 0.010 0.000 ARG F 646 *********************** 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 313 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 222 time to evaluate : 2.488 Fit side-chains 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: 0.7180 (OUTLIER) cc_final: 0.6921 (mt-10) REVERT: A 139 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6932 (tt) REVERT: A 273 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8659 (m) REVERT: A 851 MET cc_start: 0.4586 (OUTLIER) cc_final: 0.4296 (tpt) REVERT: A 988 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8083 (ptp90) REVERT: A 1090 GLN cc_start: 0.7152 (OUTLIER) cc_final: 0.6571 (tp-100) REVERT: A 1093 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6609 (mt) REVERT: A 1163 LEU cc_start: 0.7461 (mt) cc_final: 0.7169 (mt) REVERT: A 1167 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7561 (mt) REVERT: A 1199 LEU cc_start: 0.8583 (tt) cc_final: 0.8106 (mp) REVERT: A 1267 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8167 (mp) REVERT: A 1337 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.7910 (tp) REVERT: A 1374 ASN cc_start: 0.8451 (t0) cc_final: 0.8230 (t0) REVERT: E 111 SER cc_start: 0.8346 (t) cc_final: 0.7989 (p) REVERT: E 127 MET cc_start: 0.6838 (tmm) cc_final: 0.6483 (ttt) REVERT: E 133 ARG cc_start: 0.3984 (OUTLIER) cc_final: 0.3618 (mmt180) REVERT: E 151 LEU cc_start: 0.7963 (mt) cc_final: 0.7323 (pp) REVERT: E 158 MET cc_start: 0.7112 (mmp) cc_final: 0.6859 (mmp) REVERT: E 207 MET cc_start: 0.8255 (mmp) cc_final: 0.7960 (mmt) REVERT: C 292 MET cc_start: 0.3174 (mtt) cc_final: 0.2714 (tpp) REVERT: C 293 MET cc_start: 0.3311 (mtp) cc_final: 0.2659 (tmm) REVERT: C 400 LEU cc_start: 0.0281 (OUTLIER) cc_final: 0.0052 (tt) REVERT: F 39 LYS cc_start: 0.8353 (tmtt) cc_final: 0.8099 (tptp) REVERT: F 132 ASP cc_start: 0.7557 (m-30) cc_final: 0.7213 (t0) REVERT: F 508 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7610 (mt) REVERT: F 593 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8408 (mt) REVERT: F 674 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7867 (mttt) REVERT: F 689 PHE cc_start: 0.6717 (OUTLIER) cc_final: 0.6374 (m-80) REVERT: F 829 THR cc_start: 0.6296 (m) cc_final: 0.5851 (p) REVERT: F 1019 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8535 (pp) REVERT: F 1024 LYS cc_start: 0.7659 (tttt) cc_final: 0.7228 (tttp) REVERT: F 1068 LEU cc_start: 0.8926 (pt) cc_final: 0.8698 (pp) outliers start: 91 outliers final: 37 residues processed: 291 average time/residue: 1.0006 time to fit residues: 346.1429 Evaluate side-chains 265 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 211 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 182 LEU 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 637 VAL Chi-restraints excluded: chain A residue 639 ILE 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 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 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 152 ILE Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 240 VAL 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 406 CYS 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 668 ASP 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 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: chunk 249 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 147 optimal weight: 0.0270 chunk 188 optimal weight: 0.6980 chunk 146 optimal weight: 20.0000 chunk 217 optimal weight: 0.6980 chunk 144 optimal weight: 10.0000 chunk 257 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN ** A1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 644 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22466 Z= 0.165 Angle : 0.658 12.395 30427 Z= 0.316 Chirality : 0.044 0.334 3485 Planarity : 0.004 0.052 3805 Dihedral : 10.258 103.491 3650 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.64 % Allowed : 20.06 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.16), residues: 2659 helix: 0.33 (0.15), residues: 1315 sheet: -0.19 (0.29), residues: 276 loop : -1.48 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 32 HIS 0.004 0.001 HIS A 992 PHE 0.026 0.001 PHE E 113 TYR 0.012 0.001 TYR A1119 ARG 0.013 0.000 ARG F 607 *********************** 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 312 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 228 time to evaluate : 2.237 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: A 87 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6917 (mt-10) REVERT: A 273 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8676 (m) REVERT: A 851 MET cc_start: 0.4733 (OUTLIER) cc_final: 0.4470 (tpt) REVERT: A 988 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7578 (ptt180) REVERT: A 1090 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6638 (tp-100) REVERT: A 1093 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6748 (mt) REVERT: A 1163 LEU cc_start: 0.7475 (mt) cc_final: 0.7205 (mt) REVERT: A 1167 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7562 (mt) REVERT: A 1199 LEU cc_start: 0.8641 (tt) cc_final: 0.8162 (mp) REVERT: A 1267 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8163 (mp) REVERT: A 1269 TYR cc_start: 0.8562 (m-80) cc_final: 0.8242 (m-80) REVERT: A 1337 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7832 (tp) REVERT: E 17 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7125 (mt) REVERT: E 111 SER cc_start: 0.8317 (t) cc_final: 0.7977 (p) REVERT: E 126 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6619 (pp) REVERT: E 127 MET cc_start: 0.6853 (tmm) cc_final: 0.6621 (ttt) REVERT: E 133 ARG cc_start: 0.4036 (OUTLIER) cc_final: 0.3593 (mmt180) REVERT: E 207 MET cc_start: 0.8252 (mmp) cc_final: 0.7966 (mmt) REVERT: C 293 MET cc_start: 0.3351 (mtp) cc_final: 0.2640 (tmm) REVERT: C 400 LEU cc_start: 0.0550 (OUTLIER) cc_final: 0.0267 (tt) REVERT: F 39 LYS cc_start: 0.8391 (tmtt) cc_final: 0.8123 (tptt) REVERT: F 132 ASP cc_start: 0.7555 (m-30) cc_final: 0.7185 (t0) REVERT: F 593 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8454 (mt) REVERT: F 657 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6942 (mt-10) REVERT: F 689 PHE cc_start: 0.6663 (t80) cc_final: 0.6319 (m-80) REVERT: F 829 THR cc_start: 0.6124 (m) cc_final: 0.5665 (p) REVERT: F 991 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.7249 (mtpp) REVERT: F 1019 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8492 (pp) REVERT: F 1024 LYS cc_start: 0.7767 (tttt) cc_final: 0.7346 (tttp) REVERT: F 1068 LEU cc_start: 0.8952 (pt) cc_final: 0.8715 (pp) outliers start: 84 outliers final: 37 residues processed: 288 average time/residue: 1.0438 time to fit residues: 356.6292 Evaluate side-chains 268 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 215 time to evaluate : 2.763 ------------------------------------------------------------------------------- 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 273 THR Chi-restraints excluded: chain A residue 509 LEU 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 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 1352 CYS Chi-restraints excluded: chain E residue 17 LEU 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 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 333 THR Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 406 CYS 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 991 LYS 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: chunk 159 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 153 optimal weight: 0.0370 chunk 77 optimal weight: 0.0670 chunk 50 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 chunk 175 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 202 optimal weight: 4.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 644 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22466 Z= 0.156 Angle : 0.636 13.440 30427 Z= 0.306 Chirality : 0.043 0.321 3485 Planarity : 0.004 0.051 3805 Dihedral : 9.856 102.700 3648 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.99 % Allowed : 21.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.16), residues: 2659 helix: 0.54 (0.15), residues: 1316 sheet: -0.03 (0.30), residues: 263 loop : -1.39 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 32 HIS 0.004 0.001 HIS A 992 PHE 0.022 0.001 PHE A1063 TYR 0.015 0.001 TYR A1334 ARG 0.008 0.000 ARG F 646 *********************** 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 292 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 223 time to evaluate : 2.224 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 139 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6843 (tt) REVERT: A 273 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8653 (m) REVERT: A 851 MET cc_start: 0.4774 (OUTLIER) cc_final: 0.4485 (tmm) REVERT: A 988 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7933 (ptp90) REVERT: A 1090 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.6527 (tp-100) REVERT: A 1093 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6821 (mt) REVERT: A 1163 LEU cc_start: 0.7468 (mt) cc_final: 0.7197 (mt) REVERT: A 1167 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7589 (mt) REVERT: A 1199 LEU cc_start: 0.8655 (tt) cc_final: 0.8162 (mp) REVERT: A 1267 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8138 (mp) REVERT: A 1269 TYR cc_start: 0.8519 (m-80) cc_final: 0.8234 (m-80) REVERT: E 17 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7092 (mt) REVERT: E 111 SER cc_start: 0.8178 (t) cc_final: 0.7836 (p) REVERT: E 119 ILE cc_start: 0.8751 (mt) cc_final: 0.8442 (mp) REVERT: E 126 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6625 (pp) REVERT: E 127 MET cc_start: 0.6855 (tmm) cc_final: 0.6635 (ttt) REVERT: E 133 ARG cc_start: 0.4132 (OUTLIER) cc_final: 0.3633 (mmt180) REVERT: E 207 MET cc_start: 0.8212 (mmp) cc_final: 0.7983 (mmt) REVERT: C 293 MET cc_start: 0.3667 (mtp) cc_final: 0.2519 (tmm) REVERT: F 39 LYS cc_start: 0.8383 (tmtt) cc_final: 0.8121 (tptp) REVERT: F 132 ASP cc_start: 0.7526 (m-30) cc_final: 0.7148 (t0) REVERT: F 657 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6958 (mt-10) REVERT: F 689 PHE cc_start: 0.6631 (t80) cc_final: 0.6302 (m-80) REVERT: F 829 THR cc_start: 0.6104 (m) cc_final: 0.5609 (p) REVERT: F 1019 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8482 (pp) REVERT: F 1024 LYS cc_start: 0.7669 (tttt) cc_final: 0.7256 (tttp) REVERT: F 1068 LEU cc_start: 0.8938 (pt) cc_final: 0.8703 (pp) outliers start: 69 outliers final: 35 residues processed: 271 average time/residue: 0.9900 time to fit residues: 319.0314 Evaluate side-chains 256 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 209 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 142 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 486 LEU 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 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 1352 CYS Chi-restraints excluded: chain E residue 17 LEU 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 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 373 GLU Chi-restraints excluded: chain F residue 406 CYS 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 606 ASN 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 234 optimal weight: 1.9990 chunk 246 optimal weight: 7.9990 chunk 224 optimal weight: 0.0270 chunk 239 optimal weight: 3.9990 chunk 144 optimal weight: 30.0000 chunk 104 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 216 optimal weight: 0.5980 chunk 226 optimal weight: 1.9990 chunk 238 optimal weight: 0.6980 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22466 Z= 0.162 Angle : 0.644 12.367 30427 Z= 0.307 Chirality : 0.044 0.313 3485 Planarity : 0.004 0.061 3805 Dihedral : 9.479 99.528 3646 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.64 % Allowed : 21.62 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.16), residues: 2659 helix: 0.68 (0.15), residues: 1316 sheet: -0.02 (0.30), residues: 268 loop : -1.34 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 32 HIS 0.004 0.001 HIS A 992 PHE 0.033 0.001 PHE E 113 TYR 0.011 0.001 TYR A1119 ARG 0.007 0.000 ARG F 199 *********************** 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 274 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 213 time to evaluate : 2.443 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 273 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8668 (m) REVERT: A 851 MET cc_start: 0.4516 (OUTLIER) cc_final: 0.4270 (tmm) REVERT: A 894 LYS cc_start: 0.6083 (tptp) cc_final: 0.5747 (tmtm) REVERT: A 988 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7646 (ptt180) REVERT: A 1090 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6563 (tp-100) REVERT: A 1093 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6765 (mt) REVERT: A 1163 LEU cc_start: 0.7459 (mt) cc_final: 0.7217 (mt) REVERT: A 1167 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7562 (mt) REVERT: A 1199 LEU cc_start: 0.8761 (tt) cc_final: 0.8221 (mp) REVERT: A 1267 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8102 (mp) REVERT: A 1269 TYR cc_start: 0.8481 (m-80) cc_final: 0.8141 (m-80) REVERT: A 1393 ILE cc_start: 0.7595 (tt) cc_final: 0.7341 (mm) REVERT: E 17 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7129 (mt) REVERT: E 111 SER cc_start: 0.8114 (t) cc_final: 0.7770 (p) REVERT: E 119 ILE cc_start: 0.8707 (mt) cc_final: 0.8410 (mp) REVERT: E 126 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6635 (pp) REVERT: E 127 MET cc_start: 0.6893 (tmm) cc_final: 0.6631 (ttt) REVERT: E 133 ARG cc_start: 0.4100 (OUTLIER) cc_final: 0.3606 (mmt180) REVERT: E 207 MET cc_start: 0.8224 (mmp) cc_final: 0.7952 (mmt) REVERT: C 293 MET cc_start: 0.3616 (mtp) cc_final: 0.2468 (tmm) REVERT: F 39 LYS cc_start: 0.8378 (tmtt) cc_final: 0.8118 (tptp) REVERT: F 59 ASP cc_start: 0.8153 (m-30) cc_final: 0.7744 (m-30) REVERT: F 132 ASP cc_start: 0.7569 (m-30) cc_final: 0.7190 (t0) REVERT: F 657 GLU cc_start: 0.7249 (mm-30) cc_final: 0.7032 (mt-10) REVERT: F 674 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7876 (mttt) REVERT: F 689 PHE cc_start: 0.6601 (t80) cc_final: 0.6265 (m-80) REVERT: F 1019 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8470 (pp) REVERT: F 1024 LYS cc_start: 0.7707 (tttt) cc_final: 0.7258 (tttp) REVERT: F 1068 LEU cc_start: 0.8986 (pt) cc_final: 0.8782 (pp) outliers start: 61 outliers final: 35 residues processed: 261 average time/residue: 1.0090 time to fit residues: 316.7228 Evaluate side-chains 248 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 201 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 486 LEU 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 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 1352 CYS Chi-restraints excluded: chain E residue 17 LEU 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 F residue 80 GLU Chi-restraints excluded: chain F residue 178 SER 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 406 CYS 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 606 ASN 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: chunk 157 optimal weight: 20.0000 chunk 253 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 chunk 176 optimal weight: 3.9990 chunk 266 optimal weight: 6.9990 chunk 244 optimal weight: 0.4980 chunk 211 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 163 optimal weight: 20.0000 chunk 129 optimal weight: 0.2980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN A1154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22466 Z= 0.227 Angle : 0.673 13.190 30427 Z= 0.324 Chirality : 0.045 0.324 3485 Planarity : 0.005 0.065 3805 Dihedral : 9.436 99.379 3646 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.25 % Allowed : 22.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.16), residues: 2659 helix: 0.65 (0.15), residues: 1319 sheet: -0.04 (0.31), residues: 266 loop : -1.31 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 32 HIS 0.007 0.001 HIS A 992 PHE 0.021 0.001 PHE A1063 TYR 0.018 0.001 TYR F 629 ARG 0.007 0.000 ARG F 199 ********************** 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 261 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 209 time to evaluate : 2.406 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 273 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8691 (m) REVERT: A 851 MET cc_start: 0.4644 (tmt) cc_final: 0.4396 (tmm) REVERT: A 988 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7955 (ptp-170) REVERT: A 1090 GLN cc_start: 0.7082 (OUTLIER) cc_final: 0.6639 (tp-100) REVERT: A 1093 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6861 (mt) REVERT: A 1163 LEU cc_start: 0.7438 (mt) cc_final: 0.7189 (mt) REVERT: A 1167 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7585 (mt) REVERT: A 1195 ILE cc_start: 0.8168 (mm) cc_final: 0.7948 (mt) REVERT: A 1199 LEU cc_start: 0.8751 (tt) cc_final: 0.8205 (mp) REVERT: A 1393 ILE cc_start: 0.7560 (tt) cc_final: 0.7279 (mm) REVERT: E 17 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7138 (mt) REVERT: E 111 SER cc_start: 0.8132 (t) cc_final: 0.7800 (p) REVERT: E 119 ILE cc_start: 0.8729 (mt) cc_final: 0.8440 (mp) REVERT: E 126 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6658 (pp) REVERT: E 127 MET cc_start: 0.6899 (tmm) cc_final: 0.6668 (ttt) REVERT: E 133 ARG cc_start: 0.4148 (OUTLIER) cc_final: 0.3421 (mmt180) REVERT: C 293 MET cc_start: 0.3685 (mtp) cc_final: 0.2528 (tmm) REVERT: F 39 LYS cc_start: 0.8377 (tmtt) cc_final: 0.8111 (tptp) REVERT: F 59 ASP cc_start: 0.8169 (m-30) cc_final: 0.7519 (m-30) REVERT: F 132 ASP cc_start: 0.7519 (m-30) cc_final: 0.7138 (t0) REVERT: F 657 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7057 (mt-10) REVERT: F 689 PHE cc_start: 0.6624 (t80) cc_final: 0.6294 (m-80) REVERT: F 1012 MET cc_start: 0.7481 (mmm) cc_final: 0.7202 (mmt) REVERT: F 1019 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8478 (pp) REVERT: F 1024 LYS cc_start: 0.7582 (tttt) cc_final: 0.7072 (tttp) REVERT: F 1068 LEU cc_start: 0.9021 (pt) cc_final: 0.8795 (pp) outliers start: 52 outliers final: 34 residues processed: 249 average time/residue: 0.9816 time to fit residues: 290.9768 Evaluate side-chains 248 residues out of total 2378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 205 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 486 LEU 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 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 1308 THR Chi-restraints excluded: chain A residue 1352 CYS Chi-restraints excluded: chain E residue 17 LEU 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 F residue 80 GLU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 178 SER 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 406 CYS 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 606 ASN 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: chunk 168 optimal weight: 4.9990 chunk 225 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 212 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 217 optimal weight: 0.0070 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 0.4980 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN A1154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.196577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.128543 restraints weight = 33928.070| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.12 r_work: 0.3318 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22466 Z= 0.163 Angle : 0.643 12.303 30427 Z= 0.306 Chirality : 0.043 0.301 3485 Planarity : 0.004 0.058 3805 Dihedral : 9.116 96.877 3646 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.99 % Allowed : 22.88 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.16), residues: 2659 helix: 0.82 (0.15), residues: 1311 sheet: -0.03 (0.30), residues: 281 loop : -1.27 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 32 HIS 0.005 0.001 HIS A 992 PHE 0.034 0.001 PHE E 113 TYR 0.012 0.001 TYR F 629 ARG 0.008 0.000 ARG F 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8271.55 seconds wall clock time: 145 minutes 34.30 seconds (8734.30 seconds total)