Starting phenix.real_space_refine on Sat Sep 12 08:58:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6m23_30061/09_2026/6m23_30061.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m23_30061/09_2026/6m23_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6m23_30061/09_2026/6m23_30061.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6m23_30061/09_2026/6m23_30061.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6m23_30061/09_2026/6m23_30061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m23_30061/09_2026/6m23_30061.map" model { file = "/net/cci-nas-00/data/ceres_data/6m23_30061/09_2026/6m23_30061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m23_30061/09_2026/6m23_30061.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'TPO:plan-1': 2, 'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'GLU: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: {'TPO:plan-1': 2, 'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'GLU: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 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 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 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 chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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: 3.54, per 1000 atoms: 0.24 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: 1.26 Conformation dependent library (CDL) restraints added in 768.4 milliseconds 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: 0.37 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: 2.57 Time building geometry restraints manager: 1.70 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: 7760 17.36 - 34.73: 790 34.73 - 52.09: 160 52.09 - 69.46: 20 69.46 - 86.82: 14 Dihedral angle restraints: 8744 sinusoidal: 3396 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 8741 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: 0.02 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: 3.610 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.030 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 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 15072 Z= 0.434 Angle : 1.193 22.012 20480 Z= 0.618 Chirality : 0.067 0.406 2380 Planarity : 0.007 0.076 2546 Dihedral : 14.885 86.819 5314 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.84 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.006 0.001 ARG B1105 TYR 0.023 0.003 TYR A 407 PHE 0.028 0.003 PHE B1090 TRP 0.019 0.002 TRP B 318 HIS 0.008 0.002 HIS B 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00975 / 0.43 (15056) covalent geometry : angle 1.12379 / 0.60 (20434) SS BOND : bond 0.00217 / 0.11 ( 2) SS BOND : angle 0.22346 / 0.11 ( 4) hydrogen bonds : bond 0.33565 / 21.77 ( 530) hydrogen bonds : angle 10.48553 / 7.10 ( 1530) link_BETA1-4 : bond 0.01249 / 0.64 ( 6) link_BETA1-4 : angle 9.50871 / 6.70 ( 18) link_NAG-ASN : bond 0.00488 / 0.25 ( 8) link_NAG-ASN : angle 8.39750 / 4.37 ( 24) *********************** 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 : 0.554 Fit side-chains REVERT: A 866 ASP cc_start: 0.5789 (OUTLIER) cc_final: 0.5274 (m-30) REVERT: B 866 ASP cc_start: 0.5792 (OUTLIER) cc_final: 0.5276 (m-30) outliers start: 36 outliers final: 12 residues processed: 334 average time/residue: 0.1201 time to fit residues: 59.4450 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 : 0.558 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.099646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.077106 restraints weight = 32893.973| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.42 r_work: 0.3023 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15072 Z= 0.153 Angle : 0.784 13.037 20480 Z= 0.396 Chirality : 0.045 0.187 2380 Planarity : 0.005 0.057 2546 Dihedral : 6.862 55.800 2050 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.76 % Allowed : 10.18 % Favored : 89.06 % Rotamer: Outliers : 2.83 % Allowed : 14.35 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.67 (0.16), residues: 1846 helix: -2.96 (0.13), residues: 934 sheet: -1.58 (0.42), residues: 156 loop : -3.50 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 751 TYR 0.014 0.001 TYR B 880 PHE 0.020 0.001 PHE A 591 TRP 0.015 0.001 TRP A 596 HIS 0.010 0.001 HIS B 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (15056) covalent geometry : angle 0.75521 / 0.39 (20434) SS BOND : bond 0.00073 / 0.04 ( 2) SS BOND : angle 0.19852 / 0.10 ( 4) hydrogen bonds : bond 0.05187 / 3.40 ( 530) hydrogen bonds : angle 5.15068 / 3.43 ( 1530) link_BETA1-4 : bond 0.00452 / 0.24 ( 6) link_BETA1-4 : angle 2.38898 / 1.27 ( 18) link_NAG-ASN : bond 0.00355 / 0.22 ( 8) link_NAG-ASN : angle 5.85528 / 3.15 ( 24) *********************** 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 258 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 214 time to evaluate : 0.427 Fit side-chains REVERT: A 211 MET cc_start: 0.6541 (mmt) cc_final: 0.6195 (mmt) REVERT: A 241 MET cc_start: 0.8073 (mtt) cc_final: 0.7848 (mtp) REVERT: A 570 MET cc_start: 0.8967 (ttp) cc_final: 0.8666 (ttp) REVERT: A 610 MET cc_start: 0.8620 (mtp) cc_final: 0.8412 (mtp) REVERT: A 820 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8422 (mtm-85) REVERT: A 866 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6054 (m-30) REVERT: B 211 MET cc_start: 0.6555 (mmt) cc_final: 0.6199 (mmt) REVERT: B 241 MET cc_start: 0.8049 (mtt) cc_final: 0.7824 (mtp) REVERT: B 570 MET cc_start: 0.8978 (ttp) cc_final: 0.8676 (ttp) REVERT: B 610 MET cc_start: 0.8628 (mtp) cc_final: 0.8418 (mtp) REVERT: B 820 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8442 (mtm-85) REVERT: B 866 ASP cc_start: 0.7117 (OUTLIER) cc_final: 0.6054 (m-30) outliers start: 44 outliers final: 22 residues processed: 248 average time/residue: 0.1038 time to fit residues: 40.0398 Evaluate side-chains 216 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 820 ARG 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 820 ARG 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 128 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 79 optimal weight: 0.0470 chunk 132 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 HIS ** B 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.099550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.076820 restraints weight = 32633.209| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.39 r_work: 0.3025 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15072 Z= 0.130 Angle : 0.769 24.333 20480 Z= 0.365 Chirality : 0.046 0.588 2380 Planarity : 0.004 0.056 2546 Dihedral : 6.093 47.610 2044 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.46 % Favored : 89.00 % Rotamer: Outliers : 3.54 % Allowed : 15.44 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.71 (0.17), residues: 1846 helix: -1.98 (0.15), residues: 956 sheet: -1.17 (0.44), residues: 156 loop : -3.34 (0.20), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 751 TYR 0.011 0.001 TYR A 593 PHE 0.013 0.001 PHE B 591 TRP 0.014 0.001 TRP A 596 HIS 0.008 0.001 HIS B 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (15056) covalent geometry : angle 0.69945 / 0.35 (20434) SS BOND : bond 0.00041 / 0.02 ( 2) SS BOND : angle 0.31260 / 0.16 ( 4) hydrogen bonds : bond 0.04187 / 2.76 ( 530) hydrogen bonds : angle 4.48283 / 2.94 ( 1530) link_BETA1-4 : bond 0.00343 / 0.19 ( 6) link_BETA1-4 : angle 2.18927 / 1.23 ( 18) link_NAG-ASN : bond 0.01210 / 0.51 ( 8) link_NAG-ASN : angle 9.22627 / 4.59 ( 24) *********************** 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 274 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 219 time to evaluate : 0.505 Fit side-chains REVERT: A 131 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8140 (tt0) REVERT: A 211 MET cc_start: 0.6673 (mmt) cc_final: 0.6353 (mmt) REVERT: A 866 ASP cc_start: 0.7084 (OUTLIER) cc_final: 0.6149 (m-30) REVERT: A 884 ILE cc_start: 0.7145 (mt) cc_final: 0.6714 (mt) REVERT: A 905 LYS cc_start: 0.8520 (mmmt) cc_final: 0.8270 (mmmt) REVERT: A 1079 ARG cc_start: 0.7258 (ptt-90) cc_final: 0.7027 (pmt170) REVERT: B 131 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8133 (tt0) REVERT: B 211 MET cc_start: 0.6667 (mmt) cc_final: 0.6355 (mmt) REVERT: B 866 ASP cc_start: 0.7084 (OUTLIER) cc_final: 0.6151 (m-30) REVERT: B 884 ILE cc_start: 0.7158 (mt) cc_final: 0.6725 (mt) REVERT: B 905 LYS cc_start: 0.8520 (mmmt) cc_final: 0.8270 (mmmt) REVERT: B 1079 ARG cc_start: 0.7262 (ptt-90) cc_final: 0.7031 (pmt170) outliers start: 55 outliers final: 29 residues processed: 253 average time/residue: 0.0972 time to fit residues: 39.1091 Evaluate side-chains 232 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 293 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 387 MET 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 692 LEU Chi-restraints excluded: chain A residue 695 THR 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 103 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 387 MET 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 692 LEU Chi-restraints excluded: chain B residue 695 THR 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 20 optimal weight: 0.0970 chunk 1 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 147 optimal weight: 0.2980 chunk 64 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 931 GLN ** B 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 931 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.099300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.076677 restraints weight = 32613.485| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.38 r_work: 0.3021 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15072 Z= 0.122 Angle : 0.716 17.305 20480 Z= 0.343 Chirality : 0.046 0.593 2380 Planarity : 0.004 0.053 2546 Dihedral : 5.501 48.129 2038 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.70 % Favored : 89.87 % Rotamer: Outliers : 3.35 % Allowed : 17.82 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.18), residues: 1846 helix: -1.31 (0.16), residues: 950 sheet: -1.13 (0.45), residues: 158 loop : -3.12 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 751 TYR 0.018 0.001 TYR B 880 PHE 0.017 0.001 PHE B 184 TRP 0.015 0.001 TRP A 596 HIS 0.005 0.001 HIS B 833 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (15056) covalent geometry : angle 0.66841 / 0.33 (20434) SS BOND : bond 0.00045 / 0.02 ( 2) SS BOND : angle 0.25732 / 0.13 ( 4) hydrogen bonds : bond 0.03597 / 2.38 ( 530) hydrogen bonds : angle 4.26498 / 2.81 ( 1530) link_BETA1-4 : bond 0.00491 / 0.26 ( 6) link_BETA1-4 : angle 2.00609 / 1.10 ( 18) link_NAG-ASN : bond 0.01072 / 0.45 ( 8) link_NAG-ASN : angle 7.37594 / 3.76 ( 24) *********************** 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 259 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 207 time to evaluate : 0.522 Fit side-chains REVERT: A 131 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8156 (tt0) REVERT: A 211 MET cc_start: 0.6877 (mmt) cc_final: 0.6475 (mmt) REVERT: A 267 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8992 (mp) REVERT: A 866 ASP cc_start: 0.6870 (OUTLIER) cc_final: 0.5917 (m-30) REVERT: A 905 LYS cc_start: 0.8536 (mmmt) cc_final: 0.8249 (mmmt) REVERT: B 131 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8164 (tt0) REVERT: B 211 MET cc_start: 0.6857 (mmt) cc_final: 0.6473 (mmt) REVERT: B 267 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8993 (mp) REVERT: B 866 ASP cc_start: 0.6875 (OUTLIER) cc_final: 0.5918 (m-30) REVERT: B 905 LYS cc_start: 0.8534 (mmmt) cc_final: 0.8249 (mmmt) outliers start: 52 outliers final: 30 residues processed: 241 average time/residue: 0.0976 time to fit residues: 37.7736 Evaluate side-chains 224 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 267 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 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 103 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 300 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 135 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 22 optimal weight: 0.3980 chunk 82 optimal weight: 0.9990 chunk 95 optimal weight: 0.0470 chunk 157 optimal weight: 0.0970 chunk 2 optimal weight: 5.9990 chunk 168 optimal weight: 0.8980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 870 GLN ** B 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 870 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.099711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.077060 restraints weight = 32555.859| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.37 r_work: 0.3027 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15072 Z= 0.110 Angle : 0.696 17.449 20480 Z= 0.329 Chirality : 0.045 0.517 2380 Planarity : 0.004 0.054 2546 Dihedral : 5.351 48.940 2036 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.33 % Allowed : 10.40 % Favored : 89.27 % Rotamer: Outliers : 3.41 % Allowed : 18.40 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.19), residues: 1846 helix: -0.85 (0.17), residues: 954 sheet: -0.98 (0.45), residues: 158 loop : -2.98 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 912 TYR 0.011 0.001 TYR A 593 PHE 0.019 0.001 PHE A 184 TRP 0.015 0.001 TRP A 596 HIS 0.004 0.000 HIS B 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (15056) covalent geometry : angle 0.65164 / 0.32 (20434) SS BOND : bond 0.00025 / 0.01 ( 2) SS BOND : angle 0.21812 / 0.11 ( 4) hydrogen bonds : bond 0.03233 / 2.11 ( 530) hydrogen bonds : angle 4.15857 / 2.73 ( 1530) link_BETA1-4 : bond 0.00304 / 0.17 ( 6) link_BETA1-4 : angle 1.77955 / 1.01 ( 18) link_NAG-ASN : bond 0.01075 / 0.45 ( 8) link_NAG-ASN : angle 7.01090 / 3.50 ( 24) *********************** 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 263 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 210 time to evaluate : 0.550 Fit side-chains REVERT: A 131 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8095 (tt0) REVERT: A 211 MET cc_start: 0.7047 (mmt) cc_final: 0.6553 (tpt) REVERT: A 267 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.9029 (mp) REVERT: A 353 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8309 (mt) REVERT: A 468 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7861 (mm-30) REVERT: A 603 MET cc_start: 0.8513 (ttp) cc_final: 0.8310 (ttm) REVERT: A 866 ASP cc_start: 0.6855 (OUTLIER) cc_final: 0.5961 (m-30) REVERT: A 905 LYS cc_start: 0.8536 (mmmt) cc_final: 0.8266 (mmmt) REVERT: B 131 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8095 (tt0) REVERT: B 211 MET cc_start: 0.6980 (mmt) cc_final: 0.6478 (tpt) REVERT: B 267 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.9025 (mp) REVERT: B 353 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8310 (mt) REVERT: B 468 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7860 (mm-30) REVERT: B 603 MET cc_start: 0.8548 (ttp) cc_final: 0.8348 (ttm) REVERT: B 866 ASP cc_start: 0.6849 (OUTLIER) cc_final: 0.5952 (m-30) REVERT: B 905 LYS cc_start: 0.8537 (mmmt) cc_final: 0.8268 (mmmt) outliers start: 53 outliers final: 33 residues processed: 244 average time/residue: 0.1016 time to fit residues: 38.8214 Evaluate side-chains 234 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 195 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 267 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 353 LEU 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 554 LEU Chi-restraints excluded: chain A residue 593 TYR Chi-restraints excluded: chain A residue 627 LEU 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 267 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 353 LEU 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 554 LEU Chi-restraints excluded: chain B residue 593 TYR Chi-restraints excluded: chain B residue 627 LEU 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 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 120 optimal weight: 0.0020 chunk 76 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 171 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 chunk 180 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 38 optimal weight: 0.0670 chunk 90 optimal weight: 3.9990 overall best weight: 0.9930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 756 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.098320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.075542 restraints weight = 32451.660| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.36 r_work: 0.2998 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15072 Z= 0.127 Angle : 0.695 16.860 20480 Z= 0.330 Chirality : 0.045 0.500 2380 Planarity : 0.004 0.053 2546 Dihedral : 5.268 48.985 2036 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.97 % Favored : 89.60 % Rotamer: Outliers : 3.09 % Allowed : 18.60 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.20), residues: 1846 helix: -0.46 (0.17), residues: 950 sheet: -0.77 (0.46), residues: 156 loop : -2.88 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 646 TYR 0.009 0.001 TYR A 593 PHE 0.010 0.001 PHE A1090 TRP 0.013 0.001 TRP B 596 HIS 0.003 0.000 HIS B 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (15056) covalent geometry : angle 0.65383 / 0.32 (20434) SS BOND : bond 0.00016 / 0.01 ( 2) SS BOND : angle 0.18839 / 0.10 ( 4) hydrogen bonds : bond 0.03389 / 2.22 ( 530) hydrogen bonds : angle 4.11527 / 2.70 ( 1530) link_BETA1-4 : bond 0.00325 / 0.18 ( 6) link_BETA1-4 : angle 1.78009 / 1.02 ( 18) link_NAG-ASN : bond 0.01042 / 0.44 ( 8) link_NAG-ASN : angle 6.73555 / 3.35 ( 24) *********************** 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 248 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 200 time to evaluate : 0.545 Fit side-chains REVERT: A 131 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8166 (tt0) REVERT: A 211 MET cc_start: 0.7083 (mmt) cc_final: 0.6794 (tpt) REVERT: A 267 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.9057 (mp) REVERT: A 353 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8352 (mt) REVERT: A 468 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7733 (mm-30) REVERT: A 603 MET cc_start: 0.8563 (ttp) cc_final: 0.8313 (ttm) REVERT: A 866 ASP cc_start: 0.6783 (OUTLIER) cc_final: 0.6010 (m-30) REVERT: A 905 LYS cc_start: 0.8549 (mmmt) cc_final: 0.8300 (mmmt) REVERT: A 1089 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8400 (mm-30) REVERT: B 131 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8160 (tt0) REVERT: B 211 MET cc_start: 0.7084 (mmt) cc_final: 0.6795 (tpt) REVERT: B 267 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.9059 (mp) REVERT: B 353 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8348 (mt) REVERT: B 468 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7746 (mm-30) REVERT: B 603 MET cc_start: 0.8573 (ttp) cc_final: 0.8324 (ttm) REVERT: B 866 ASP cc_start: 0.6780 (OUTLIER) cc_final: 0.6007 (m-30) REVERT: B 905 LYS cc_start: 0.8548 (mmmt) cc_final: 0.8301 (mmmt) REVERT: B 1089 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8411 (mm-30) outliers start: 48 outliers final: 34 residues processed: 234 average time/residue: 0.0914 time to fit residues: 34.4957 Evaluate side-chains 235 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 267 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 353 LEU 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 676 VAL Chi-restraints excluded: chain A residue 695 THR 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 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 267 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 353 LEU 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 676 VAL Chi-restraints excluded: chain B residue 695 THR 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 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 106 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 2 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 160 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1057 ASN B1057 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.094957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.072170 restraints weight = 32888.260| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.32 r_work: 0.2933 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15072 Z= 0.194 Angle : 0.741 16.787 20480 Z= 0.357 Chirality : 0.048 0.499 2380 Planarity : 0.004 0.051 2546 Dihedral : 5.510 47.463 2036 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.35 % Favored : 89.22 % Rotamer: Outliers : 3.15 % Allowed : 19.18 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.19), residues: 1846 helix: -0.44 (0.17), residues: 970 sheet: -0.93 (0.44), residues: 158 loop : -2.76 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 646 TYR 0.019 0.002 TYR B 880 PHE 0.018 0.002 PHE A 184 TRP 0.017 0.002 TRP A 830 HIS 0.003 0.001 HIS B 719 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (15056) covalent geometry : angle 0.70407 / 0.35 (20434) SS BOND : bond 0.00083 / 0.04 ( 2) SS BOND : angle 0.28722 / 0.15 ( 4) hydrogen bonds : bond 0.04069 / 2.67 ( 530) hydrogen bonds : angle 4.29236 / 2.83 ( 1530) link_BETA1-4 : bond 0.00459 / 0.25 ( 6) link_BETA1-4 : angle 2.03827 / 1.15 ( 18) link_NAG-ASN : bond 0.01004 / 0.42 ( 8) link_NAG-ASN : angle 6.59756 / 3.28 ( 24) *********************** 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 232 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 183 time to evaluate : 0.520 Fit side-chains REVERT: A 131 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8324 (tt0) REVERT: A 211 MET cc_start: 0.7278 (mmt) cc_final: 0.7003 (tpt) REVERT: A 353 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8455 (mt) REVERT: A 468 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7920 (mm-30) REVERT: A 603 MET cc_start: 0.8605 (ttp) cc_final: 0.8367 (ttm) REVERT: A 866 ASP cc_start: 0.6771 (OUTLIER) cc_final: 0.5999 (m-30) REVERT: A 1089 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8419 (mm-30) REVERT: B 131 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8324 (tt0) REVERT: B 211 MET cc_start: 0.7266 (mmt) cc_final: 0.7001 (tpt) REVERT: B 353 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8458 (mt) REVERT: B 468 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7941 (mm-30) REVERT: B 603 MET cc_start: 0.8613 (ttp) cc_final: 0.8375 (ttm) REVERT: B 866 ASP cc_start: 0.6763 (OUTLIER) cc_final: 0.5987 (m-30) REVERT: B 1089 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8443 (mm-30) outliers start: 49 outliers final: 37 residues processed: 223 average time/residue: 0.0957 time to fit residues: 33.9878 Evaluate side-chains 214 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 249 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 360 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 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 249 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 360 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 695 THR Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 750 LEU 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 27 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 137 optimal weight: 0.2980 chunk 54 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 176 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.097732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.075104 restraints weight = 32317.337| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.27 r_work: 0.2987 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15072 Z= 0.127 Angle : 0.687 16.332 20480 Z= 0.329 Chirality : 0.045 0.470 2380 Planarity : 0.004 0.052 2546 Dihedral : 5.352 48.858 2036 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.18 % Favored : 89.38 % Rotamer: Outliers : 3.09 % Allowed : 20.21 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.20), residues: 1846 helix: -0.09 (0.17), residues: 962 sheet: -0.84 (0.45), residues: 156 loop : -2.73 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 646 TYR 0.009 0.001 TYR A 593 PHE 0.012 0.001 PHE B 611 TRP 0.013 0.001 TRP B 596 HIS 0.003 0.001 HIS B 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (15056) covalent geometry : angle 0.64858 / 0.32 (20434) SS BOND : bond 0.00007 / 0.00 ( 2) SS BOND : angle 0.27122 / 0.13 ( 4) hydrogen bonds : bond 0.03493 / 2.27 ( 530) hydrogen bonds : angle 4.13515 / 2.72 ( 1530) link_BETA1-4 : bond 0.00262 / 0.15 ( 6) link_BETA1-4 : angle 1.80216 / 1.06 ( 18) link_NAG-ASN : bond 0.01062 / 0.44 ( 8) link_NAG-ASN : angle 6.45977 / 3.20 ( 24) *********************** 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 235 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 187 time to evaluate : 0.372 Fit side-chains REVERT: A 131 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8320 (tt0) REVERT: A 211 MET cc_start: 0.7253 (mmt) cc_final: 0.6968 (tpt) REVERT: A 267 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.9131 (mp) REVERT: A 353 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8447 (mt) REVERT: A 468 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7941 (mm-30) REVERT: A 603 MET cc_start: 0.8522 (ttp) cc_final: 0.8289 (ttm) REVERT: A 866 ASP cc_start: 0.6651 (OUTLIER) cc_final: 0.5945 (m-30) REVERT: A 912 ARG cc_start: 0.8240 (ttt90) cc_final: 0.7759 (ptm160) REVERT: A 1089 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8416 (mm-30) REVERT: B 131 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8317 (tt0) REVERT: B 211 MET cc_start: 0.7237 (mmt) cc_final: 0.6964 (tpt) REVERT: B 267 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9130 (mp) REVERT: B 353 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8432 (mt) REVERT: B 468 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7952 (mm-30) REVERT: B 603 MET cc_start: 0.8535 (ttp) cc_final: 0.8303 (ttm) REVERT: B 866 ASP cc_start: 0.6641 (OUTLIER) cc_final: 0.5931 (m-30) REVERT: B 912 ARG cc_start: 0.8239 (ttt90) cc_final: 0.7757 (ptm160) REVERT: B 1089 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8424 (mm-30) outliers start: 48 outliers final: 34 residues processed: 223 average time/residue: 0.0915 time to fit residues: 32.9057 Evaluate side-chains 218 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 267 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 353 LEU 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 695 THR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 733 MET Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 871 MET 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 267 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 353 LEU 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 695 THR Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 733 MET Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 871 MET 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 185 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 0.0370 chunk 126 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 85 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 120 optimal weight: 0.0670 chunk 167 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 110 optimal weight: 0.6980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.099607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.078283 restraints weight = 32170.715| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.14 r_work: 0.3023 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15072 Z= 0.108 Angle : 0.671 15.826 20480 Z= 0.320 Chirality : 0.044 0.446 2380 Planarity : 0.004 0.054 2546 Dihedral : 5.151 49.987 2036 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.56 % Favored : 89.00 % Rotamer: Outliers : 3.09 % Allowed : 19.82 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.20), residues: 1846 helix: 0.19 (0.18), residues: 948 sheet: -0.76 (0.45), residues: 156 loop : -2.62 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 646 TYR 0.022 0.001 TYR A 880 PHE 0.010 0.001 PHE B 611 TRP 0.016 0.001 TRP A 122 HIS 0.004 0.000 HIS B 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (15056) covalent geometry : angle 0.63483 / 0.31 (20434) SS BOND : bond 0.00038 / 0.02 ( 2) SS BOND : angle 0.17134 / 0.09 ( 4) hydrogen bonds : bond 0.03223 / 2.09 ( 530) hydrogen bonds : angle 4.01554 / 2.63 ( 1530) link_BETA1-4 : bond 0.00370 / 0.20 ( 6) link_BETA1-4 : angle 1.61090 / 0.96 ( 18) link_NAG-ASN : bond 0.01048 / 0.44 ( 8) link_NAG-ASN : angle 6.24840 / 3.10 ( 24) *********************** 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 242 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 0.460 Fit side-chains REVERT: A 131 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8310 (tt0) REVERT: A 267 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.9131 (mp) REVERT: A 468 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7901 (mm-30) REVERT: A 603 MET cc_start: 0.8390 (ttp) cc_final: 0.8158 (ttm) REVERT: A 866 ASP cc_start: 0.6533 (OUTLIER) cc_final: 0.5822 (m-30) REVERT: A 912 ARG cc_start: 0.8211 (ttt90) cc_final: 0.7743 (ptm160) REVERT: A 1089 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8370 (mm-30) REVERT: B 131 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8298 (tt0) REVERT: B 267 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9135 (mp) REVERT: B 468 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7888 (mm-30) REVERT: B 603 MET cc_start: 0.8436 (ttp) cc_final: 0.8204 (ttm) REVERT: B 866 ASP cc_start: 0.6528 (OUTLIER) cc_final: 0.5819 (m-30) REVERT: B 881 HIS cc_start: 0.8777 (t-170) cc_final: 0.8309 (t-170) REVERT: B 912 ARG cc_start: 0.8210 (ttt90) cc_final: 0.7737 (ptm160) REVERT: B 1089 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8379 (mm-30) outliers start: 48 outliers final: 38 residues processed: 230 average time/residue: 0.0935 time to fit residues: 34.8189 Evaluate side-chains 230 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 227 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 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 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 601 LEU Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 733 MET Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 871 MET 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 129 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 300 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 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 695 THR Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 871 MET 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 179 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 180 optimal weight: 0.0370 chunk 48 optimal weight: 0.9980 chunk 148 optimal weight: 0.8980 chunk 178 optimal weight: 0.0980 chunk 109 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.099208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.076736 restraints weight = 31975.422| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.26 r_work: 0.3021 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15072 Z= 0.111 Angle : 0.682 15.687 20480 Z= 0.322 Chirality : 0.045 0.441 2380 Planarity : 0.004 0.056 2546 Dihedral : 5.072 50.108 2036 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.08 % Favored : 89.49 % Rotamer: Outliers : 2.57 % Allowed : 20.72 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.20), residues: 1846 helix: 0.30 (0.18), residues: 950 sheet: -0.73 (0.45), residues: 156 loop : -2.63 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 646 TYR 0.009 0.001 TYR A 593 PHE 0.010 0.001 PHE A1090 TRP 0.016 0.001 TRP B 596 HIS 0.004 0.000 HIS B 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (15056) covalent geometry : angle 0.64814 / 0.31 (20434) SS BOND : bond 0.00030 / 0.01 ( 2) SS BOND : angle 0.11386 / 0.06 ( 4) hydrogen bonds : bond 0.03215 / 2.09 ( 530) hydrogen bonds : angle 3.99685 / 2.62 ( 1530) link_BETA1-4 : bond 0.00300 / 0.17 ( 6) link_BETA1-4 : angle 1.53977 / 0.92 ( 18) link_NAG-ASN : bond 0.01030 / 0.43 ( 8) link_NAG-ASN : angle 6.16544 / 3.05 ( 24) ********************** 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 231 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8371 (tt0) REVERT: A 194 MET cc_start: 0.9072 (ttp) cc_final: 0.8744 (tmm) REVERT: A 267 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.9095 (mp) REVERT: A 468 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7877 (mm-30) REVERT: A 603 MET cc_start: 0.8481 (ttp) cc_final: 0.8267 (ttm) REVERT: A 866 ASP cc_start: 0.6499 (OUTLIER) cc_final: 0.5767 (m-30) REVERT: A 912 ARG cc_start: 0.8240 (ttt90) cc_final: 0.7754 (ptm160) REVERT: A 1089 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8402 (mm-30) REVERT: B 131 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8366 (tt0) REVERT: B 194 MET cc_start: 0.9055 (ttp) cc_final: 0.8726 (tmm) REVERT: B 468 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7870 (mm-30) REVERT: B 603 MET cc_start: 0.8466 (ttp) cc_final: 0.8249 (ttm) REVERT: B 866 ASP cc_start: 0.6495 (OUTLIER) cc_final: 0.5762 (m-30) REVERT: B 881 HIS cc_start: 0.8801 (t-170) cc_final: 0.8329 (t-170) REVERT: B 912 ARG cc_start: 0.8240 (ttt90) cc_final: 0.7751 (ptm160) REVERT: B 1089 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8405 (mm-30) outliers start: 40 outliers final: 36 residues processed: 221 average time/residue: 0.1036 time to fit residues: 37.1783 Evaluate side-chains 224 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 227 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 387 MET 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 695 THR Chi-restraints excluded: chain A residue 733 MET Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 871 MET 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 129 ILE 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 341 THR Chi-restraints excluded: chain B residue 387 MET 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 695 THR Chi-restraints excluded: chain B residue 733 MET Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 871 MET 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 170 optimal weight: 0.1980 chunk 38 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 185 optimal weight: 7.9990 chunk 153 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.099466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.076940 restraints weight = 32001.771| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.25 r_work: 0.3027 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 15072 Z= 0.111 Angle : 0.676 15.440 20480 Z= 0.319 Chirality : 0.045 0.430 2380 Planarity : 0.004 0.052 2546 Dihedral : 5.009 50.541 2036 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.46 % Favored : 89.11 % Rotamer: Outliers : 2.83 % Allowed : 20.46 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.20), residues: 1846 helix: 0.42 (0.18), residues: 948 sheet: -0.73 (0.45), residues: 156 loop : -2.61 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 646 TYR 0.009 0.001 TYR B 593 PHE 0.010 0.001 PHE A1090 TRP 0.016 0.001 TRP B 122 HIS 0.004 0.000 HIS B 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (15056) covalent geometry : angle 0.64335 / 0.31 (20434) SS BOND : bond 0.00092 / 0.05 ( 2) SS BOND : angle 0.10768 / 0.06 ( 4) hydrogen bonds : bond 0.03156 / 2.04 ( 530) hydrogen bonds : angle 3.98002 / 2.60 ( 1530) link_BETA1-4 : bond 0.00287 / 0.16 ( 6) link_BETA1-4 : angle 1.48925 / 0.89 ( 18) link_NAG-ASN : bond 0.01031 / 0.43 ( 8) link_NAG-ASN : angle 6.02927 / 2.98 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3446.93 seconds wall clock time: 59 minutes 53.73 seconds (3593.73 seconds total)