Starting phenix.real_space_refine on Thu Sep 18 07:08:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m23_30061/09_2025/6m23_30061.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m23_30061/09_2025/6m23_30061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m23_30061/09_2025/6m23_30061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m23_30061/09_2025/6m23_30061.map" model { file = "/net/cci-nas-00/data/ceres_data/6m23_30061/09_2025/6m23_30061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m23_30061/09_2025/6m23_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' K': 1, ' CL': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' K': 1, ' CL': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.73, per 1000 atoms: 0.25 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: 1.27 Conformation dependent library (CDL) restraints added in 679.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.62 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: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4016 1.33 - 1.45: 2756 1.45 - 1.57: 8082 1.57 - 1.69: 16 1.69 - 1.81: 186 Bond restraints: 15056 Sorted by residual: bond pdb=" OG1 TPO A 906 " pdb=" P TPO A 906 " ideal model delta sigma weight residual 1.717 1.605 0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" OG1 TPO B 906 " pdb=" P TPO B 906 " ideal model delta sigma weight residual 1.717 1.605 0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C ARG B 671 " pdb=" N PRO B 672 " ideal model delta sigma weight residual 1.332 1.389 -0.057 1.12e-02 7.97e+03 2.55e+01 bond pdb=" C ARG A 671 " pdb=" N PRO A 672 " ideal model delta sigma weight residual 1.332 1.389 -0.057 1.12e-02 7.97e+03 2.55e+01 bond pdb=" OG1 TPO A1007 " pdb=" P TPO A1007 " ideal model delta sigma weight residual 1.717 1.618 0.099 2.00e-02 2.50e+03 2.46e+01 ... (remaining 15051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 19776 2.66 - 5.31: 542 5.31 - 7.97: 88 7.97 - 10.62: 24 10.62 - 13.28: 4 Bond angle restraints: 20434 Sorted by residual: angle pdb=" C ARG B 671 " pdb=" N PRO B 672 " pdb=" CA PRO B 672 " ideal model delta sigma weight residual 119.98 114.21 5.77 1.16e+00 7.43e-01 2.48e+01 angle pdb=" C ARG A 671 " pdb=" N PRO A 672 " pdb=" CA PRO A 672 " ideal model delta sigma weight residual 119.98 114.21 5.77 1.16e+00 7.43e-01 2.48e+01 angle pdb=" C ALA A 329 " pdb=" N THR A 330 " pdb=" CA THR A 330 " ideal model delta sigma weight residual 122.82 129.73 -6.91 1.42e+00 4.96e-01 2.37e+01 angle pdb=" C ALA B 329 " pdb=" N THR B 330 " pdb=" CA THR B 330 " ideal model delta sigma weight residual 122.82 129.73 -6.91 1.42e+00 4.96e-01 2.37e+01 angle pdb=" N VAL A1054 " pdb=" CA VAL A1054 " pdb=" C VAL A1054 " ideal model delta sigma weight residual 112.12 108.06 4.06 8.40e-01 1.42e+00 2.33e+01 ... (remaining 20429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 8014 17.36 - 34.73: 804 34.73 - 52.09: 182 52.09 - 69.46: 24 69.46 - 86.82: 14 Dihedral angle restraints: 9038 sinusoidal: 3690 harmonic: 5348 Sorted by residual: dihedral pdb=" CA ILE B 612 " pdb=" C ILE B 612 " pdb=" N CYS B 613 " pdb=" CA CYS B 613 " ideal model delta harmonic sigma weight residual 180.00 150.21 29.79 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA ILE A 612 " pdb=" C ILE A 612 " pdb=" N CYS A 613 " pdb=" CA CYS A 613 " ideal model delta harmonic sigma weight residual 180.00 150.21 29.79 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA CYS B 302 " pdb=" C CYS B 302 " pdb=" N ALA B 303 " pdb=" CA ALA B 303 " ideal model delta harmonic sigma weight residual 180.00 153.92 26.08 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 9035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1950 0.081 - 0.162: 378 0.162 - 0.243: 42 0.243 - 0.325: 8 0.325 - 0.406: 2 Chirality restraints: 2380 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" CB TPO B1007 " pdb=" CA TPO B1007 " pdb=" OG1 TPO B1007 " pdb=" CG2 TPO B1007 " both_signs ideal model delta sigma weight residual False 2.48 2.08 0.41 2.00e-01 2.50e+01 4.12e+00 ... (remaining 2377 not shown) Planarity restraints: 2554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 291 " -0.030 2.00e-02 2.50e+03 3.91e-02 1.91e+01 pdb=" CG ASN A 291 " 0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN A 291 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 291 " 0.068 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 291 " 0.030 2.00e-02 2.50e+03 3.91e-02 1.91e+01 pdb=" CG ASN B 291 " -0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN B 291 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B 291 " -0.068 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 663 " -0.051 5.00e-02 4.00e+02 7.63e-02 9.32e+00 pdb=" N PRO A 664 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 664 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 664 " -0.042 5.00e-02 4.00e+02 ... (remaining 2551 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.80: 4274 2.80 - 3.39: 14583 3.39 - 3.97: 25399 3.97 - 4.56: 37402 4.56 - 5.14: 54639 Nonbonded interactions: 136297 Sorted by model distance: nonbonded pdb=" O GLN A 673 " pdb=" O LEU A 704 " model vdw 2.216 3.040 nonbonded pdb=" O GLN B 673 " pdb=" O LEU B 704 " model vdw 2.216 3.040 nonbonded pdb=" OG SER A 151 " pdb=" CE2 PHE A 591 " model vdw 2.245 3.340 nonbonded pdb=" OG SER B 151 " pdb=" CE2 PHE B 591 " model vdw 2.245 3.340 nonbonded pdb=" O THR B 934 " pdb=" N GLU B 936 " model vdw 2.253 3.120 ... (remaining 136292 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 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: 2.130 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.330 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.112 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 : 14.890 86.819 5608 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 aren 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 covalent geometry : bond 0.00975 (15056) covalent geometry : angle 1.12379 (20434) SS BOND : bond 0.00217 ( 2) SS BOND : angle 0.22346 ( 4) hydrogen bonds : bond 0.33565 ( 530) hydrogen bonds : angle 10.48553 ( 1530) link_BETA1-4 : bond 0.01249 ( 6) link_BETA1-4 : angle 9.50871 ( 18) link_NAG-ASN : bond 0.00488 ( 8) link_NAG-ASN : angle 8.39750 ( 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 : 0.587 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: 0.1361 time to fit residues: 66.5761 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 : 0.601 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 A1051 HIS B 338 ASN B 344 GLN B 419 ASN B 573 ASN B 579 GLN B 673 GLN B 688 HIS B 719 HIS B 723 GLN B 778 ASN B 790 ASN B 848 HIS ** B 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1051 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.099480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.076947 restraints weight = 32906.587| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.42 r_work: 0.3021 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2438 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= 0.155 Angle : 0.789 12.864 20480 Z= 0.398 Chirality : 0.045 0.199 2380 Planarity : 0.006 0.058 2546 Dihedral : 7.924 56.542 2344 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.76 % Allowed : 9.97 % Favored : 89.27 % Rotamer: Outliers : 2.70 % Allowed : 14.22 % Favored : 83.08 % 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 aren not related in a simple way. whole: -4.65 (0.16), residues: 1846 helix: -2.92 (0.13), residues: 934 sheet: -1.63 (0.42), residues: 156 loop : -3.51 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 751 TYR 0.014 0.001 TYR B 880 PHE 0.022 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 covalent geometry : bond 0.00330 (15056) covalent geometry : angle 0.75863 (20434) SS BOND : bond 0.00077 ( 2) SS BOND : angle 0.24502 ( 4) hydrogen bonds : bond 0.05452 ( 530) hydrogen bonds : angle 5.17328 ( 1530) link_BETA1-4 : bond 0.00532 ( 6) link_BETA1-4 : angle 2.53017 ( 18) link_NAG-ASN : bond 0.00237 ( 8) link_NAG-ASN : angle 6.04209 ( 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 250 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 0.568 Fit side-chains REVERT: A 211 MET cc_start: 0.6668 (mmt) cc_final: 0.6142 (mmt) REVERT: A 241 MET cc_start: 0.8075 (mtt) cc_final: 0.7857 (mtp) REVERT: A 570 MET cc_start: 0.8965 (ttp) cc_final: 0.8623 (ttp) REVERT: A 610 MET cc_start: 0.8659 (mtp) cc_final: 0.8436 (mtp) REVERT: A 820 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8412 (mtm-85) REVERT: A 866 ASP cc_start: 0.7120 (OUTLIER) cc_final: 0.6058 (m-30) REVERT: B 211 MET cc_start: 0.6678 (mmt) cc_final: 0.6145 (mmt) REVERT: B 241 MET cc_start: 0.8050 (mtt) cc_final: 0.7832 (mtp) REVERT: B 570 MET cc_start: 0.8986 (ttp) cc_final: 0.8645 (ttp) REVERT: B 610 MET cc_start: 0.8659 (mtp) cc_final: 0.8434 (mtp) REVERT: B 820 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8431 (mtm-85) REVERT: B 866 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6056 (m-30) outliers start: 42 outliers final: 24 residues processed: 240 average time/residue: 0.1143 time to fit residues: 42.3285 Evaluate side-chains 218 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 A residue 933 ILE 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 Chi-restraints excluded: chain B residue 933 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 128 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 132 optimal weight: 0.0040 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.098882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.076161 restraints weight = 32730.406| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 3.40 r_work: 0.3010 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3024 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= 0.134 Angle : 0.701 11.629 20480 Z= 0.350 Chirality : 0.043 0.166 2380 Planarity : 0.004 0.055 2546 Dihedral : 7.168 55.721 2342 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.83 % Favored : 88.62 % Rotamer: Outliers : 3.60 % Allowed : 14.93 % Favored : 81.47 % 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 aren not related in a simple way. whole: -3.71 (0.17), residues: 1846 helix: -1.99 (0.15), residues: 968 sheet: -1.22 (0.44), residues: 156 loop : -3.31 (0.20), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 912 TYR 0.011 0.001 TYR A 593 PHE 0.012 0.001 PHE B 591 TRP 0.014 0.001 TRP A 596 HIS 0.007 0.001 HIS B 756 Details of bonding type rmsd covalent geometry : bond 0.00299 (15056) covalent geometry : angle 0.67709 (20434) SS BOND : bond 0.00016 ( 2) SS BOND : angle 0.30330 ( 4) hydrogen bonds : bond 0.04249 ( 530) hydrogen bonds : angle 4.47775 ( 1530) link_BETA1-4 : bond 0.00483 ( 6) link_BETA1-4 : angle 2.32799 ( 18) link_NAG-ASN : bond 0.00199 ( 8) link_NAG-ASN : angle 4.96527 ( 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 276 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 220 time to evaluate : 0.569 Fit side-chains REVERT: A 131 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8131 (tt0) REVERT: A 184 PHE cc_start: 0.8276 (t80) cc_final: 0.8044 (t80) REVERT: A 211 MET cc_start: 0.6713 (mmt) cc_final: 0.6399 (mmt) REVERT: A 346 ILE cc_start: 0.9535 (OUTLIER) cc_final: 0.9267 (mm) REVERT: A 353 LEU cc_start: 0.8426 (mt) cc_final: 0.8144 (mt) REVERT: A 866 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6187 (m-30) REVERT: A 884 ILE cc_start: 0.7143 (mt) cc_final: 0.6796 (mt) REVERT: A 905 LYS cc_start: 0.8442 (mmmt) cc_final: 0.8175 (mmmt) REVERT: A 931 GLN cc_start: 0.7588 (tp40) cc_final: 0.7216 (tt0) REVERT: B 131 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8120 (tt0) REVERT: B 184 PHE cc_start: 0.8288 (t80) cc_final: 0.8057 (t80) REVERT: B 211 MET cc_start: 0.6705 (mmt) cc_final: 0.6397 (mmt) REVERT: B 346 ILE cc_start: 0.9535 (OUTLIER) cc_final: 0.9270 (mm) REVERT: B 353 LEU cc_start: 0.8426 (mt) cc_final: 0.8147 (mt) REVERT: B 866 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6186 (m-30) REVERT: B 884 ILE cc_start: 0.7150 (mt) cc_final: 0.6805 (mt) REVERT: B 905 LYS cc_start: 0.8442 (mmmt) cc_final: 0.8177 (mmmt) REVERT: B 931 GLN cc_start: 0.7591 (tp40) cc_final: 0.7219 (tt0) outliers start: 56 outliers final: 26 residues processed: 256 average time/residue: 0.1048 time to fit residues: 42.0969 Evaluate side-chains 232 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 200 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 346 ILE 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 833 HIS Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 932 SER Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 346 ILE 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 833 HIS Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 932 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 84 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1057 ASN B 73 GLN ** B 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1057 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.096862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.074081 restraints weight = 32865.537| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.39 r_work: 0.2973 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15072 Z= 0.162 Angle : 0.716 11.262 20480 Z= 0.353 Chirality : 0.044 0.161 2380 Planarity : 0.004 0.051 2546 Dihedral : 6.425 46.587 2332 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.24 % Favored : 89.22 % Rotamer: Outliers : 3.60 % Allowed : 17.12 % Favored : 79.28 % 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 aren not related in a simple way. whole: -3.10 (0.18), residues: 1846 helix: -1.39 (0.16), residues: 942 sheet: -1.23 (0.44), residues: 160 loop : -3.09 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 751 TYR 0.015 0.001 TYR B 880 PHE 0.011 0.001 PHE B1090 TRP 0.014 0.001 TRP B 596 HIS 0.004 0.001 HIS B 756 Details of bonding type rmsd covalent geometry : bond 0.00367 (15056) covalent geometry : angle 0.69507 (20434) SS BOND : bond 0.00002 ( 2) SS BOND : angle 0.28785 ( 4) hydrogen bonds : bond 0.04037 ( 530) hydrogen bonds : angle 4.41855 ( 1530) link_BETA1-4 : bond 0.00400 ( 6) link_BETA1-4 : angle 2.28177 ( 18) link_NAG-ASN : bond 0.00184 ( 8) link_NAG-ASN : angle 4.68914 ( 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 250 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 194 time to evaluate : 0.578 Fit side-chains REVERT: A 131 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8235 (tt0) REVERT: A 211 MET cc_start: 0.6997 (mmt) cc_final: 0.6678 (mmt) REVERT: A 353 LEU cc_start: 0.8586 (mt) cc_final: 0.8300 (mt) REVERT: A 468 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7780 (mm-30) REVERT: A 866 ASP cc_start: 0.6892 (OUTLIER) cc_final: 0.5936 (m-30) REVERT: A 905 LYS cc_start: 0.8601 (mmmt) cc_final: 0.8317 (mmmt) REVERT: B 131 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8222 (tt0) REVERT: B 211 MET cc_start: 0.6982 (mmt) cc_final: 0.6677 (mmt) REVERT: B 353 LEU cc_start: 0.8593 (mt) cc_final: 0.8309 (mt) REVERT: B 468 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7779 (mm-30) REVERT: B 866 ASP cc_start: 0.6895 (OUTLIER) cc_final: 0.5941 (m-30) REVERT: B 905 LYS cc_start: 0.8598 (mmmt) cc_final: 0.8317 (mmmt) outliers start: 56 outliers final: 38 residues processed: 238 average time/residue: 0.1075 time to fit residues: 40.4728 Evaluate side-chains 224 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 332 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 461 VAL 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 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 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 332 ASP Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 461 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 135 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 86 optimal weight: 0.2980 chunk 78 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 82 optimal weight: 0.1980 chunk 95 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 931 GLN ** B 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 931 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.098105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.075464 restraints weight = 32567.516| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.36 r_work: 0.3002 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3708 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= 0.115 Angle : 0.666 11.694 20480 Z= 0.326 Chirality : 0.043 0.155 2380 Planarity : 0.004 0.054 2546 Dihedral : 5.985 47.664 2332 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.51 % Favored : 89.06 % Rotamer: Outliers : 3.09 % Allowed : 16.99 % Favored : 79.92 % 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 aren not related in a simple way. whole: -2.51 (0.19), residues: 1846 helix: -0.85 (0.17), residues: 954 sheet: -0.95 (0.45), residues: 158 loop : -2.91 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 912 TYR 0.011 0.001 TYR A 593 PHE 0.017 0.001 PHE A 184 TRP 0.014 0.001 TRP B 596 HIS 0.005 0.000 HIS B 756 Details of bonding type rmsd covalent geometry : bond 0.00252 (15056) covalent geometry : angle 0.64752 (20434) SS BOND : bond 0.00034 ( 2) SS BOND : angle 0.24402 ( 4) hydrogen bonds : bond 0.03371 ( 530) hydrogen bonds : angle 4.18467 ( 1530) link_BETA1-4 : bond 0.00434 ( 6) link_BETA1-4 : angle 1.86212 ( 18) link_NAG-ASN : bond 0.00227 ( 8) link_NAG-ASN : angle 4.33610 ( 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 266 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 218 time to evaluate : 0.779 Fit side-chains REVERT: A 131 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8192 (tt0) REVERT: A 211 MET cc_start: 0.7096 (mmt) cc_final: 0.6829 (mmt) REVERT: A 468 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7770 (mm-30) REVERT: A 866 ASP cc_start: 0.6846 (OUTLIER) cc_final: 0.6146 (m-30) REVERT: A 905 LYS cc_start: 0.8549 (mmmt) cc_final: 0.8278 (mmmt) REVERT: A 1089 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8426 (mm-30) REVERT: B 131 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8192 (tt0) REVERT: B 211 MET cc_start: 0.7084 (mmt) cc_final: 0.6828 (mmt) REVERT: B 468 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7773 (mm-30) REVERT: B 866 ASP cc_start: 0.6850 (OUTLIER) cc_final: 0.6151 (m-30) REVERT: B 905 LYS cc_start: 0.8547 (mmmt) cc_final: 0.8278 (mmmt) REVERT: B 1089 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8433 (mm-30) outliers start: 48 outliers final: 32 residues processed: 252 average time/residue: 0.1158 time to fit residues: 45.5912 Evaluate side-chains 220 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 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 676 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 930 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 293 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 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 807 VAL Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 930 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: 0.6980 chunk 76 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 82 optimal weight: 0.0050 chunk 171 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 180 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 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 = 0.3511 r_free = 0.3511 target = 0.097446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.074668 restraints weight = 32402.465| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.33 r_work: 0.2989 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15072 Z= 0.122 Angle : 0.651 10.764 20480 Z= 0.321 Chirality : 0.043 0.223 2380 Planarity : 0.004 0.053 2546 Dihedral : 5.862 48.146 2330 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.18 % Favored : 89.38 % Rotamer: Outliers : 3.80 % Allowed : 17.44 % Favored : 78.76 % 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 aren not related in a simple way. whole: -2.16 (0.20), residues: 1846 helix: -0.50 (0.17), residues: 950 sheet: -0.80 (0.46), residues: 156 loop : -2.83 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 646 TYR 0.018 0.001 TYR B 880 PHE 0.011 0.001 PHE A 611 TRP 0.015 0.001 TRP B 596 HIS 0.003 0.000 HIS B 756 Details of bonding type rmsd covalent geometry : bond 0.00275 (15056) covalent geometry : angle 0.63269 (20434) SS BOND : bond 0.00005 ( 2) SS BOND : angle 0.20718 ( 4) hydrogen bonds : bond 0.03416 ( 530) hydrogen bonds : angle 4.14781 ( 1530) link_BETA1-4 : bond 0.00383 ( 6) link_BETA1-4 : angle 1.79825 ( 18) link_NAG-ASN : bond 0.00141 ( 8) link_NAG-ASN : angle 4.28690 ( 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 263 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 204 time to evaluate : 0.734 Fit side-chains REVERT: A 131 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8274 (tt0) REVERT: A 211 MET cc_start: 0.7119 (mmt) cc_final: 0.6780 (tpt) REVERT: A 468 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7840 (mm-30) REVERT: A 834 ASP cc_start: 0.7680 (p0) cc_final: 0.7453 (p0) REVERT: A 866 ASP cc_start: 0.6781 (OUTLIER) cc_final: 0.6071 (m-30) REVERT: A 905 LYS cc_start: 0.8597 (mmmt) cc_final: 0.8349 (mmmt) REVERT: A 910 GLU cc_start: 0.8080 (mp0) cc_final: 0.7810 (pm20) REVERT: A 1089 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8390 (mm-30) REVERT: B 131 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8260 (tt0) REVERT: B 211 MET cc_start: 0.7111 (mmt) cc_final: 0.6786 (tpt) REVERT: B 468 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7836 (mm-30) REVERT: B 834 ASP cc_start: 0.7688 (p0) cc_final: 0.7465 (p0) REVERT: B 866 ASP cc_start: 0.6782 (OUTLIER) cc_final: 0.6075 (m-30) REVERT: B 905 LYS cc_start: 0.8595 (mmmt) cc_final: 0.8350 (mmmt) REVERT: B 910 GLU cc_start: 0.8091 (mp0) cc_final: 0.7823 (pm20) REVERT: B 1089 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8398 (mm-30) outliers start: 59 outliers final: 39 residues processed: 242 average time/residue: 0.1176 time to fit residues: 44.2243 Evaluate side-chains 229 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 274 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 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 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 807 VAL Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 897 ASP Chi-restraints excluded: chain A residue 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 274 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 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 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 807 VAL Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 897 ASP 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: 0.0070 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 172 optimal weight: 0.0170 chunk 131 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.9838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.098647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.076026 restraints weight = 31950.349| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.26 r_work: 0.3013 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15072 Z= 0.124 Angle : 0.649 10.890 20480 Z= 0.318 Chirality : 0.044 0.270 2380 Planarity : 0.004 0.053 2546 Dihedral : 5.785 48.300 2330 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.35 % Favored : 89.22 % Rotamer: Outliers : 3.41 % Allowed : 18.85 % Favored : 77.73 % 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 aren not related in a simple way. whole: -1.94 (0.20), residues: 1846 helix: -0.27 (0.17), residues: 950 sheet: -0.78 (0.46), residues: 156 loop : -2.78 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 646 TYR 0.009 0.001 TYR A 593 PHE 0.014 0.001 PHE A 184 TRP 0.014 0.001 TRP B 596 HIS 0.004 0.001 HIS B 756 Details of bonding type rmsd covalent geometry : bond 0.00281 (15056) covalent geometry : angle 0.63129 (20434) SS BOND : bond 0.00014 ( 2) SS BOND : angle 0.23022 ( 4) hydrogen bonds : bond 0.03454 ( 530) hydrogen bonds : angle 4.09501 ( 1530) link_BETA1-4 : bond 0.00423 ( 6) link_BETA1-4 : angle 1.71985 ( 18) link_NAG-ASN : bond 0.00183 ( 8) link_NAG-ASN : angle 4.18461 ( 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 247 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 194 time to evaluate : 0.578 Fit side-chains REVERT: A 131 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8239 (tt0) REVERT: A 211 MET cc_start: 0.7229 (mmt) cc_final: 0.6897 (tpt) REVERT: A 468 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7893 (mm-30) REVERT: A 866 ASP cc_start: 0.6697 (OUTLIER) cc_final: 0.6046 (m-30) REVERT: A 905 LYS cc_start: 0.8600 (mmmt) cc_final: 0.8351 (mmmt) REVERT: A 910 GLU cc_start: 0.8148 (mp0) cc_final: 0.7784 (pm20) REVERT: A 912 ARG cc_start: 0.8210 (ttt90) cc_final: 0.7738 (ptm160) REVERT: A 1089 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8335 (mm-30) REVERT: B 131 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8230 (tt0) REVERT: B 211 MET cc_start: 0.7223 (mmt) cc_final: 0.6895 (tpt) REVERT: B 468 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7898 (mm-30) REVERT: B 866 ASP cc_start: 0.6681 (OUTLIER) cc_final: 0.6029 (m-30) REVERT: B 905 LYS cc_start: 0.8602 (mmmt) cc_final: 0.8356 (mmmt) REVERT: B 910 GLU cc_start: 0.8143 (mp0) cc_final: 0.7776 (pm20) REVERT: B 912 ARG cc_start: 0.8207 (ttt90) cc_final: 0.7735 (ptm160) REVERT: B 1089 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8336 (mm-30) outliers start: 53 outliers final: 41 residues processed: 234 average time/residue: 0.1105 time to fit residues: 40.4736 Evaluate side-chains 232 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 593 TYR Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 897 ASP Chi-restraints excluded: chain A residue 898 ILE 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 293 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 593 TYR Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 695 THR Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 897 ASP Chi-restraints excluded: chain B residue 898 ILE Chi-restraints excluded: chain B residue 933 ILE Chi-restraints excluded: chain B residue 1072 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 27 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 83 optimal weight: 8.9990 chunk 176 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.095261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.072627 restraints weight = 32583.497| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.27 r_work: 0.2941 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15072 Z= 0.206 Angle : 0.724 12.679 20480 Z= 0.356 Chirality : 0.047 0.318 2380 Planarity : 0.005 0.049 2546 Dihedral : 5.972 46.758 2330 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.62 % Favored : 88.95 % Rotamer: Outliers : 3.09 % Allowed : 19.43 % Favored : 77.48 % 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 aren not related in a simple way. whole: -1.91 (0.20), residues: 1846 helix: -0.27 (0.17), residues: 956 sheet: -0.79 (0.45), residues: 158 loop : -2.75 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 646 TYR 0.016 0.002 TYR B 880 PHE 0.018 0.002 PHE B 611 TRP 0.012 0.002 TRP B 481 HIS 0.004 0.001 HIS A 719 Details of bonding type rmsd covalent geometry : bond 0.00471 (15056) covalent geometry : angle 0.70674 (20434) SS BOND : bond 0.00091 ( 2) SS BOND : angle 0.25983 ( 4) hydrogen bonds : bond 0.04315 ( 530) hydrogen bonds : angle 4.30810 ( 1530) link_BETA1-4 : bond 0.00351 ( 6) link_BETA1-4 : angle 2.04794 ( 18) link_NAG-ASN : bond 0.00069 ( 8) link_NAG-ASN : angle 4.35027 ( 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 234 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 186 time to evaluate : 0.613 Fit side-chains REVERT: A 130 MET cc_start: 0.8043 (mmm) cc_final: 0.7815 (mmm) REVERT: A 131 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8434 (tt0) REVERT: A 468 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8009 (mm-30) REVERT: A 866 ASP cc_start: 0.6746 (OUTLIER) cc_final: 0.6013 (m-30) REVERT: A 905 LYS cc_start: 0.8643 (mmmt) cc_final: 0.8375 (mmmt) REVERT: A 910 GLU cc_start: 0.8151 (mp0) cc_final: 0.7816 (pm20) REVERT: A 912 ARG cc_start: 0.8233 (ttt90) cc_final: 0.7695 (ptm160) REVERT: A 1089 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8406 (mm-30) REVERT: B 130 MET cc_start: 0.8053 (mmm) cc_final: 0.7826 (mmm) REVERT: B 131 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8422 (tt0) REVERT: B 468 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8021 (mm-30) REVERT: B 866 ASP cc_start: 0.6737 (OUTLIER) cc_final: 0.6002 (m-30) REVERT: B 905 LYS cc_start: 0.8642 (mmmt) cc_final: 0.8375 (mmmt) REVERT: B 910 GLU cc_start: 0.8148 (mp0) cc_final: 0.7814 (pm20) REVERT: B 912 ARG cc_start: 0.8246 (ttt90) cc_final: 0.7705 (ptm160) REVERT: B 1089 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8417 (mm-30) outliers start: 48 outliers final: 38 residues processed: 224 average time/residue: 0.1163 time to fit residues: 40.5622 Evaluate side-chains 216 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 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 750 LEU Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 897 ASP Chi-restraints excluded: chain A residue 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 293 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 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 897 ASP Chi-restraints excluded: chain B residue 933 ILE Chi-restraints excluded: chain B residue 1072 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 185 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 10 optimal weight: 0.0050 chunk 126 optimal weight: 0.0030 chunk 141 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 167 optimal weight: 0.0970 chunk 86 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 870 GLN B 870 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.099048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.076594 restraints weight = 32134.045| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.27 r_work: 0.3018 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15072 Z= 0.109 Angle : 0.657 12.200 20480 Z= 0.321 Chirality : 0.044 0.413 2380 Planarity : 0.004 0.053 2546 Dihedral : 5.726 49.076 2330 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.97 % Favored : 89.60 % Rotamer: Outliers : 2.25 % Allowed : 20.91 % Favored : 76.83 % 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 aren not related in a simple way. whole: -1.62 (0.20), residues: 1846 helix: 0.11 (0.17), residues: 944 sheet: -0.84 (0.45), residues: 158 loop : -2.73 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 646 TYR 0.010 0.001 TYR A 593 PHE 0.009 0.001 PHE B 521 TRP 0.015 0.001 TRP A 122 HIS 0.004 0.000 HIS B 756 Details of bonding type rmsd covalent geometry : bond 0.00232 (15056) covalent geometry : angle 0.64163 (20434) SS BOND : bond 0.00056 ( 2) SS BOND : angle 0.24988 ( 4) hydrogen bonds : bond 0.03356 ( 530) hydrogen bonds : angle 4.08853 ( 1530) link_BETA1-4 : bond 0.00474 ( 6) link_BETA1-4 : angle 1.55249 ( 18) link_NAG-ASN : bond 0.00286 ( 8) link_NAG-ASN : angle 4.03358 ( 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 233 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 198 time to evaluate : 0.593 Fit side-chains REVERT: A 130 MET cc_start: 0.8017 (mmm) cc_final: 0.7796 (mmm) REVERT: A 131 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8453 (tt0) REVERT: A 468 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7953 (mm-30) REVERT: A 866 ASP cc_start: 0.6631 (OUTLIER) cc_final: 0.6048 (m-30) REVERT: A 905 LYS cc_start: 0.8567 (mmmt) cc_final: 0.8329 (mmmt) REVERT: A 910 GLU cc_start: 0.8232 (mp0) cc_final: 0.7868 (pm20) REVERT: A 912 ARG cc_start: 0.8282 (ttt90) cc_final: 0.7733 (ptm160) REVERT: A 1089 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8424 (mm-30) REVERT: B 130 MET cc_start: 0.8029 (mmm) cc_final: 0.7809 (mmm) REVERT: B 131 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8446 (tt0) REVERT: B 468 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7948 (mm-30) REVERT: B 866 ASP cc_start: 0.6624 (OUTLIER) cc_final: 0.6042 (m-30) REVERT: B 905 LYS cc_start: 0.8567 (mmmt) cc_final: 0.8328 (mmmt) REVERT: B 910 GLU cc_start: 0.8235 (mp0) cc_final: 0.7871 (pm20) REVERT: B 912 ARG cc_start: 0.8285 (ttt90) cc_final: 0.7734 (ptm160) REVERT: B 1089 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8425 (mm-30) outliers start: 35 outliers final: 31 residues processed: 228 average time/residue: 0.1142 time to fit residues: 40.8758 Evaluate side-chains 226 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 461 VAL 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 897 ASP 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 293 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 461 VAL 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 866 ASP Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 897 ASP 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: 5.9990 chunk 180 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 178 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 144 optimal weight: 0.0050 chunk 47 optimal weight: 0.0030 chunk 133 optimal weight: 0.6980 chunk 2 optimal weight: 0.0050 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.099575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.077025 restraints weight = 31957.174| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 3.26 r_work: 0.3032 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 15072 Z= 0.108 Angle : 0.660 12.511 20480 Z= 0.318 Chirality : 0.044 0.367 2380 Planarity : 0.004 0.054 2546 Dihedral : 5.492 49.543 2330 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.97 % Favored : 89.60 % Rotamer: Outliers : 2.57 % Allowed : 20.85 % Favored : 76.58 % 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 aren not related in a simple way. whole: -1.43 (0.20), residues: 1846 helix: 0.29 (0.17), residues: 948 sheet: -0.86 (0.45), residues: 158 loop : -2.67 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 646 TYR 0.022 0.001 TYR B 880 PHE 0.010 0.001 PHE B 611 TRP 0.018 0.001 TRP B 596 HIS 0.004 0.001 HIS B 756 Details of bonding type rmsd covalent geometry : bond 0.00244 (15056) covalent geometry : angle 0.64520 (20434) SS BOND : bond 0.00080 ( 2) SS BOND : angle 0.17017 ( 4) hydrogen bonds : bond 0.03201 ( 530) hydrogen bonds : angle 4.03725 ( 1530) link_BETA1-4 : bond 0.00394 ( 6) link_BETA1-4 : angle 1.41452 ( 18) link_NAG-ASN : bond 0.00170 ( 8) link_NAG-ASN : angle 3.97320 ( 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 253 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 0.593 Fit side-chains REVERT: A 97 MET cc_start: 0.8563 (mmp) cc_final: 0.7854 (mmm) REVERT: A 108 LEU cc_start: 0.8293 (tt) cc_final: 0.7993 (tt) REVERT: A 131 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8441 (tt0) REVERT: A 468 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7921 (mm-30) REVERT: A 866 ASP cc_start: 0.6551 (OUTLIER) cc_final: 0.5989 (m-30) REVERT: A 905 LYS cc_start: 0.8562 (mmmt) cc_final: 0.8327 (mmmt) REVERT: A 910 GLU cc_start: 0.8176 (mp0) cc_final: 0.7815 (pm20) REVERT: A 912 ARG cc_start: 0.8278 (ttt90) cc_final: 0.7725 (ptm160) REVERT: A 1089 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8433 (mm-30) REVERT: B 97 MET cc_start: 0.8556 (mmp) cc_final: 0.7850 (mmm) REVERT: B 108 LEU cc_start: 0.8293 (tt) cc_final: 0.7994 (tt) REVERT: B 131 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8433 (tt0) REVERT: B 468 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7911 (mm-30) REVERT: B 866 ASP cc_start: 0.6542 (OUTLIER) cc_final: 0.5981 (m-30) REVERT: B 905 LYS cc_start: 0.8560 (mmmt) cc_final: 0.8325 (mmmt) REVERT: B 910 GLU cc_start: 0.8179 (mp0) cc_final: 0.7817 (pm20) REVERT: B 912 ARG cc_start: 0.8280 (ttt90) cc_final: 0.7729 (ptm160) REVERT: B 1089 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8420 (mm-30) outliers start: 40 outliers final: 30 residues processed: 245 average time/residue: 0.1214 time to fit residues: 45.5769 Evaluate side-chains 226 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 461 VAL 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 897 ASP 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 293 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 461 VAL 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 866 ASP Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 897 ASP 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: 0.0270 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 chunk 185 optimal weight: 5.9990 chunk 153 optimal weight: 0.8980 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.099381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.076986 restraints weight = 31930.122| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.22 r_work: 0.3030 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15072 Z= 0.112 Angle : 0.684 14.750 20480 Z= 0.326 Chirality : 0.045 0.380 2380 Planarity : 0.004 0.054 2546 Dihedral : 5.451 49.649 2330 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.24 % Favored : 89.33 % Rotamer: Outliers : 2.32 % Allowed : 21.49 % Favored : 76.19 % 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 aren not related in a simple way. whole: -1.34 (0.20), residues: 1846 helix: 0.37 (0.18), residues: 948 sheet: -0.84 (0.45), residues: 158 loop : -2.62 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 646 TYR 0.009 0.001 TYR B 593 PHE 0.013 0.001 PHE B 611 TRP 0.020 0.001 TRP A 830 HIS 0.004 0.000 HIS B 756 Details of bonding type rmsd covalent geometry : bond 0.00256 (15056) covalent geometry : angle 0.67048 (20434) SS BOND : bond 0.00097 ( 2) SS BOND : angle 0.14920 ( 4) hydrogen bonds : bond 0.03186 ( 530) hydrogen bonds : angle 4.07031 ( 1530) link_BETA1-4 : bond 0.00418 ( 6) link_BETA1-4 : angle 1.37883 ( 18) link_NAG-ASN : bond 0.00187 ( 8) link_NAG-ASN : angle 3.89869 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4021.38 seconds wall clock time: 69 minutes 41.69 seconds (4181.69 seconds total)