Starting phenix.real_space_refine on Tue Dec 31 05:24:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m23_30061/12_2024/6m23_30061.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m23_30061/12_2024/6m23_30061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m23_30061/12_2024/6m23_30061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m23_30061/12_2024/6m23_30061.map" model { file = "/net/cci-nas-00/data/ceres_data/6m23_30061/12_2024/6m23_30061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m23_30061/12_2024/6m23_30061.cif" } resolution = 3.2 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= 0.002 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 S 116 5.16 5 Cl 2 4.86 5 C 9452 2.51 5 N 2480 2.21 5 O 2688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 14744 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 936, 7271 Classifications: {'peptide': 936} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 33, 'TRANS': 902} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'TPO:plan-1': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 7271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 936, 7271 Classifications: {'peptide': 936} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 33, 'TRANS': 902} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'TPO:plan-1': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" 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: "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: "E" 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: "F" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' K': 1, ' CL': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' K': 1, ' CL': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 9.64, per 1000 atoms: 0.65 Number of scatterers: 14744 At special positions: 0 Unit cell: (96.743, 114.135, 158.702, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 Cl 2 17.00 S 116 16.00 P 4 15.00 O 2688 8.00 N 2480 7.00 C 9452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 331 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1209 " - " ASN A 310 " " NAG B1209 " - " ASN B 310 " " NAG C 1 " - " ASN A 291 " " NAG D 1 " - " ASN A 328 " " NAG E 1 " - " ASN A 339 " " NAG F 1 " - " ASN B 291 " " NAG G 1 " - " ASN B 328 " " NAG H 1 " - " ASN B 339 " Time building additional restraints: 4.59 Conformation dependent library (CDL) restraints added in 2.1 seconds 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3424 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 10 sheets defined 53.7% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.563A pdb=" N GLN A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 111 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 119 removed outlier: 3.928A pdb=" N PHE A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 139 through 155 removed outlier: 3.809A pdb=" N THR A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 174 through 179 removed outlier: 3.545A pdb=" N ALA A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 206 removed outlier: 3.683A pdb=" N TYR A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 196 " --> pdb=" O GLY A 192 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 248 removed outlier: 4.180A pdb=" N ALA A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 232 " --> pdb=" O ASN A 228 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS A 240 " --> pdb=" O CYS A 236 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N PHE A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 255 Processing helix chain 'A' and resid 255 through 277 removed outlier: 3.856A pdb=" N PHE A 259 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 275 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 322 removed outlier: 3.778A pdb=" N PHE A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 354 through 358 removed outlier: 3.515A pdb=" N LEU A 358 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 408 removed outlier: 3.569A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 413 through 419 removed outlier: 3.502A pdb=" N ALA A 416 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY A 417 " --> pdb=" O ILE A 414 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 418 " --> pdb=" O MET A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 441 removed outlier: 3.608A pdb=" N ILE A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) Proline residue: A 432 - end of helix removed outlier: 3.746A pdb=" N ALA A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 454 removed outlier: 3.713A pdb=" N SER A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 476 through 480 removed outlier: 3.564A pdb=" N LEU A 479 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 498 removed outlier: 3.998A pdb=" N SER A 494 " --> pdb=" O GLY A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 516 Proline residue: A 507 - end of helix removed outlier: 3.580A pdb=" N GLN A 511 " --> pdb=" O PRO A 507 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 removed outlier: 3.676A pdb=" N GLN A 523 " --> pdb=" O PRO A 520 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL A 524 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY A 526 " --> pdb=" O GLN A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 545 removed outlier: 4.103A pdb=" N LEU A 539 " --> pdb=" O THR A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 549 Processing helix chain 'A' and resid 557 through 583 removed outlier: 3.517A pdb=" N SER A 562 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 564 " --> pdb=" O ILE A 560 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN A 573 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 577 " --> pdb=" O ASN A 573 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A 579 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR A 580 " --> pdb=" O CYS A 576 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 612 removed outlier: 3.887A pdb=" N ALA A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 622 removed outlier: 4.337A pdb=" N VAL A 620 " --> pdb=" O TYR A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 641 removed outlier: 3.636A pdb=" N LYS A 630 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 639 " --> pdb=" O ARG A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 659 removed outlier: 4.351A pdb=" N SER A 649 " --> pdb=" O ILE A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.747A pdb=" N SER A 693 " --> pdb=" O PRO A 689 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 694 " --> pdb=" O GLN A 690 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 719 Processing helix chain 'A' and resid 719 through 734 removed outlier: 3.602A pdb=" N ARG A 724 " --> pdb=" O PRO A 720 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 725 " --> pdb=" O GLN A 721 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE A 729 " --> pdb=" O ALA A 725 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 732 " --> pdb=" O SER A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 removed outlier: 3.547A pdb=" N GLY A 753 " --> pdb=" O ASN A 749 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 757 " --> pdb=" O GLY A 753 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 801 removed outlier: 3.517A pdb=" N ILE A 792 " --> pdb=" O TRP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 814 Processing helix chain 'A' and resid 835 through 846 removed outlier: 3.902A pdb=" N LEU A 841 " --> pdb=" O MET A 837 " (cutoff:3.500A) Proline residue: A 842 - end of helix Processing helix chain 'A' and resid 870 through 881 Processing helix chain 'A' and resid 907 through 918 removed outlier: 3.702A pdb=" N SER A 913 " --> pdb=" O MET A 909 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN A 914 " --> pdb=" O GLU A 910 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN A 918 " --> pdb=" O GLN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1065 removed outlier: 3.769A pdb=" N VAL A1059 " --> pdb=" O ARG A1055 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS A1063 " --> pdb=" O VAL A1059 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG A1065 " --> pdb=" O VAL A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1084 removed outlier: 3.530A pdb=" N GLY A1083 " --> pdb=" O ASN A1080 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP A1084 " --> pdb=" O ARG A1081 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1080 through 1084' Processing helix chain 'A' and resid 1087 through 1095 removed outlier: 3.985A pdb=" N VAL A1093 " --> pdb=" O GLU A1089 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A1095 " --> pdb=" O LEU A1091 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 98 through 103 Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.563A pdb=" N GLN B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN B 110 " --> pdb=" O PRO B 106 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 111 " --> pdb=" O CYS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 119 removed outlier: 3.928A pdb=" N PHE B 117 " --> pdb=" O GLY B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 139 through 155 removed outlier: 3.809A pdb=" N THR B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 174 through 179 removed outlier: 3.545A pdb=" N ALA B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 206 removed outlier: 3.683A pdb=" N TYR B 185 " --> pdb=" O GLY B 181 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 196 " --> pdb=" O GLY B 192 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 248 removed outlier: 4.180A pdb=" N ALA B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL B 232 " --> pdb=" O ASN B 228 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR B 235 " --> pdb=" O ARG B 231 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS B 240 " --> pdb=" O CYS B 236 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 245 " --> pdb=" O MET B 241 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N PHE B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 247 " --> pdb=" O THR B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 255 Processing helix chain 'B' and resid 255 through 277 removed outlier: 3.856A pdb=" N PHE B 259 " --> pdb=" O PHE B 255 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 260 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 274 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE B 275 " --> pdb=" O TYR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 322 removed outlier: 3.778A pdb=" N PHE B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 354 through 358 removed outlier: 3.515A pdb=" N LEU B 358 " --> pdb=" O LYS B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 408 removed outlier: 3.569A pdb=" N VAL B 404 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY B 405 " --> pdb=" O THR B 401 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 406 " --> pdb=" O LEU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 411 No H-bonds generated for 'chain 'B' and resid 409 through 411' Processing helix chain 'B' and resid 413 through 419 removed outlier: 3.502A pdb=" N ALA B 416 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY B 417 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER B 418 " --> pdb=" O MET B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 441 removed outlier: 3.608A pdb=" N ILE B 431 " --> pdb=" O ALA B 427 " (cutoff:3.500A) Proline residue: B 432 - end of helix removed outlier: 3.746A pdb=" N ALA B 438 " --> pdb=" O GLY B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 454 removed outlier: 3.713A pdb=" N SER B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 451 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 476 through 480 removed outlier: 3.564A pdb=" N LEU B 479 " --> pdb=" O VAL B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 498 removed outlier: 3.998A pdb=" N SER B 494 " --> pdb=" O GLY B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 516 Proline residue: B 507 - end of helix removed outlier: 3.580A pdb=" N GLN B 511 " --> pdb=" O PRO B 507 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 removed outlier: 3.676A pdb=" N GLN B 523 " --> pdb=" O PRO B 520 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL B 524 " --> pdb=" O PHE B 521 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY B 526 " --> pdb=" O GLN B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 545 removed outlier: 4.103A pdb=" N LEU B 539 " --> pdb=" O THR B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 549 Processing helix chain 'B' and resid 557 through 583 removed outlier: 3.517A pdb=" N SER B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET B 563 " --> pdb=" O PRO B 559 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 564 " --> pdb=" O ILE B 560 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN B 573 " --> pdb=" O TYR B 569 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA B 577 " --> pdb=" O ASN B 573 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN B 579 " --> pdb=" O ALA B 575 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR B 580 " --> pdb=" O CYS B 576 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 581 " --> pdb=" O ALA B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 612 removed outlier: 3.887A pdb=" N ALA B 608 " --> pdb=" O SER B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 622 removed outlier: 4.337A pdb=" N VAL B 620 " --> pdb=" O TYR B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 641 removed outlier: 3.636A pdb=" N LYS B 630 " --> pdb=" O GLY B 626 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS B 639 " --> pdb=" O ARG B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 659 removed outlier: 4.351A pdb=" N SER B 649 " --> pdb=" O ILE B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 700 removed outlier: 3.747A pdb=" N SER B 693 " --> pdb=" O PRO B 689 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 694 " --> pdb=" O GLN B 690 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B 695 " --> pdb=" O LEU B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 719 Processing helix chain 'B' and resid 719 through 734 removed outlier: 3.602A pdb=" N ARG B 724 " --> pdb=" O PRO B 720 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 725 " --> pdb=" O GLN B 721 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE B 729 " --> pdb=" O ALA B 725 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 732 " --> pdb=" O SER B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 removed outlier: 3.547A pdb=" N GLY B 753 " --> pdb=" O ASN B 749 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 757 " --> pdb=" O GLY B 753 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN B 759 " --> pdb=" O SER B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 801 removed outlier: 3.517A pdb=" N ILE B 792 " --> pdb=" O TRP B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 814 Processing helix chain 'B' and resid 835 through 846 removed outlier: 3.902A pdb=" N LEU B 841 " --> pdb=" O MET B 837 " (cutoff:3.500A) Proline residue: B 842 - end of helix Processing helix chain 'B' and resid 870 through 881 Processing helix chain 'B' and resid 907 through 918 removed outlier: 3.702A pdb=" N SER B 913 " --> pdb=" O MET B 909 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 914 " --> pdb=" O GLU B 910 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN B 918 " --> pdb=" O GLN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1065 removed outlier: 3.769A pdb=" N VAL B1059 " --> pdb=" O ARG B1055 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS B1063 " --> pdb=" O VAL B1059 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B1065 " --> pdb=" O VAL B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1080 through 1084 removed outlier: 3.530A pdb=" N GLY B1083 " --> pdb=" O ASN B1080 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP B1084 " --> pdb=" O ARG B1081 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1080 through 1084' Processing helix chain 'B' and resid 1087 through 1095 removed outlier: 3.985A pdb=" N VAL B1093 " --> pdb=" O GLU B1089 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B1095 " --> pdb=" O LEU B1091 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 285 through 288 Processing sheet with id=AA2, first strand: chain 'A' and resid 528 through 529 removed outlier: 3.886A pdb=" N GLY A 532 " --> pdb=" O LYS A 529 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 675 through 677 removed outlier: 6.398A pdb=" N VAL A 676 " --> pdb=" O GLY A 708 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N VAL A 710 " --> pdb=" O VAL A 676 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 762 through 763 removed outlier: 3.524A pdb=" N LEU A 763 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 770 through 773 removed outlier: 6.342A pdb=" N VAL A 771 " --> pdb=" O LEU A 806 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N THR A 808 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL A 773 " --> pdb=" O THR A 808 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A1101 " --> pdb=" O LYS A 809 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL A1070 " --> pdb=" O MET A1102 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL A1104 " --> pdb=" O VAL A1070 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU A1072 " --> pdb=" O VAL A1104 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN A1073 " --> pdb=" O TRP A 829 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL A 828 " --> pdb=" O PHE A 859 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL A 861 " --> pdb=" O VAL A 828 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 285 through 288 Processing sheet with id=AA7, first strand: chain 'B' and resid 528 through 529 removed outlier: 3.886A pdb=" N GLY B 532 " --> pdb=" O LYS B 529 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 675 through 677 removed outlier: 6.398A pdb=" N VAL B 676 " --> pdb=" O GLY B 708 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N VAL B 710 " --> pdb=" O VAL B 676 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 762 through 763 removed outlier: 3.524A pdb=" N LEU B 763 " --> pdb=" O LEU B 766 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 770 through 773 removed outlier: 6.342A pdb=" N VAL B 771 " --> pdb=" O LEU B 806 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N THR B 808 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL B 773 " --> pdb=" O THR B 808 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL B1101 " --> pdb=" O LYS B 809 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL B1070 " --> pdb=" O MET B1102 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL B1104 " --> pdb=" O VAL B1070 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU B1072 " --> pdb=" O VAL B1104 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN B1073 " --> pdb=" O TRP B 829 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL B 828 " --> pdb=" O PHE B 859 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL B 861 " --> pdb=" O VAL B 828 " (cutoff:3.500A) 530 hydrogen bonds defined for protein. 1530 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: 7.17 Time building geometry restraints manager: 4.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4016 1.33 - 1.45: 2756 1.45 - 1.57: 8082 1.57 - 1.69: 16 1.69 - 1.81: 186 Bond restraints: 15056 Sorted by residual: bond pdb=" OG1 TPO A 906 " pdb=" P TPO A 906 " ideal model delta sigma weight residual 1.717 1.605 0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" OG1 TPO B 906 " pdb=" P TPO B 906 " ideal model delta sigma weight residual 1.717 1.605 0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C ARG B 671 " pdb=" N PRO B 672 " ideal model delta sigma weight residual 1.332 1.389 -0.057 1.12e-02 7.97e+03 2.55e+01 bond pdb=" C ARG A 671 " pdb=" N PRO A 672 " ideal model delta sigma weight residual 1.332 1.389 -0.057 1.12e-02 7.97e+03 2.55e+01 bond pdb=" OG1 TPO A1007 " pdb=" P TPO A1007 " ideal model delta sigma weight residual 1.717 1.618 0.099 2.00e-02 2.50e+03 2.46e+01 ... (remaining 15051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 19776 2.66 - 5.31: 542 5.31 - 7.97: 88 7.97 - 10.62: 24 10.62 - 13.28: 4 Bond angle restraints: 20434 Sorted by residual: angle pdb=" C ARG B 671 " pdb=" N PRO B 672 " pdb=" CA PRO B 672 " ideal model delta sigma weight residual 119.98 114.21 5.77 1.16e+00 7.43e-01 2.48e+01 angle pdb=" C ARG A 671 " pdb=" N PRO A 672 " pdb=" CA PRO A 672 " ideal model delta sigma weight residual 119.98 114.21 5.77 1.16e+00 7.43e-01 2.48e+01 angle pdb=" C ALA A 329 " pdb=" N THR A 330 " pdb=" CA THR A 330 " ideal model delta sigma weight residual 122.82 129.73 -6.91 1.42e+00 4.96e-01 2.37e+01 angle pdb=" C ALA B 329 " pdb=" N THR B 330 " pdb=" CA THR B 330 " ideal model delta sigma weight residual 122.82 129.73 -6.91 1.42e+00 4.96e-01 2.37e+01 angle pdb=" N VAL A1054 " pdb=" CA VAL A1054 " pdb=" C VAL A1054 " ideal model delta sigma weight residual 112.12 108.06 4.06 8.40e-01 1.42e+00 2.33e+01 ... (remaining 20429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 8014 17.36 - 34.73: 804 34.73 - 52.09: 182 52.09 - 69.46: 24 69.46 - 86.82: 14 Dihedral angle restraints: 9038 sinusoidal: 3690 harmonic: 5348 Sorted by residual: dihedral pdb=" CA ILE B 612 " pdb=" C ILE B 612 " pdb=" N CYS B 613 " pdb=" CA CYS B 613 " ideal model delta harmonic sigma weight residual 180.00 150.21 29.79 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA ILE A 612 " pdb=" C ILE A 612 " pdb=" N CYS A 613 " pdb=" CA CYS A 613 " ideal model delta harmonic sigma weight residual 180.00 150.21 29.79 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA CYS B 302 " pdb=" C CYS B 302 " pdb=" N ALA B 303 " pdb=" CA ALA B 303 " ideal model delta harmonic sigma weight residual 180.00 153.92 26.08 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 9035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1950 0.081 - 0.162: 378 0.162 - 0.243: 42 0.243 - 0.325: 8 0.325 - 0.406: 2 Chirality restraints: 2380 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" CB TPO B1007 " pdb=" CA TPO B1007 " pdb=" OG1 TPO B1007 " pdb=" CG2 TPO B1007 " both_signs ideal model delta sigma weight residual False 2.48 2.08 0.41 2.00e-01 2.50e+01 4.12e+00 ... (remaining 2377 not shown) Planarity restraints: 2554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 291 " -0.030 2.00e-02 2.50e+03 3.91e-02 1.91e+01 pdb=" CG ASN A 291 " 0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN A 291 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 291 " 0.068 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 291 " 0.030 2.00e-02 2.50e+03 3.91e-02 1.91e+01 pdb=" CG ASN B 291 " -0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN B 291 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B 291 " -0.068 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 663 " -0.051 5.00e-02 4.00e+02 7.63e-02 9.32e+00 pdb=" N PRO A 664 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 664 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 664 " -0.042 5.00e-02 4.00e+02 ... (remaining 2551 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.80: 4274 2.80 - 3.39: 14583 3.39 - 3.97: 25399 3.97 - 4.56: 37402 4.56 - 5.14: 54639 Nonbonded interactions: 136297 Sorted by model distance: nonbonded pdb=" O GLN A 673 " pdb=" O LEU A 704 " model vdw 2.216 3.040 nonbonded pdb=" O GLN B 673 " pdb=" O LEU B 704 " model vdw 2.216 3.040 nonbonded pdb=" OG SER A 151 " pdb=" CE2 PHE A 591 " model vdw 2.245 3.340 nonbonded pdb=" OG SER B 151 " pdb=" CE2 PHE B 591 " model vdw 2.245 3.340 nonbonded pdb=" O THR B 934 " pdb=" N GLU B 936 " model vdw 2.253 3.120 ... (remaining 136292 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.860 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: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 41.140 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.100 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:3.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 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 : 0.010 0.112 15056 Z= 0.626 Angle : 1.124 13.275 20434 Z= 0.604 Chirality : 0.067 0.406 2380 Planarity : 0.007 0.076 2546 Dihedral : 14.890 86.819 5608 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 1.52 % Allowed : 10.73 % Favored : 87.76 % Rotamer: Outliers : 2.32 % Allowed : 9.52 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -6.36 (0.12), residues: 1846 helix: -4.62 (0.07), residues: 938 sheet: -2.30 (0.38), residues: 160 loop : -3.92 (0.16), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 318 HIS 0.008 0.002 HIS B 756 PHE 0.028 0.003 PHE B1090 TYR 0.023 0.003 TYR A 407 ARG 0.006 0.001 ARG B1105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 306 time to evaluate : 1.789 Fit side-chains REVERT: A 866 ASP cc_start: 0.5789 (OUTLIER) cc_final: 0.5209 (m-30) REVERT: B 866 ASP cc_start: 0.5792 (OUTLIER) cc_final: 0.5211 (m-30) outliers start: 36 outliers final: 12 residues processed: 334 average time/residue: 0.3090 time to fit residues: 152.7752 Evaluate side-chains 198 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 593 TYR Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 593 TYR Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 932 SER Chi-restraints excluded: chain B residue 933 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN A 338 ASN A 344 GLN A 419 ASN A 573 ASN A 579 GLN A 673 GLN A 688 HIS A 719 HIS A 723 GLN A 778 ASN A 790 ASN A 848 HIS ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 HIS B 73 GLN B 338 ASN B 344 GLN B 419 ASN B 573 ASN B 579 GLN B 673 GLN B 688 HIS B 719 HIS B 723 GLN B 778 ASN B 790 ASN B 848 HIS ** B 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1051 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15056 Z= 0.227 Angle : 0.766 13.100 20434 Z= 0.396 Chirality : 0.045 0.207 2380 Planarity : 0.006 0.057 2546 Dihedral : 7.927 55.860 2344 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.76 % Allowed : 9.97 % Favored : 89.27 % Rotamer: Outliers : 2.45 % Allowed : 14.35 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.62 (0.16), residues: 1846 helix: -2.89 (0.13), residues: 934 sheet: -1.60 (0.42), residues: 156 loop : -3.51 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 596 HIS 0.009 0.001 HIS B 756 PHE 0.020 0.001 PHE B 591 TYR 0.014 0.001 TYR A 880 ARG 0.004 0.000 ARG A 751 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 1.752 Fit side-chains REVERT: A 866 ASP cc_start: 0.5854 (OUTLIER) cc_final: 0.5048 (m-30) REVERT: B 866 ASP cc_start: 0.5856 (OUTLIER) cc_final: 0.5053 (m-30) outliers start: 38 outliers final: 22 residues processed: 232 average time/residue: 0.2437 time to fit residues: 88.2627 Evaluate side-chains 208 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 593 TYR Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 833 HIS Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 593 TYR Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 833 HIS Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 932 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 8.9990 chunk 52 optimal weight: 0.0370 chunk 140 optimal weight: 0.5980 chunk 115 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 182 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 167 optimal weight: 0.0270 chunk 57 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 870 GLN ** B 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15056 Z= 0.175 Angle : 0.679 11.771 20434 Z= 0.345 Chirality : 0.042 0.167 2380 Planarity : 0.004 0.056 2546 Dihedral : 7.015 46.437 2338 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.62 % Favored : 88.84 % Rotamer: Outliers : 3.99 % Allowed : 14.74 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.17), residues: 1846 helix: -2.05 (0.15), residues: 962 sheet: -1.25 (0.44), residues: 156 loop : -3.43 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 596 HIS 0.007 0.000 HIS B 756 PHE 0.012 0.001 PHE B 591 TYR 0.012 0.001 TYR A 593 ARG 0.007 0.000 ARG B 912 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 222 time to evaluate : 1.771 Fit side-chains REVERT: A 866 ASP cc_start: 0.5980 (OUTLIER) cc_final: 0.5373 (m-30) REVERT: A 884 ILE cc_start: 0.6738 (mt) cc_final: 0.6249 (mt) REVERT: B 866 ASP cc_start: 0.5987 (OUTLIER) cc_final: 0.5377 (m-30) REVERT: B 884 ILE cc_start: 0.6740 (mt) cc_final: 0.6248 (mt) outliers start: 62 outliers final: 36 residues processed: 264 average time/residue: 0.2221 time to fit residues: 93.6367 Evaluate side-chains 230 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 593 TYR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 833 HIS Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 593 TYR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 833 HIS Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 932 SER Chi-restraints excluded: chain B residue 933 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 0.2980 chunk 127 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 169 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 160 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 931 GLN ** B 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 931 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15056 Z= 0.212 Angle : 0.714 11.455 20434 Z= 0.353 Chirality : 0.047 0.591 2380 Planarity : 0.004 0.053 2546 Dihedral : 7.424 59.873 2332 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.97 % Favored : 89.60 % Rotamer: Outliers : 3.73 % Allowed : 17.76 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.10 (0.18), residues: 1846 helix: -1.37 (0.16), residues: 956 sheet: -1.20 (0.44), residues: 158 loop : -3.15 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 596 HIS 0.004 0.001 HIS B 756 PHE 0.018 0.001 PHE A 184 TYR 0.018 0.001 TYR B 880 ARG 0.004 0.000 ARG A 751 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 192 time to evaluate : 1.783 Fit side-chains REVERT: A 866 ASP cc_start: 0.5580 (OUTLIER) cc_final: 0.4893 (m-30) REVERT: B 866 ASP cc_start: 0.5590 (OUTLIER) cc_final: 0.4895 (m-30) outliers start: 58 outliers final: 36 residues processed: 234 average time/residue: 0.2271 time to fit residues: 83.6119 Evaluate side-chains 216 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 593 TYR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 593 TYR Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 933 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 133 optimal weight: 0.0060 chunk 74 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1057 ASN ** B 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1057 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15056 Z= 0.259 Angle : 0.709 11.054 20434 Z= 0.352 Chirality : 0.049 0.657 2380 Planarity : 0.004 0.050 2546 Dihedral : 7.082 54.011 2330 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.56 % Favored : 88.89 % Rotamer: Outliers : 4.12 % Allowed : 17.18 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.65 (0.19), residues: 1846 helix: -1.04 (0.16), residues: 972 sheet: -1.03 (0.45), residues: 158 loop : -2.90 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 596 HIS 0.005 0.001 HIS A 833 PHE 0.019 0.001 PHE A 184 TYR 0.010 0.001 TYR B 629 ARG 0.005 0.000 ARG B 912 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 192 time to evaluate : 1.731 Fit side-chains REVERT: A 241 MET cc_start: 0.6784 (OUTLIER) cc_final: 0.6438 (mtp) REVERT: A 866 ASP cc_start: 0.5641 (OUTLIER) cc_final: 0.5120 (m-30) REVERT: B 241 MET cc_start: 0.6782 (OUTLIER) cc_final: 0.6433 (mtp) REVERT: B 866 ASP cc_start: 0.5642 (OUTLIER) cc_final: 0.5116 (m-30) outliers start: 64 outliers final: 44 residues processed: 236 average time/residue: 0.2437 time to fit residues: 91.2173 Evaluate side-chains 220 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 172 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 593 TYR Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 593 TYR Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 898 ILE Chi-restraints excluded: chain B residue 933 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 105 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15056 Z= 0.178 Angle : 0.663 10.874 20434 Z= 0.328 Chirality : 0.046 0.594 2380 Planarity : 0.004 0.052 2546 Dihedral : 6.860 47.911 2330 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.56 % Favored : 89.00 % Rotamer: Outliers : 3.47 % Allowed : 18.73 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.26 (0.19), residues: 1846 helix: -0.64 (0.17), residues: 964 sheet: -0.95 (0.45), residues: 158 loop : -2.80 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 596 HIS 0.004 0.000 HIS B 756 PHE 0.011 0.001 PHE B 184 TYR 0.010 0.001 TYR A 593 ARG 0.007 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 204 time to evaluate : 1.707 Fit side-chains REVERT: A 866 ASP cc_start: 0.5436 (OUTLIER) cc_final: 0.4984 (m-30) REVERT: B 866 ASP cc_start: 0.5441 (OUTLIER) cc_final: 0.4982 (m-30) outliers start: 54 outliers final: 42 residues processed: 234 average time/residue: 0.2316 time to fit residues: 86.0044 Evaluate side-chains 226 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 593 TYR Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 593 TYR Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 898 ILE Chi-restraints excluded: chain B residue 933 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 101 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 179 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15056 Z= 0.191 Angle : 0.672 11.674 20434 Z= 0.330 Chirality : 0.047 0.596 2380 Planarity : 0.004 0.052 2546 Dihedral : 6.635 48.091 2330 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.62 % Favored : 88.95 % Rotamer: Outliers : 3.73 % Allowed : 19.37 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.04 (0.20), residues: 1846 helix: -0.41 (0.17), residues: 962 sheet: -0.76 (0.45), residues: 156 loop : -2.79 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 596 HIS 0.003 0.001 HIS B 756 PHE 0.021 0.001 PHE A 184 TYR 0.018 0.001 TYR A 880 ARG 0.006 0.000 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 192 time to evaluate : 1.791 Fit side-chains REVERT: A 866 ASP cc_start: 0.5380 (OUTLIER) cc_final: 0.4956 (m-30) REVERT: B 866 ASP cc_start: 0.5408 (OUTLIER) cc_final: 0.4970 (m-30) outliers start: 58 outliers final: 38 residues processed: 234 average time/residue: 0.2332 time to fit residues: 86.7957 Evaluate side-chains 214 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 593 TYR Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 910 GLU Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 593 TYR Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 898 ILE Chi-restraints excluded: chain B residue 910 GLU Chi-restraints excluded: chain B residue 933 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.0970 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 34 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 88 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 140 optimal weight: 0.5980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 HIS B 870 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 15056 Z= 0.154 Angle : 0.658 11.095 20434 Z= 0.326 Chirality : 0.047 0.567 2380 Planarity : 0.004 0.055 2546 Dihedral : 6.343 49.246 2330 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.67 % Favored : 88.89 % Rotamer: Outliers : 2.77 % Allowed : 20.53 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.20), residues: 1846 helix: -0.10 (0.17), residues: 960 sheet: -0.78 (0.45), residues: 156 loop : -2.77 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 596 HIS 0.003 0.000 HIS B 756 PHE 0.027 0.001 PHE B 184 TYR 0.010 0.001 TYR A 593 ARG 0.006 0.000 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 202 time to evaluate : 1.808 Fit side-chains REVERT: A 101 MET cc_start: 0.7234 (mmm) cc_final: 0.6989 (mmm) REVERT: A 866 ASP cc_start: 0.5251 (OUTLIER) cc_final: 0.4881 (m-30) REVERT: B 101 MET cc_start: 0.7235 (mmm) cc_final: 0.6992 (mmm) REVERT: B 866 ASP cc_start: 0.5259 (OUTLIER) cc_final: 0.4882 (m-30) outliers start: 43 outliers final: 29 residues processed: 228 average time/residue: 0.2346 time to fit residues: 84.2078 Evaluate side-chains 217 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 593 TYR Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 897 ASP Chi-restraints excluded: chain A residue 910 GLU Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 593 TYR Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 897 ASP Chi-restraints excluded: chain B residue 910 GLU Chi-restraints excluded: chain B residue 933 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 0.0010 chunk 171 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- 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: 0.8007 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15056 Z= 0.184 Angle : 0.668 10.847 20434 Z= 0.330 Chirality : 0.048 0.572 2380 Planarity : 0.004 0.053 2546 Dihedral : 6.201 49.121 2330 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.02 % Favored : 89.54 % Rotamer: Outliers : 2.57 % Allowed : 21.49 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.66 (0.20), residues: 1846 helix: 0.03 (0.17), residues: 952 sheet: -0.78 (0.45), residues: 156 loop : -2.74 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 596 HIS 0.004 0.000 HIS B 756 PHE 0.020 0.001 PHE B 184 TYR 0.019 0.001 TYR B 880 ARG 0.006 0.000 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 2.231 Fit side-chains REVERT: A 866 ASP cc_start: 0.5138 (OUTLIER) cc_final: 0.4736 (m-30) REVERT: B 726 GLU cc_start: 0.7615 (tp30) cc_final: 0.7415 (tp30) REVERT: B 866 ASP cc_start: 0.5323 (OUTLIER) cc_final: 0.4904 (m-30) outliers start: 40 outliers final: 36 residues processed: 210 average time/residue: 0.2401 time to fit residues: 80.8203 Evaluate side-chains 216 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 593 TYR Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 897 ASP Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 910 GLU Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 593 TYR Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 897 ASP Chi-restraints excluded: chain B residue 898 ILE Chi-restraints excluded: chain B residue 910 GLU Chi-restraints excluded: chain B residue 933 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 107 optimal weight: 0.0040 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 overall best weight: 1.0394 ------------------------------------------------------------------------------- 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: 0.8019 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15056 Z= 0.191 Angle : 0.681 13.693 20434 Z= 0.333 Chirality : 0.048 0.563 2380 Planarity : 0.004 0.053 2546 Dihedral : 6.138 49.141 2330 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.24 % Favored : 89.33 % Rotamer: Outliers : 2.70 % Allowed : 21.49 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.58 (0.20), residues: 1846 helix: 0.10 (0.17), residues: 952 sheet: -0.74 (0.45), residues: 156 loop : -2.69 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 122 HIS 0.004 0.001 HIS B 756 PHE 0.020 0.001 PHE A 184 TYR 0.009 0.001 TYR A 593 ARG 0.006 0.000 ARG A 646 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 1.854 Fit side-chains REVERT: A 241 MET cc_start: 0.6942 (mmm) cc_final: 0.6656 (mtp) REVERT: A 866 ASP cc_start: 0.5314 (OUTLIER) cc_final: 0.4922 (m-30) REVERT: B 241 MET cc_start: 0.6938 (mmm) cc_final: 0.6652 (mtp) REVERT: B 866 ASP cc_start: 0.5315 (OUTLIER) cc_final: 0.4918 (m-30) outliers start: 42 outliers final: 37 residues processed: 216 average time/residue: 0.2272 time to fit residues: 78.5021 Evaluate side-chains 214 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 593 TYR Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 897 ASP Chi-restraints excluded: chain A residue 910 GLU Chi-restraints excluded: chain A residue 933 ILE Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 593 TYR Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 897 ASP Chi-restraints excluded: chain B residue 910 GLU Chi-restraints excluded: chain B residue 933 ILE Chi-restraints excluded: chain B residue 1072 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 9.9990 chunk 157 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 136 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 41 optimal weight: 0.0970 chunk 147 optimal weight: 1.9990 chunk 61 optimal weight: 0.0020 chunk 151 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.099943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.078612 restraints weight = 32201.628| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.14 r_work: 0.3041 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15056 Z= 0.161 Angle : 0.667 13.185 20434 Z= 0.326 Chirality : 0.047 0.544 2380 Planarity : 0.004 0.054 2546 Dihedral : 6.019 49.964 2330 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.86 % Favored : 89.71 % Rotamer: Outliers : 2.90 % Allowed : 21.30 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.45 (0.20), residues: 1846 helix: 0.25 (0.17), residues: 954 sheet: -0.66 (0.45), residues: 156 loop : -2.72 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 122 HIS 0.004 0.001 HIS B 756 PHE 0.019 0.001 PHE A 184 TYR 0.021 0.001 TYR B 880 ARG 0.005 0.000 ARG B 646 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3129.11 seconds wall clock time: 59 minutes 25.73 seconds (3565.73 seconds total)