Starting phenix.real_space_refine on Sat Jun 28 15:41:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5uow_8579/06_2025/5uow_8579_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5uow_8579/06_2025/5uow_8579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5uow_8579/06_2025/5uow_8579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5uow_8579/06_2025/5uow_8579.map" model { file = "/net/cci-nas-00/data/ceres_data/5uow_8579/06_2025/5uow_8579_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5uow_8579/06_2025/5uow_8579_neut.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10586 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 15525 2.51 5 N 4158 2.21 5 O 4554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24347 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 797, 5758 Classifications: {'peptide': 797} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PTRANS': 35, 'TRANS': 761} Chain breaks: 1 Unresolved non-hydrogen bonds: 565 Unresolved non-hydrogen angles: 689 Unresolved non-hydrogen dihedrals: 456 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 15, 'ASP:plan': 14, 'PHE:plan': 2, 'GLU:plan': 25, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 367 Chain: "B" Number of atoms: 5582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 5582 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 203} Link IDs: {'PTRANS': 28, 'TRANS': 766} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 750 Unresolved non-hydrogen angles: 937 Unresolved non-hydrogen dihedrals: 625 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 18, 'ASP:plan': 21, 'PHE:plan': 14, 'GLU:plan': 20, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 453 Chain: "C" Number of atoms: 5484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 798, 5484 Classifications: {'peptide': 798} Incomplete info: {'truncation_to_alanine': 216} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 762} Chain breaks: 1 Unresolved non-hydrogen bonds: 872 Unresolved non-hydrogen angles: 1095 Unresolved non-hydrogen dihedrals: 735 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 15, 'TRP:plan': 6, 'ASP:plan': 15, 'PHE:plan': 9, 'GLU:plan': 31, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 556 Chain: "D" Number of atoms: 5127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 5127 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 327} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 765} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1224 Unresolved non-hydrogen angles: 1520 Unresolved non-hydrogen dihedrals: 1021 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 4, 'TYR:plan': 12, 'ASN:plan1': 18, 'TRP:plan': 2, 'ASP:plan': 30, 'PHE:plan': 17, 'GLU:plan': 42, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 731 Chain: "F" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1070 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'CIS': 3, 'TRANS': 210} Unresolved non-hydrogen bonds: 428 Unresolved non-hydrogen angles: 642 Unresolved non-hydrogen dihedrals: 214 Planarities with less than four sites: {'UNK:plan-1': 214} Unresolved non-hydrogen planarities: 214 Chain: "G" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1075 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 215} Link IDs: {'CIS': 3, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 430 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 215 Planarities with less than four sites: {'UNK:plan-1': 215} Unresolved non-hydrogen planarities: 215 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: "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: "I" 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 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: "M" 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: "N" 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: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'BMK': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.95, per 1000 atoms: 0.61 Number of scatterers: 24347 At special positions: 0 Unit cell: (197.2, 113.9, 185.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 4554 8.00 N 4158 7.00 C 15525 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.04 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 452 " distance=2.06 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 453 " distance=2.03 Simple disulfide: pdb=" SG CYS A 742 " - pdb=" SG CYS A 796 " distance=2.08 Simple disulfide: pdb=" SG CYS B 79 " - pdb=" SG CYS B 312 " distance=2.01 Simple disulfide: pdb=" SG CYS B 417 " - pdb=" SG CYS B 443 " distance=2.03 Simple disulfide: pdb=" SG CYS B 424 " - pdb=" SG CYS B 444 " distance=2.02 Simple disulfide: pdb=" SG CYS B 733 " - pdb=" SG CYS B 788 " distance=2.08 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.05 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 452 " distance=2.04 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 453 " distance=2.04 Simple disulfide: pdb=" SG CYS C 742 " - pdb=" SG CYS C 796 " distance=2.03 Simple disulfide: pdb=" SG CYS D 81 " - pdb=" SG CYS D 316 " distance=2.04 Simple disulfide: pdb=" SG CYS D 422 " - pdb=" SG CYS D 449 " distance=2.02 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 450 " distance=2.03 Simple disulfide: pdb=" SG CYS D 739 " - pdb=" SG CYS D 794 " 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=2, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG E 1 " - " ASN A 61 " " NAG H 1 " - " ASN A 203 " " NAG I 1 " - " ASN A 276 " " NAG J 1 " - " ASN C 61 " " NAG K 1 " - " ASN C 203 " " NAG L 1 " - " ASN C 276 " " NAG M 1 " - " ASN D 336 " " NAG N 1 " - " ASN D 681 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.57 Conformation dependent library (CDL) restraints added in 3.3 seconds 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6834 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 39 sheets defined 47.0% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.80 Creating SS restraints... Processing helix chain 'A' and resid 35 through 53 removed outlier: 4.364A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 82 Processing helix chain 'A' and resid 105 through 115 removed outlier: 3.597A pdb=" N TYR A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.862A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 147 through 159 Processing helix chain 'A' and resid 170 through 187 removed outlier: 3.790A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 removed outlier: 4.116A pdb=" N LEU A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.608A pdb=" N ALA A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET A 237 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.586A pdb=" N ILE A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 276 through 296 removed outlier: 3.976A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 327 removed outlier: 4.547A pdb=" N LEU A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 360 Processing helix chain 'A' and resid 455 through 468 Processing helix chain 'A' and resid 497 through 506 Processing helix chain 'A' and resid 518 through 523 Processing helix chain 'A' and resid 549 through 559 removed outlier: 3.596A pdb=" N MET A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) Proline residue: A 555 - end of helix Processing helix chain 'A' and resid 559 through 580 removed outlier: 3.917A pdb=" N LEU A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY A 565 " --> pdb=" O TRP A 561 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA A 572 " --> pdb=" O VAL A 568 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL A 573 " --> pdb=" O HIS A 569 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 614 Processing helix chain 'A' and resid 624 through 654 removed outlier: 4.163A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.524A pdb=" N ARG A 671 " --> pdb=" O ASP A 667 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN A 672 " --> pdb=" O PRO A 668 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 667 through 672' Processing helix chain 'A' and resid 686 through 694 removed outlier: 3.502A pdb=" N TYR A 690 " --> pdb=" O SER A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 706 Processing helix chain 'A' and resid 711 through 721 removed outlier: 3.869A pdb=" N VAL A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 742 removed outlier: 4.256A pdb=" N PHE A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU A 737 " --> pdb=" O VAL A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 780 Processing helix chain 'A' and resid 781 through 792 Processing helix chain 'A' and resid 808 through 835 removed outlier: 3.574A pdb=" N ILE A 826 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE A 827 " --> pdb=" O VAL A 823 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 832 " --> pdb=" O LEU A 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 54 removed outlier: 3.538A pdb=" N ILE B 45 " --> pdb=" O THR B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 85 removed outlier: 3.717A pdb=" N GLY B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 113 Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 142 through 158 Processing helix chain 'B' and resid 171 through 185 removed outlier: 3.520A pdb=" N ILE B 176 " --> pdb=" O TYR B 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE B 178 " --> pdb=" O ASP B 174 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS B 180 " --> pdb=" O ILE B 176 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 removed outlier: 3.508A pdb=" N LYS B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE B 214 " --> pdb=" O GLN B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 239 removed outlier: 3.575A pdb=" N SER B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 279 through 299 removed outlier: 4.065A pdb=" N VAL B 284 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 removed outlier: 3.536A pdb=" N ASN B 319 " --> pdb=" O ASN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 459 Processing helix chain 'B' and resid 483 through 490 Processing helix chain 'B' and resid 503 through 510 Processing helix chain 'B' and resid 532 through 568 removed outlier: 3.916A pdb=" N ALA B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU B 538 " --> pdb=" O PRO B 534 " (cutoff:3.500A) Proline residue: B 540 - end of helix removed outlier: 4.052A pdb=" N SER B 544 " --> pdb=" O PRO B 540 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL B 547 " --> pdb=" O ALA B 543 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA B 558 " --> pdb=" O LEU B 554 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU B 565 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR B 566 " --> pdb=" O PHE B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 601 removed outlier: 4.622A pdb=" N GLY B 590 " --> pdb=" O SER B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 644 removed outlier: 3.670A pdb=" N LYS B 616 " --> pdb=" O GLY B 612 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE B 617 " --> pdb=" O THR B 613 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE B 642 " --> pdb=" O ALA B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 660 Processing helix chain 'B' and resid 661 through 664 removed outlier: 3.626A pdb=" N TYR B 664 " --> pdb=" O PRO B 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 661 through 664' Processing helix chain 'B' and resid 676 through 684 removed outlier: 4.339A pdb=" N ARG B 680 " --> pdb=" O GLY B 676 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN B 681 " --> pdb=" O SER B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 696 Processing helix chain 'B' and resid 700 through 710 Processing helix chain 'B' and resid 720 through 730 Processing helix chain 'B' and resid 759 through 773 removed outlier: 3.920A pdb=" N LEU B 765 " --> pdb=" O ARG B 761 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA B 766 " --> pdb=" O PRO B 762 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN B 769 " --> pdb=" O LEU B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 784 Processing helix chain 'B' and resid 801 through 828 Processing helix chain 'C' and resid 35 through 53 Processing helix chain 'C' and resid 70 through 80 removed outlier: 4.130A pdb=" N MET C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 78 " --> pdb=" O MET C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 114 removed outlier: 3.598A pdb=" N TYR C 109 " --> pdb=" O THR C 105 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 removed outlier: 3.950A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 159 removed outlier: 4.165A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 removed outlier: 3.531A pdb=" N LEU C 183 " --> pdb=" O LYS C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 214 removed outlier: 3.990A pdb=" N LEU C 208 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU C 214 " --> pdb=" O GLU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 238 removed outlier: 4.162A pdb=" N THR C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET C 237 " --> pdb=" O LYS C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.625A pdb=" N SER C 255 " --> pdb=" O GLU C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 261 removed outlier: 3.696A pdb=" N ARG C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR C 261 " --> pdb=" O SER C 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 261' Processing helix chain 'C' and resid 276 through 296 removed outlier: 3.522A pdb=" N ASP C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 455 through 468 Processing helix chain 'C' and resid 478 through 481 removed outlier: 4.297A pdb=" N LYS C 481 " --> pdb=" O ALA C 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 478 through 481' Processing helix chain 'C' and resid 497 through 505 removed outlier: 3.744A pdb=" N GLY C 501 " --> pdb=" O ASN C 497 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU C 502 " --> pdb=" O GLY C 498 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 503 " --> pdb=" O MET C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 523 Processing helix chain 'C' and resid 548 through 582 Proline residue: C 555 - end of helix removed outlier: 4.643A pdb=" N SER C 558 " --> pdb=" O GLN C 554 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR C 559 " --> pdb=" O PRO C 555 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU C 560 " --> pdb=" O PHE C 556 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS C 569 " --> pdb=" O GLY C 565 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 570 " --> pdb=" O LEU C 566 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 576 " --> pdb=" O ALA C 572 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 614 removed outlier: 4.059A pdb=" N VAL C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU C 612 " --> pdb=" O SER C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 652 removed outlier: 3.561A pdb=" N LEU C 636 " --> pdb=" O MET C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 655 No H-bonds generated for 'chain 'C' and resid 653 through 655' Processing helix chain 'C' and resid 667 through 672 Processing helix chain 'C' and resid 685 through 694 Processing helix chain 'C' and resid 698 through 705 Processing helix chain 'C' and resid 711 through 721 Processing helix chain 'C' and resid 731 through 741 removed outlier: 3.825A pdb=" N PHE C 736 " --> pdb=" O ALA C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 781 Processing helix chain 'C' and resid 781 through 792 Processing helix chain 'C' and resid 804 through 836 removed outlier: 4.367A pdb=" N ASN C 810 " --> pdb=" O LEU C 806 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N MET C 811 " --> pdb=" O THR C 807 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY C 813 " --> pdb=" O GLU C 809 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA C 819 " --> pdb=" O PHE C 815 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY C 821 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE C 822 " --> pdb=" O VAL C 818 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL C 823 " --> pdb=" O ALA C 819 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA C 824 " --> pdb=" O GLY C 820 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY C 825 " --> pdb=" O GLY C 821 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE C 827 " --> pdb=" O VAL C 823 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 55 removed outlier: 3.652A pdb=" N ASP D 47 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N HIS D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 88 removed outlier: 3.805A pdb=" N CYS D 81 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP D 86 " --> pdb=" O ASP D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 115 removed outlier: 4.180A pdb=" N GLN D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 127 Processing helix chain 'D' and resid 144 through 159 Processing helix chain 'D' and resid 173 through 188 removed outlier: 4.087A pdb=" N SER D 188 " --> pdb=" O THR D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 217 removed outlier: 3.937A pdb=" N LYS D 217 " --> pdb=" O ASN D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 243 Processing helix chain 'D' and resid 254 through 259 removed outlier: 4.609A pdb=" N ALA D 258 " --> pdb=" O PRO D 254 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 259 " --> pdb=" O SER D 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 254 through 259' Processing helix chain 'D' and resid 283 through 305 Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 326 through 336 removed outlier: 4.278A pdb=" N ARG D 332 " --> pdb=" O HIS D 328 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TYR D 333 " --> pdb=" O MET D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 466 removed outlier: 3.618A pdb=" N THR D 464 " --> pdb=" O LYS D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 496 removed outlier: 3.717A pdb=" N GLU D 493 " --> pdb=" O GLY D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 516 Processing helix chain 'D' and resid 543 through 549 removed outlier: 3.774A pdb=" N ALA D 549 " --> pdb=" O GLU D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 574 removed outlier: 3.920A pdb=" N VAL D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 607 removed outlier: 3.698A pdb=" N ILE D 599 " --> pdb=" O ILE D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 649 removed outlier: 3.668A pdb=" N ILE D 623 " --> pdb=" O THR D 619 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN D 649 " --> pdb=" O ALA D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 692 Processing helix chain 'D' and resid 692 through 700 removed outlier: 3.599A pdb=" N HIS D 696 " --> pdb=" O TYR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 703 No H-bonds generated for 'chain 'D' and resid 701 through 703' Processing helix chain 'D' and resid 706 through 716 Processing helix chain 'D' and resid 726 through 735 Processing helix chain 'D' and resid 765 through 780 removed outlier: 3.953A pdb=" N VAL D 769 " --> pdb=" O TRP D 765 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA D 772 " --> pdb=" O GLN D 768 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE D 773 " --> pdb=" O VAL D 769 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE D 777 " --> pdb=" O ILE D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 780 through 790 removed outlier: 3.898A pdb=" N GLU D 784 " --> pdb=" O GLY D 780 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 837 removed outlier: 3.647A pdb=" N TYR D 836 " --> pdb=" O GLU D 832 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS D 837 " --> pdb=" O HIS D 833 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.864A pdb=" N UNK F 84 " --> pdb=" O UNK F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 128 Processing helix chain 'F' and resid 184 through 189 removed outlier: 3.707A pdb=" N UNK F 189 " --> pdb=" O UNK F 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 56 No H-bonds generated for 'chain 'G' and resid 54 through 56' Processing helix chain 'G' and resid 61 through 66 removed outlier: 4.671A pdb=" N UNK G 66 " --> pdb=" O UNK G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 158 through 160 No H-bonds generated for 'chain 'G' and resid 158 through 160' Processing helix chain 'G' and resid 203 through 205 No H-bonds generated for 'chain 'G' and resid 203 through 205' Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 65 removed outlier: 6.458A pdb=" N ILE A 90 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 197 removed outlier: 6.052A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 268 through 271 removed outlier: 4.119A pdb=" N GLY A 365 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 368 " --> pdb=" O TYR A 371 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR A 371 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 471 through 474 removed outlier: 8.092A pdb=" N MET A 510 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LYS A 399 " --> pdb=" O MET A 510 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 526 " --> pdb=" O MET A 760 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA6, first strand: chain 'A' and resid 679 through 680 removed outlier: 6.719A pdb=" N ALA A 680 " --> pdb=" O ILE A 728 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N ASP A 730 " --> pdb=" O ALA A 680 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N PHE A 727 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLN A 534 " --> pdb=" O ARG A 753 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ARG A 753 " --> pdb=" O GLN A 534 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE A 538 " --> pdb=" O GLU A 749 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N GLU A 749 " --> pdb=" O ILE A 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 65 removed outlier: 6.626A pdb=" N ASN B 29 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N VAL B 91 " --> pdb=" O ASN B 29 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA B 31 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N GLY B 93 " --> pdb=" O ALA B 31 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE B 33 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 163 through 165 removed outlier: 5.932A pdb=" N SER B 163 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 332 through 335 removed outlier: 4.268A pdb=" N VAL B 333 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 353 through 358 removed outlier: 3.606A pdb=" N LEU B 353 " --> pdb=" O TRP B 370 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU B 357 " --> pdb=" O LYS B 366 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LYS B 366 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU B 371 " --> pdb=" O SER B 374 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 463 through 466 removed outlier: 3.645A pdb=" N THR B 398 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL B 497 " --> pdb=" O SER B 395 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL B 397 " --> pdb=" O VAL B 497 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 406 through 409 removed outlier: 6.047A pdb=" N CYS B 424 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N CYS B 443 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL B 422 " --> pdb=" O CYS B 443 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 475 through 477 removed outlier: 3.740A pdb=" N ILE B 477 " --> pdb=" O VAL B 480 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 521 through 524 removed outlier: 6.210A pdb=" N GLY B 671 " --> pdb=" O ILE B 717 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N ASP B 719 " --> pdb=" O GLY B 671 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 60 through 66 removed outlier: 6.113A pdb=" N VAL C 27 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N THR C 63 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE C 29 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N VAL C 65 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ALA C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE C 90 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 194 through 197 removed outlier: 6.105A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 267 through 271 removed outlier: 4.112A pdb=" N GLY C 365 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 410 through 413 removed outlier: 6.580A pdb=" N ILE C 435 " --> pdb=" O VAL C 474 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N LEU C 476 " --> pdb=" O ILE C 435 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN C 437 " --> pdb=" O LEU C 476 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 516 through 517 removed outlier: 4.772A pdb=" N GLY C 755 " --> pdb=" O ILE C 517 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N PHE C 752 " --> pdb=" O LEU C 536 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU C 536 " --> pdb=" O PHE C 752 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS C 532 " --> pdb=" O PHE C 756 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA C 680 " --> pdb=" O ILE C 728 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N ASP C 730 " --> pdb=" O ALA C 680 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 516 through 517 removed outlier: 4.772A pdb=" N GLY C 755 " --> pdb=" O ILE C 517 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N PHE C 752 " --> pdb=" O LEU C 536 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU C 536 " --> pdb=" O PHE C 752 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS C 532 " --> pdb=" O PHE C 756 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 525 through 527 Processing sheet with id=AC4, first strand: chain 'D' and resid 60 through 68 removed outlier: 3.533A pdb=" N VAL D 34 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY D 91 " --> pdb=" O ASP D 31 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE D 118 " --> pdb=" O PHE D 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 193 through 200 removed outlier: 6.731A pdb=" N PHE D 164 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLU D 196 " --> pdb=" O PHE D 164 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU D 200 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL D 222 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE D 223 " --> pdb=" O ILE D 252 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N TRP D 251 " --> pdb=" O ILE D 273 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N VAL D 275 " --> pdb=" O TRP D 251 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL D 253 " --> pdb=" O VAL D 275 " (cutoff:3.500A) removed outlier: 9.842A pdb=" N TYR D 277 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU D 357 " --> pdb=" O TYR D 374 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU D 361 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ARG D 370 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS D 375 " --> pdb=" O SER D 378 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 338 through 339 Processing sheet with id=AC7, first strand: chain 'D' and resid 470 through 473 removed outlier: 4.013A pdb=" N MET D 501 " --> pdb=" O SER D 400 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL D 402 " --> pdb=" O MET D 501 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 411 through 414 removed outlier: 3.856A pdb=" N ARG D 448 " --> pdb=" O CYS D 429 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 481 through 483 Processing sheet with id=AD1, first strand: chain 'D' and resid 524 through 525 Processing sheet with id=AD2, first strand: chain 'D' and resid 676 through 677 removed outlier: 6.218A pdb=" N GLY D 677 " --> pdb=" O ILE D 723 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N ASP D 725 " --> pdb=" O GLY D 677 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL D 531 " --> pdb=" O VAL D 742 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AD4, first strand: chain 'F' and resid 10 through 13 removed outlier: 5.553A pdb=" N UNK F 11 " --> pdb=" O UNK F 106 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N UNK F 34 " --> pdb=" O UNK F 50 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N UNK F 50 " --> pdb=" O UNK F 34 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N UNK F 36 " --> pdb=" O UNK F 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 10 through 13 removed outlier: 5.553A pdb=" N UNK F 11 " --> pdb=" O UNK F 106 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.330A pdb=" N UNK F 174 " --> pdb=" O UNK F 139 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N UNK F 175 " --> pdb=" O UNK F 165 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 154 through 156 removed outlier: 4.022A pdb=" N UNK F 149 " --> pdb=" O UNK F 156 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.435A pdb=" N UNK G 34 " --> pdb=" O UNK G 50 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N UNK G 50 " --> pdb=" O UNK G 34 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N UNK G 36 " --> pdb=" O UNK G 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 11 through 12 removed outlier: 4.189A pdb=" N UNK G 108 " --> pdb=" O UNK G 98 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 126 through 131 removed outlier: 5.418A pdb=" N UNK G 177 " --> pdb=" O UNK G 146 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N UNK G 180 " --> pdb=" O UNK G 169 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N UNK G 169 " --> pdb=" O UNK G 180 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N UNK G 182 " --> pdb=" O UNK G 167 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N UNK G 167 " --> pdb=" O UNK G 182 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N UNK G 184 " --> pdb=" O UNK G 165 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N UNK G 165 " --> pdb=" O UNK G 184 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 152 through 156 1220 hydrogen bonds defined for protein. 3483 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: 10.06 Time building geometry restraints manager: 7.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5513 1.33 - 1.45: 6659 1.45 - 1.58: 12465 1.58 - 1.71: 1 1.71 - 1.84: 182 Bond restraints: 24820 Sorted by residual: bond pdb=" CA PRO A 263 " pdb=" C PRO A 263 " ideal model delta sigma weight residual 1.520 1.684 -0.164 1.42e-02 4.96e+03 1.34e+02 bond pdb=" N PRO A 263 " pdb=" CA PRO A 263 " ideal model delta sigma weight residual 1.469 1.550 -0.081 1.28e-02 6.10e+03 4.00e+01 bond pdb=" CA ALA B 141 " pdb=" C ALA B 141 " ideal model delta sigma weight residual 1.520 1.450 0.070 1.22e-02 6.72e+03 3.32e+01 bond pdb=" N PHE B 178 " pdb=" CA PHE B 178 " ideal model delta sigma weight residual 1.459 1.394 0.065 1.19e-02 7.06e+03 3.01e+01 bond pdb=" N UNK F 78 " pdb=" CA UNK F 78 " ideal model delta sigma weight residual 1.458 1.361 0.097 1.90e-02 2.77e+03 2.63e+01 ... (remaining 24815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.34: 33889 7.34 - 14.67: 226 14.67 - 22.01: 8 22.01 - 29.35: 7 29.35 - 36.68: 1 Bond angle restraints: 34131 Sorted by residual: angle pdb=" N THR B 200 " pdb=" CA THR B 200 " pdb=" C THR B 200 " ideal model delta sigma weight residual 111.28 126.70 -15.42 1.09e+00 8.42e-01 2.00e+02 angle pdb=" N VAL D 613 " pdb=" CA VAL D 613 " pdb=" C VAL D 613 " ideal model delta sigma weight residual 110.42 122.44 -12.02 9.60e-01 1.09e+00 1.57e+02 angle pdb=" C SER A 754 " pdb=" N GLY A 755 " pdb=" CA GLY A 755 " ideal model delta sigma weight residual 121.45 133.95 -12.50 1.06e+00 8.90e-01 1.39e+02 angle pdb=" N SER D 534 " pdb=" CA SER D 534 " pdb=" C SER D 534 " ideal model delta sigma weight residual 111.14 123.15 -12.01 1.08e+00 8.57e-01 1.24e+02 angle pdb=" N GLN B 67 " pdb=" CA GLN B 67 " pdb=" C GLN B 67 " ideal model delta sigma weight residual 111.36 122.92 -11.56 1.09e+00 8.42e-01 1.13e+02 ... (remaining 34126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 13574 17.83 - 35.66: 751 35.66 - 53.49: 326 53.49 - 71.32: 84 71.32 - 89.15: 19 Dihedral angle restraints: 14754 sinusoidal: 4233 harmonic: 10521 Sorted by residual: dihedral pdb=" CA UNK G 148 " pdb=" C UNK G 148 " pdb=" N UNK G 149 " pdb=" CA UNK G 149 " ideal model delta harmonic sigma weight residual 180.00 107.65 72.35 0 5.00e+00 4.00e-02 2.09e+02 dihedral pdb=" C UNK F 67 " pdb=" N UNK F 67 " pdb=" CA UNK F 67 " pdb=" CB UNK F 67 " ideal model delta harmonic sigma weight residual -122.60 -157.68 35.08 0 2.50e+00 1.60e-01 1.97e+02 dihedral pdb=" N UNK F 67 " pdb=" C UNK F 67 " pdb=" CA UNK F 67 " pdb=" CB UNK F 67 " ideal model delta harmonic sigma weight residual 122.80 157.40 -34.60 0 2.50e+00 1.60e-01 1.92e+02 ... (remaining 14751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.312: 4177 0.312 - 0.625: 72 0.625 - 0.937: 2 0.937 - 1.249: 0 1.249 - 1.561: 1 Chirality restraints: 4252 Sorted by residual: chirality pdb=" CA UNK F 67 " pdb=" N UNK F 67 " pdb=" C UNK F 67 " pdb=" CB UNK F 67 " both_signs ideal model delta sigma weight residual False 2.52 0.96 1.56 2.00e-01 2.50e+01 6.09e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.73e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.68e+01 ... (remaining 4249 not shown) Planarity restraints: 4426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " 0.336 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG N 1 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " 0.044 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " -0.508 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " 0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.335 2.00e-02 2.50e+03 2.85e-01 1.01e+03 pdb=" C7 NAG H 1 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " -0.180 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.499 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 1 " -0.315 2.00e-02 2.50e+03 2.71e-01 9.18e+02 pdb=" C7 NAG K 1 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG K 1 " -0.011 2.00e-02 2.50e+03 pdb=" N2 NAG K 1 " 0.467 2.00e-02 2.50e+03 pdb=" O7 NAG K 1 " -0.211 2.00e-02 2.50e+03 ... (remaining 4423 not shown) Histogram of nonbonded interaction distances: 1.07 - 1.84: 16 1.84 - 2.60: 665 2.60 - 3.37: 34998 3.37 - 4.13: 55434 4.13 - 4.90: 96189 Nonbonded interactions: 187302 Sorted by model distance: nonbonded pdb=" OH TYR A 679 " pdb=" CD1 ILE A 728 " model vdw 1.072 3.460 nonbonded pdb=" CZ TYR A 679 " pdb=" CD1 ILE A 728 " model vdw 1.142 3.680 nonbonded pdb=" SD MET D 302 " pdb=" CG PRO D 310 " model vdw 1.215 3.800 nonbonded pdb=" O GLY C 825 " pdb=" CG2 ILE C 829 " model vdw 1.425 3.460 nonbonded pdb=" O ASN C 273 " pdb=" CD2 HIS C 280 " model vdw 1.427 3.260 ... (remaining 187297 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 50 or (resid 51 and (name N or name CA or name \ C or name O or name CB )) or resid 52 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 75 or (resid 76 and ( \ name N or name CA or name C or name O or name CB )) or resid 77 through 79 or (r \ esid 80 and (name N or name CA or name C or name O or name CB )) or resid 81 thr \ ough 93 or (resid 94 and (name N or name CA or name C or name O or name CB )) or \ resid 95 through 100 or (resid 101 through 103 and (name N or name CA or name C \ or name O or name CB )) or resid 104 through 129 or (resid 130 and (name N or n \ ame CA or name C or name O or name CB )) or resid 131 through 143 or (resid 144 \ and (name N or name CA or name C or name O or name CB )) or resid 145 or (resid \ 146 through 149 and (name N or name CA or name C or name O or name CB )) or resi \ d 150 or (resid 151 through 155 and (name N or name CA or name C or name O or na \ me CB )) or resid 156 or (resid 157 through 162 and (name N or name CA or name C \ or name O or name CB )) or resid 163 through 168 or (resid 169 and (name N or n \ ame CA or name C or name O or name CB )) or resid 170 through 176 or (resid 177 \ through 178 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 9 through 180 or (resid 181 through 182 and (name N or name CA or name C or name \ O or name CB )) or resid 183 or (resid 184 through 193 and (name N or name CA o \ r name C or name O or name CB )) or resid 194 through 197 or (resid 198 and (nam \ e N or name CA or name C or name O or name CB )) or resid 199 through 200 or (re \ sid 201 through 202 and (name N or name CA or name C or name O or name CB )) or \ resid 203 through 209 or (resid 210 through 211 and (name N or name CA or name C \ or name O or name CB )) or resid 212 or (resid 213 through 220 and (name N or n \ ame CA or name C or name O or name CB )) or resid 221 through 223 or (resid 224 \ through 225 and (name N or name CA or name C or name O or name CB )) or resid 22 \ 6 through 231 or (resid 232 through 233 and (name N or name CA or name C or name \ O or name CB )) or resid 234 through 239 or (resid 240 and (name N or name CA o \ r name C or name O or name CB )) or resid 241 through 244 or (resid 245 through \ 249 and (name N or name CA or name C or name O or name CB )) or resid 250 or (re \ sid 251 through 255 and (name N or name CA or name C or name O or name CB )) or \ resid 256 through 258 or (resid 259 and (name N or name CA or name C or name O o \ r name CB )) or resid 260 through 265 or (resid 266 through 267 and (name N or n \ ame CA or name C or name O or name CB )) or resid 268 or (resid 269 through 272 \ and (name N or name CA or name C or name O or name CB )) or resid 273 through 34 \ 5 or (resid 346 through 347 and (name N or name CA or name C or name O or name C \ B )) or resid 348 through 350 or (resid 351 and (name N or name CA or name C or \ name O or name CB )) or resid 352 through 355 or (resid 356 through 363 and (nam \ e N or name CA or name C or name O or name CB )) or resid 364 through 372 or (re \ sid 373 through 381 and (name N or name CA or name C or name O or name CB )) or \ resid 382 through 415 or (resid 416 and (name N or name CA or name C or name O o \ r name CB )) or resid 417 through 447 or (resid 448 and (name N or name CA or na \ me C or name O or name CB )) or resid 449 through 466 or (resid 467 and (name N \ or name CA or name C or name O or name CB )) or resid 468 through 495 or (resid \ 496 through 497 and (name N or name CA or name C or name O or name CB )) or resi \ d 498 through 547 or (resid 548 through 554 and (name N or name CA or name C or \ name O or name CB )) or resid 555 or (resid 556 through 557 and (name N or name \ CA or name C or name O or name CB )) or resid 558 through 560 or (resid 561 and \ (name N or name CA or name C or name O or name CB )) or resid 562 through 577 or \ (resid 578 and (name N or name CA or name C or name O or name CB )) or resid 57 \ 9 or (resid 580 through 581 and (name N or name CA or name C or name O or name C \ B )) or resid 582 through 601 or (resid 602 and (name N or name CA or name C or \ name O or name CB )) or resid 603 through 606 or (resid 607 and (name N or name \ CA or name C or name O or name CB )) or resid 608 through 610 or (resid 611 thro \ ugh 615 and (name N or name CA or name C or name O or name CB )) or resid 616 th \ rough 624 or (resid 625 through 628 and (name N or name CA or name C or name O o \ r name CB )) or resid 629 through 653 or (resid 654 through 657 and (name N or n \ ame CA or name C or name O or name CB )) or resid 658 through 662 or (resid 663 \ and (name N or name CA or name C or name O or name CB )) or resid 664 through 67 \ 4 or (resid 675 through 676 and (name N or name CA or name C or name O or name C \ B )) or resid 677 through 692 or (resid 693 and (name N or name CA or name C or \ name O or name CB )) or resid 694 through 699 or (resid 700 and (name N or name \ CA or name C or name O or name CB )) or resid 701 or (resid 702 and (name N or n \ ame CA or name C or name O or name CB )) or resid 703 through 704 or (resid 705 \ through 706 and (name N or name CA or name C or name O or name CB )) or resid 70 \ 7 through 738 or (resid 739 through 741 and (name N or name CA or name C or name \ O or name CB )) or resid 742 through 792 or (resid 793 and (name N or name CA o \ r name C or name O or name CB )) or resid 794 through 805 or (resid 806 through \ 810 and (name N or name CA or name C or name O or name CB )) or resid 811 throug \ h 832 or (resid 833 through 836 and (name N or name CA or name C or name O or na \ me CB )))) selection = (chain 'C' and (resid 23 through 27 or (resid 28 and (name N or name CA or name \ C or name O or name CB )) or resid 29 through 113 or (resid 114 and (name N or n \ ame CA or name C or name O or name CB )) or resid 115 through 271 or (resid 272 \ and (name N or name CA or name C or name O or name CB )) or resid 273 through 32 \ 2 or (resid 323 and (name N or name CA or name C or name O or name CB )) or resi \ d 324 through 389 or (resid 390 and (name N or name CA or name C or name O or na \ me CB )) or resid 391 through 394 or (resid 395 through 396 and (name N or name \ CA or name C or name O or name CB )) or resid 397 through 402 or (resid 403 and \ (name N or name CA or name C or name O or name CB )) or resid 404 or (resid 405 \ and (name N or name CA or name C or name O or name CB )) or resid 406 through 41 \ 1 or (resid 412 and (name N or name CA or name C or name O or name CB )) or resi \ d 413 or (resid 414 through 416 and (name N or name CA or name C or name O or na \ me CB )) or resid 417 through 420 or (resid 421 through 424 and (name N or name \ CA or name C or name O or name CB )) or resid 425 through 426 or (resid 427 and \ (name N or name CA or name C or name O or name CB )) or resid 428 or (resid 429 \ and (name N or name CA or name C or name O or name CB )) or resid 430 or (resid \ 431 and (name N or name CA or name C or name O or name CB )) or resid 432 or (re \ sid 433 and (name N or name CA or name C or name O or name CB )) or resid 434 th \ rough 471 or (resid 472 through 473 and (name N or name CA or name C or name O o \ r name CB )) or resid 474 through 475 or (resid 476 and (name N or name CA or na \ me C or name O or name CB )) or resid 477 through 478 or (resid 479 and (name N \ or name CA or name C or name O or name CB )) or resid 480 or (resid 481 and (nam \ e N or name CA or name C or name O or name CB )) or resid 482 through 483 or (re \ sid 484 through 497 and (name N or name CA or name C or name O or name CB )) or \ resid 498 or (resid 499 and (name N or name CA or name C or name O or name CB )) \ or resid 500 through 506 or (resid 507 through 508 and (name N or name CA or na \ me C or name O or name CB )) or resid 509 through 518 or (resid 519 through 520 \ and (name N or name CA or name C or name O or name CB )) or resid 521 through 52 \ 5 or (resid 526 and (name N or name CA or name C or name O or name CB )) or resi \ d 527 through 528 or (resid 529 and (name N or name CA or name C or name O or na \ me CB )) or resid 530 through 582 or resid 600 through 623 or (resid 624 through \ 628 and (name N or name CA or name C or name O or name CB )) or resid 629 throu \ gh 631 or (resid 632 and (name N or name CA or name C or name O or name CB )) or \ resid 633 through 713 or (resid 714 through 716 and (name N or name CA or name \ C or name O or name CB )) or resid 717 through 719 or (resid 720 through 723 and \ (name N or name CA or name C or name O or name CB )) or resid 724 or (resid 725 \ through 727 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 28 through 733 or (resid 734 and (name N or name CA or name C or name O or name \ CB )) or resid 735 through 736 or (resid 737 through 741 and (name N or name CA \ or name C or name O or name CB )) or resid 742 or (resid 743 and (name N or name \ CA or name C or name O or name CB )) or resid 744 through 749 or (resid 750 thr \ ough 751 and (name N or name CA or name C or name O or name CB )) or resid 752 t \ hrough 782 or (resid 783 through 784 and (name N or name CA or name C or name O \ or name CB )) or resid 785 through 804 or (resid 805 through 810 and (name N or \ name CA or name C or name O or name CB )) or resid 811 through 836)) } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 2 through 215) } 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 group one per residue 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.220 Construct map_model_manager: 0.020 Extract box with map and model: 0.970 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 58.600 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5590 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 : 0.012 0.406 24854 Z= 0.764 Angle : 1.944 52.275 34211 Z= 1.241 Chirality : 0.104 1.561 4252 Planarity : 0.018 0.290 4418 Dihedral : 14.829 84.607 7872 Min Nonbonded Distance : 1.072 Molprobity Statistics. All-atom Clashscore : 54.88 Ramachandran Plot: Outliers : 1.01 % Allowed : 4.48 % Favored : 94.51 % Rotamer: Outliers : 10.98 % Allowed : 8.69 % Favored : 80.33 % Cbeta Deviations : 0.50 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3169 helix: 0.51 (0.14), residues: 1178 sheet: -0.26 (0.29), residues: 319 loop : -1.02 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 766 HIS 0.010 0.001 HIS A 101 PHE 0.036 0.002 PHE C 408 TYR 0.058 0.004 TYR C 472 ARG 0.018 0.001 ARG C 156 Details of bonding type rmsd link_NAG-ASN : bond 0.08542 ( 8) link_NAG-ASN : angle 9.52877 ( 24) link_BETA1-4 : bond 0.00042 ( 8) link_BETA1-4 : angle 0.03537 ( 24) hydrogen bonds : bond 0.23418 ( 1209) hydrogen bonds : angle 9.79281 ( 3483) SS BOND : bond 0.02009 ( 16) SS BOND : angle 19.33525 ( 32) covalent geometry : bond 0.01115 (24820) covalent geometry : angle 1.83668 (34131) Misc. bond : bond 0.33588 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 113 time to evaluate : 2.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.5454 (mm) REVERT: A 469 ASP cc_start: 0.9253 (OUTLIER) cc_final: 0.8976 (p0) REVERT: C 477 VAL cc_start: 0.6223 (OUTLIER) cc_final: 0.5565 (p) REVERT: C 695 VAL cc_start: 0.8169 (OUTLIER) cc_final: 0.7901 (p) REVERT: D 72 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7420 (t0) REVERT: D 152 MET cc_start: 0.8053 (mtp) cc_final: 0.6806 (mmm) REVERT: D 543 PHE cc_start: 0.6502 (OUTLIER) cc_final: 0.6280 (p90) REVERT: D 558 MET cc_start: 0.8425 (tpt) cc_final: 0.8097 (ttt) REVERT: D 794 CYS cc_start: 0.6619 (OUTLIER) cc_final: 0.6325 (p) outliers start: 206 outliers final: 49 residues processed: 304 average time/residue: 0.3389 time to fit residues: 162.7051 Evaluate side-chains 166 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 110 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 302 optimal weight: 2.9990 chunk 271 optimal weight: 7.9990 chunk 150 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 280 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 170 optimal weight: 30.0000 chunk 208 optimal weight: 6.9990 chunk 325 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 HIS A 146 HIS ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 GLN ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 ASN A 810 ASN ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN B 194 ASN B 350 ASN B 389 HIS B 503 ASN B 662 HIS B 675 GLN B 690 HIS ** B 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 HIS C 86 GLN ** C 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 GLN C 404 HIS C 451 GLN ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 717 GLN C 725 HIS D 55 HIS D 154 ASN D 306 HIS D 354 HIS D 691 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.030672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.022636 restraints weight = 461994.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.022750 restraints weight = 432324.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.022753 restraints weight = 385399.140| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 24854 Z= 0.237 Angle : 0.834 19.746 34211 Z= 0.432 Chirality : 0.049 0.760 4252 Planarity : 0.008 0.178 4418 Dihedral : 7.191 59.570 4104 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.88 % Favored : 95.83 % Rotamer: Outliers : 0.37 % Allowed : 3.73 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3169 helix: 0.39 (0.13), residues: 1308 sheet: -0.86 (0.24), residues: 390 loop : -1.11 (0.15), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 160 HIS 0.016 0.002 HIS D 55 PHE 0.033 0.003 PHE B 178 TYR 0.029 0.003 TYR D 333 ARG 0.008 0.001 ARG A 139 Details of bonding type rmsd link_NAG-ASN : bond 0.00443 ( 8) link_NAG-ASN : angle 5.87737 ( 24) link_BETA1-4 : bond 0.01600 ( 8) link_BETA1-4 : angle 1.79757 ( 24) hydrogen bonds : bond 0.06257 ( 1209) hydrogen bonds : angle 7.22720 ( 3483) SS BOND : bond 0.00699 ( 16) SS BOND : angle 1.86739 ( 32) covalent geometry : bond 0.00479 (24820) covalent geometry : angle 0.81700 (34131) Misc. bond : bond 0.00309 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9433 (tmm) cc_final: 0.8974 (tmm) REVERT: A 240 MET cc_start: 0.9120 (mmt) cc_final: 0.8214 (mmm) REVERT: A 298 MET cc_start: 0.8938 (mpp) cc_final: 0.8735 (mpp) REVERT: A 553 MET cc_start: 0.9007 (tpt) cc_final: 0.8658 (tpp) REVERT: A 700 MET cc_start: 0.9400 (mpp) cc_final: 0.9009 (mmm) REVERT: A 704 MET cc_start: 0.8846 (tmm) cc_final: 0.8566 (tmm) REVERT: B 552 MET cc_start: 0.9561 (mmm) cc_final: 0.9262 (mmm) REVERT: C 354 MET cc_start: 0.9078 (mmp) cc_final: 0.8498 (mmm) REVERT: C 394 MET cc_start: 0.8651 (tpp) cc_final: 0.8178 (tpt) REVERT: C 499 MET cc_start: 0.9166 (ttm) cc_final: 0.8687 (mtp) REVERT: D 152 MET cc_start: 0.8587 (mtp) cc_final: 0.8139 (mmm) REVERT: D 202 MET cc_start: 0.5116 (ppp) cc_final: 0.4723 (ppp) REVERT: D 555 MET cc_start: 0.8200 (tpt) cc_final: 0.7869 (tpt) REVERT: D 558 MET cc_start: 0.9421 (tpt) cc_final: 0.8730 (ttt) outliers start: 7 outliers final: 2 residues processed: 118 average time/residue: 0.3229 time to fit residues: 66.2043 Evaluate side-chains 113 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 148 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 177 optimal weight: 50.0000 chunk 168 optimal weight: 9.9990 chunk 32 optimal weight: 0.5980 chunk 308 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 280 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 195 optimal weight: 9.9990 overall best weight: 6.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN A 280 HIS A 311 ASN ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS B 146 GLN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 HIS C 707 HIS ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.029350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.021492 restraints weight = 470089.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.021469 restraints weight = 476688.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.021557 restraints weight = 398100.718| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 24854 Z= 0.245 Angle : 0.784 15.256 34211 Z= 0.404 Chirality : 0.046 0.599 4252 Planarity : 0.006 0.160 4418 Dihedral : 6.622 59.654 4104 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.40 % Favored : 94.38 % Rotamer: Outliers : 0.21 % Allowed : 3.68 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.14), residues: 3169 helix: 0.42 (0.13), residues: 1325 sheet: -1.04 (0.24), residues: 386 loop : -1.14 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 496 HIS 0.015 0.002 HIS D 55 PHE 0.025 0.002 PHE B 178 TYR 0.022 0.002 TYR A 679 ARG 0.019 0.001 ARG A 260 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 8) link_NAG-ASN : angle 4.26975 ( 24) link_BETA1-4 : bond 0.00361 ( 8) link_BETA1-4 : angle 1.63922 ( 24) hydrogen bonds : bond 0.05446 ( 1209) hydrogen bonds : angle 6.75225 ( 3483) SS BOND : bond 0.00427 ( 16) SS BOND : angle 1.83558 ( 32) covalent geometry : bond 0.00482 (24820) covalent geometry : angle 0.77353 (34131) Misc. bond : bond 0.00204 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9472 (tmm) cc_final: 0.8964 (tmm) REVERT: A 240 MET cc_start: 0.9384 (mmt) cc_final: 0.8247 (mmm) REVERT: A 354 MET cc_start: 0.9326 (mmm) cc_final: 0.8933 (mmm) REVERT: A 553 MET cc_start: 0.9078 (tpt) cc_final: 0.8841 (tpp) REVERT: B 776 MET cc_start: 0.9715 (mpp) cc_final: 0.9262 (pmm) REVERT: C 354 MET cc_start: 0.9253 (mmp) cc_final: 0.8897 (mmm) REVERT: C 394 MET cc_start: 0.8875 (tpp) cc_final: 0.8424 (tpt) REVERT: C 499 MET cc_start: 0.9100 (ttm) cc_final: 0.8421 (mtp) REVERT: C 760 MET cc_start: 0.9539 (ptp) cc_final: 0.9034 (ptp) REVERT: D 152 MET cc_start: 0.8701 (mtp) cc_final: 0.8270 (mmm) REVERT: D 558 MET cc_start: 0.9212 (tpt) cc_final: 0.8718 (ttt) outliers start: 4 outliers final: 1 residues processed: 114 average time/residue: 0.3169 time to fit residues: 62.7395 Evaluate side-chains 110 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 347 optimal weight: 20.0000 chunk 68 optimal weight: 0.7980 chunk 300 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 180 optimal weight: 9.9990 chunk 52 optimal weight: 30.0000 chunk 191 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 HIS A 196 GLN ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 ASN A 684 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 GLN ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 HIS ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.028837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 172)---------------| | r_work = 0.2862 r_free = 0.2862 target = 0.021012 restraints weight = 479797.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.021107 restraints weight = 397959.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.021129 restraints weight = 380851.876| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 24854 Z= 0.170 Angle : 0.654 13.999 34211 Z= 0.334 Chirality : 0.043 0.540 4252 Planarity : 0.005 0.153 4418 Dihedral : 6.300 59.007 4104 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.18 % Favored : 94.60 % Rotamer: Outliers : 0.11 % Allowed : 2.29 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3169 helix: 0.60 (0.14), residues: 1348 sheet: -0.98 (0.24), residues: 390 loop : -1.15 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 790 HIS 0.013 0.001 HIS D 55 PHE 0.023 0.002 PHE D 631 TYR 0.023 0.002 TYR B 157 ARG 0.007 0.001 ARG A 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 8) link_NAG-ASN : angle 3.69429 ( 24) link_BETA1-4 : bond 0.00543 ( 8) link_BETA1-4 : angle 1.76425 ( 24) hydrogen bonds : bond 0.04567 ( 1209) hydrogen bonds : angle 6.39932 ( 3483) SS BOND : bond 0.00319 ( 16) SS BOND : angle 1.71827 ( 32) covalent geometry : bond 0.00345 (24820) covalent geometry : angle 0.64315 (34131) Misc. bond : bond 0.00133 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9404 (tmm) cc_final: 0.9085 (tmm) REVERT: A 240 MET cc_start: 0.9412 (mmt) cc_final: 0.8339 (mmm) REVERT: A 354 MET cc_start: 0.9327 (mmm) cc_final: 0.8519 (mmm) REVERT: A 553 MET cc_start: 0.9083 (tpt) cc_final: 0.8850 (tpp) REVERT: A 704 MET cc_start: 0.8604 (tmm) cc_final: 0.8270 (tmm) REVERT: B 552 MET cc_start: 0.9521 (mmm) cc_final: 0.9251 (mtp) REVERT: B 689 MET cc_start: 0.9711 (ptp) cc_final: 0.9461 (tpt) REVERT: B 776 MET cc_start: 0.9609 (mpp) cc_final: 0.9395 (mpp) REVERT: C 394 MET cc_start: 0.8689 (tpp) cc_final: 0.8359 (tpt) REVERT: C 499 MET cc_start: 0.9237 (ttm) cc_final: 0.8499 (mtp) REVERT: C 500 MET cc_start: 0.9159 (ptt) cc_final: 0.8746 (ptt) REVERT: D 152 MET cc_start: 0.8680 (mtp) cc_final: 0.8435 (mmt) REVERT: D 558 MET cc_start: 0.9326 (tpt) cc_final: 0.8759 (ttt) outliers start: 2 outliers final: 1 residues processed: 111 average time/residue: 0.3080 time to fit residues: 59.8886 Evaluate side-chains 110 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 201 optimal weight: 6.9990 chunk 109 optimal weight: 30.0000 chunk 34 optimal weight: 0.3980 chunk 147 optimal weight: 0.8980 chunk 263 optimal weight: 10.0000 chunk 158 optimal weight: 50.0000 chunk 40 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 330 optimal weight: 50.0000 chunk 41 optimal weight: 9.9990 chunk 206 optimal weight: 3.9990 overall best weight: 4.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 GLN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 773 ASN D 55 HIS D 199 HIS D 214 GLN ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.028448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.2852 r_free = 0.2852 target = 0.020660 restraints weight = 483851.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.020898 restraints weight = 408572.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.021076 restraints weight = 350499.764| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 24854 Z= 0.167 Angle : 0.642 13.328 34211 Z= 0.327 Chirality : 0.043 0.469 4252 Planarity : 0.005 0.146 4418 Dihedral : 6.003 59.664 4104 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.90 % Favored : 93.91 % Rotamer: Outliers : 0.11 % Allowed : 3.09 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 3169 helix: 0.71 (0.14), residues: 1346 sheet: -1.03 (0.23), residues: 410 loop : -1.03 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 790 HIS 0.011 0.001 HIS D 55 PHE 0.022 0.002 PHE D 631 TYR 0.014 0.001 TYR B 490 ARG 0.010 0.001 ARG A 260 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 8) link_NAG-ASN : angle 3.38043 ( 24) link_BETA1-4 : bond 0.00407 ( 8) link_BETA1-4 : angle 1.65313 ( 24) hydrogen bonds : bond 0.04248 ( 1209) hydrogen bonds : angle 6.16657 ( 3483) SS BOND : bond 0.00314 ( 16) SS BOND : angle 1.60620 ( 32) covalent geometry : bond 0.00333 (24820) covalent geometry : angle 0.63281 (34131) Misc. bond : bond 0.00109 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9372 (tmm) cc_final: 0.8932 (tmm) REVERT: A 240 MET cc_start: 0.9460 (mmt) cc_final: 0.8833 (mmt) REVERT: A 298 MET cc_start: 0.9280 (mpp) cc_final: 0.9065 (mpp) REVERT: A 354 MET cc_start: 0.9299 (mmm) cc_final: 0.8485 (mmm) REVERT: A 553 MET cc_start: 0.9090 (tpt) cc_final: 0.8835 (tpp) REVERT: A 704 MET cc_start: 0.8910 (tmm) cc_final: 0.8588 (tmm) REVERT: B 495 MET cc_start: 0.9168 (mmp) cc_final: 0.8841 (mmp) REVERT: B 689 MET cc_start: 0.9663 (ptp) cc_final: 0.9411 (ptp) REVERT: C 499 MET cc_start: 0.9236 (ttm) cc_final: 0.8360 (mtp) REVERT: C 500 MET cc_start: 0.9261 (ptt) cc_final: 0.8717 (ptt) REVERT: C 510 MET cc_start: 0.9562 (tpt) cc_final: 0.9144 (tpp) REVERT: C 760 MET cc_start: 0.9505 (ptp) cc_final: 0.9298 (ptp) REVERT: D 152 MET cc_start: 0.8827 (mtp) cc_final: 0.8590 (mmm) outliers start: 2 outliers final: 1 residues processed: 111 average time/residue: 0.3260 time to fit residues: 63.7550 Evaluate side-chains 110 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 92 optimal weight: 0.9990 chunk 311 optimal weight: 9.9990 chunk 224 optimal weight: 7.9990 chunk 236 optimal weight: 30.0000 chunk 7 optimal weight: 9.9990 chunk 336 optimal weight: 50.0000 chunk 6 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 301 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN B 681 ASN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 HIS ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 760 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.028102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.020466 restraints weight = 484895.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.020553 restraints weight = 443733.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.020565 restraints weight = 404091.457| |-----------------------------------------------------------------------------| r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.6043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 24854 Z= 0.187 Angle : 0.652 13.115 34211 Z= 0.333 Chirality : 0.044 0.747 4252 Planarity : 0.005 0.140 4418 Dihedral : 6.034 59.892 4104 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.90 % Favored : 93.88 % Rotamer: Outliers : 0.05 % Allowed : 1.81 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 3169 helix: 0.67 (0.14), residues: 1357 sheet: -1.07 (0.24), residues: 401 loop : -1.04 (0.17), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 634 HIS 0.006 0.001 HIS B 160 PHE 0.023 0.002 PHE C 637 TYR 0.029 0.002 TYR A 679 ARG 0.014 0.001 ARG A 260 Details of bonding type rmsd link_NAG-ASN : bond 0.00766 ( 8) link_NAG-ASN : angle 3.78586 ( 24) link_BETA1-4 : bond 0.00327 ( 8) link_BETA1-4 : angle 1.84921 ( 24) hydrogen bonds : bond 0.04292 ( 1209) hydrogen bonds : angle 6.18909 ( 3483) SS BOND : bond 0.00580 ( 16) SS BOND : angle 1.61467 ( 32) covalent geometry : bond 0.00368 (24820) covalent geometry : angle 0.64170 (34131) Misc. bond : bond 0.00113 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.9559 (mmt) cc_final: 0.9086 (mmt) REVERT: A 298 MET cc_start: 0.8935 (mpp) cc_final: 0.8712 (mpp) REVERT: A 354 MET cc_start: 0.9159 (mmm) cc_final: 0.8547 (mmm) REVERT: B 495 MET cc_start: 0.9496 (mmp) cc_final: 0.9283 (mmp) REVERT: B 689 MET cc_start: 0.9792 (ptp) cc_final: 0.9584 (tpt) REVERT: B 816 MET cc_start: 0.9024 (ptp) cc_final: 0.8729 (ptp) REVERT: C 499 MET cc_start: 0.9488 (ttm) cc_final: 0.8691 (mtp) REVERT: C 510 MET cc_start: 0.9744 (tpt) cc_final: 0.9533 (tpp) REVERT: D 152 MET cc_start: 0.8975 (mtp) cc_final: 0.8652 (mmm) REVERT: D 817 MET cc_start: 0.3998 (pmm) cc_final: 0.3777 (pmm) outliers start: 1 outliers final: 1 residues processed: 110 average time/residue: 0.2902 time to fit residues: 55.6722 Evaluate side-chains 110 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 346 optimal weight: 50.0000 chunk 64 optimal weight: 7.9990 chunk 322 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 chunk 332 optimal weight: 50.0000 chunk 321 optimal weight: 10.0000 chunk 268 optimal weight: 50.0000 chunk 303 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 chunk 280 optimal weight: 5.9990 chunk 295 optimal weight: 10.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 HIS A 196 GLN ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 ASN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 717 GLN D 122 HIS ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 775 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.027962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.020230 restraints weight = 489950.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.020473 restraints weight = 416216.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.020689 restraints weight = 352431.550| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.6485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 24854 Z= 0.200 Angle : 0.670 13.112 34211 Z= 0.343 Chirality : 0.043 0.664 4252 Planarity : 0.005 0.144 4418 Dihedral : 5.992 59.848 4104 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.72 % Favored : 93.06 % Rotamer: Outliers : 0.05 % Allowed : 1.17 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 3169 helix: 0.71 (0.14), residues: 1351 sheet: -1.14 (0.25), residues: 399 loop : -1.06 (0.17), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 790 HIS 0.007 0.001 HIS B 690 PHE 0.019 0.002 PHE D 631 TYR 0.024 0.002 TYR A 679 ARG 0.009 0.001 ARG A 260 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 8) link_NAG-ASN : angle 3.76764 ( 24) link_BETA1-4 : bond 0.00354 ( 8) link_BETA1-4 : angle 1.57386 ( 24) hydrogen bonds : bond 0.04317 ( 1209) hydrogen bonds : angle 6.23331 ( 3483) SS BOND : bond 0.00407 ( 16) SS BOND : angle 2.38385 ( 32) covalent geometry : bond 0.00390 (24820) covalent geometry : angle 0.65786 (34131) Misc. bond : bond 0.00184 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.9480 (mmt) cc_final: 0.8911 (mmt) REVERT: A 298 MET cc_start: 0.9371 (mpp) cc_final: 0.9141 (mpp) REVERT: A 354 MET cc_start: 0.9244 (mmm) cc_final: 0.8520 (mmm) REVERT: A 553 MET cc_start: 0.8856 (tpp) cc_final: 0.8567 (tpp) REVERT: B 495 MET cc_start: 0.9177 (mmp) cc_final: 0.8875 (mmp) REVERT: B 689 MET cc_start: 0.9650 (ptp) cc_final: 0.9398 (tpt) REVERT: B 816 MET cc_start: 0.9614 (ptp) cc_final: 0.9346 (ptp) REVERT: C 125 MET cc_start: 0.8868 (mpp) cc_final: 0.8557 (mpp) REVERT: C 499 MET cc_start: 0.9397 (ttm) cc_final: 0.8761 (mtp) REVERT: C 510 MET cc_start: 0.9621 (tpt) cc_final: 0.9376 (tpp) REVERT: C 760 MET cc_start: 0.8015 (ptt) cc_final: 0.7624 (pmm) REVERT: D 152 MET cc_start: 0.8891 (mtp) cc_final: 0.8666 (mmm) REVERT: D 558 MET cc_start: 0.9382 (tpt) cc_final: 0.8449 (ttt) REVERT: D 817 MET cc_start: 0.4267 (pmm) cc_final: 0.3970 (pmm) outliers start: 1 outliers final: 1 residues processed: 109 average time/residue: 0.2998 time to fit residues: 57.6198 Evaluate side-chains 109 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 212 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 201 optimal weight: 6.9990 chunk 329 optimal weight: 90.0000 chunk 43 optimal weight: 2.9990 chunk 325 optimal weight: 30.0000 chunk 337 optimal weight: 40.0000 chunk 283 optimal weight: 8.9990 chunk 321 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 244 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 GLN ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 GLN ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.027521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.020147 restraints weight = 498034.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.020147 restraints weight = 444623.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.020147 restraints weight = 442994.339| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.7180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 24854 Z= 0.199 Angle : 0.667 11.904 34211 Z= 0.344 Chirality : 0.044 0.633 4252 Planarity : 0.005 0.136 4418 Dihedral : 6.055 59.607 4104 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.25 % Favored : 93.53 % Rotamer: Outliers : 0.05 % Allowed : 1.07 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 3169 helix: 0.73 (0.14), residues: 1369 sheet: -1.32 (0.25), residues: 397 loop : -1.18 (0.17), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 335 HIS 0.006 0.001 HIS A 146 PHE 0.045 0.002 PHE D 630 TYR 0.049 0.002 TYR B 686 ARG 0.013 0.001 ARG A 260 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 8) link_NAG-ASN : angle 3.41428 ( 24) link_BETA1-4 : bond 0.00225 ( 8) link_BETA1-4 : angle 1.61939 ( 24) hydrogen bonds : bond 0.04256 ( 1209) hydrogen bonds : angle 6.22604 ( 3483) SS BOND : bond 0.00508 ( 16) SS BOND : angle 1.82677 ( 32) covalent geometry : bond 0.00388 (24820) covalent geometry : angle 0.65811 (34131) Misc. bond : bond 0.00161 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.9441 (mmt) cc_final: 0.8988 (mmt) REVERT: A 298 MET cc_start: 0.9577 (mpp) cc_final: 0.9341 (mpp) REVERT: A 354 MET cc_start: 0.9224 (mmm) cc_final: 0.8234 (mmm) REVERT: A 553 MET cc_start: 0.8898 (tpp) cc_final: 0.8648 (tpp) REVERT: A 605 MET cc_start: 0.8985 (ptp) cc_final: 0.8709 (ppp) REVERT: B 495 MET cc_start: 0.9294 (mmp) cc_final: 0.9043 (mmp) REVERT: B 689 MET cc_start: 0.9652 (ptp) cc_final: 0.9343 (mpp) REVERT: B 693 MET cc_start: 0.8549 (tpt) cc_final: 0.8204 (tpt) REVERT: C 125 MET cc_start: 0.8765 (mpp) cc_final: 0.8491 (mpp) REVERT: C 298 MET cc_start: 0.9080 (mpp) cc_final: 0.8865 (mpp) REVERT: C 499 MET cc_start: 0.9420 (ttm) cc_final: 0.8728 (mtp) REVERT: C 574 MET cc_start: 0.9599 (tmm) cc_final: 0.9294 (ptp) REVERT: C 760 MET cc_start: 0.7738 (ptt) cc_final: 0.7296 (pmm) REVERT: D 152 MET cc_start: 0.9022 (mtp) cc_final: 0.8597 (mmm) REVERT: D 558 MET cc_start: 0.9630 (tpt) cc_final: 0.8747 (ttt) REVERT: D 817 MET cc_start: 0.3199 (pmm) cc_final: 0.2959 (pmm) outliers start: 1 outliers final: 1 residues processed: 109 average time/residue: 0.3004 time to fit residues: 58.2487 Evaluate side-chains 109 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 313 optimal weight: 20.0000 chunk 208 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 316 optimal weight: 50.0000 chunk 2 optimal weight: 7.9990 chunk 179 optimal weight: 0.0070 chunk 131 optimal weight: 7.9990 chunk 204 optimal weight: 30.0000 chunk 49 optimal weight: 20.0000 chunk 235 optimal weight: 20.0000 overall best weight: 6.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 HIS ** D 642 ASN ** 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 = 0.3219 r_free = 0.3219 target = 0.027390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.020027 restraints weight = 500329.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.020027 restraints weight = 456355.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.020027 restraints weight = 454181.578| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.7486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 24854 Z= 0.203 Angle : 0.676 12.148 34211 Z= 0.347 Chirality : 0.043 0.606 4252 Planarity : 0.005 0.133 4418 Dihedral : 6.035 59.978 4104 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.94 % Favored : 92.84 % Rotamer: Outliers : 0.05 % Allowed : 0.59 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.15), residues: 3169 helix: 0.73 (0.14), residues: 1372 sheet: -1.38 (0.25), residues: 390 loop : -1.24 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 603 HIS 0.006 0.001 HIS A 146 PHE 0.033 0.002 PHE A 691 TYR 0.025 0.002 TYR B 157 ARG 0.016 0.001 ARG A 260 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 8) link_NAG-ASN : angle 3.47883 ( 24) link_BETA1-4 : bond 0.00299 ( 8) link_BETA1-4 : angle 1.51862 ( 24) hydrogen bonds : bond 0.04327 ( 1209) hydrogen bonds : angle 6.27322 ( 3483) SS BOND : bond 0.00490 ( 16) SS BOND : angle 1.77302 ( 32) covalent geometry : bond 0.00396 (24820) covalent geometry : angle 0.66681 (34131) Misc. bond : bond 0.00137 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.9429 (mmt) cc_final: 0.8977 (mmt) REVERT: A 298 MET cc_start: 0.9590 (mpp) cc_final: 0.9350 (mpp) REVERT: A 354 MET cc_start: 0.9270 (mmm) cc_final: 0.8317 (mmm) REVERT: A 605 MET cc_start: 0.8878 (ptp) cc_final: 0.8506 (ppp) REVERT: B 549 MET cc_start: 0.9756 (tmm) cc_final: 0.9532 (mtp) REVERT: B 689 MET cc_start: 0.9593 (ptp) cc_final: 0.9201 (mpp) REVERT: C 125 MET cc_start: 0.8916 (mpp) cc_final: 0.8578 (mpp) REVERT: C 298 MET cc_start: 0.9068 (mpp) cc_final: 0.8800 (mpp) REVERT: C 499 MET cc_start: 0.9452 (ttm) cc_final: 0.8668 (mtp) REVERT: C 574 MET cc_start: 0.9607 (tmm) cc_final: 0.9279 (ptp) REVERT: C 760 MET cc_start: 0.7874 (ptt) cc_final: 0.6853 (pmm) REVERT: D 152 MET cc_start: 0.8922 (mtp) cc_final: 0.8471 (mmt) REVERT: D 558 MET cc_start: 0.9552 (tpt) cc_final: 0.8744 (ttt) outliers start: 1 outliers final: 1 residues processed: 109 average time/residue: 0.2969 time to fit residues: 57.1638 Evaluate side-chains 109 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 185 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 314 optimal weight: 10.0000 chunk 341 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 239 optimal weight: 9.9990 chunk 279 optimal weight: 30.0000 chunk 214 optimal weight: 30.0000 chunk 170 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 GLN D 105 GLN ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 833 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.027299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.019903 restraints weight = 502871.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.019912 restraints weight = 465405.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.019915 restraints weight = 456176.514| |-----------------------------------------------------------------------------| r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.8134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 24854 Z= 0.262 Angle : 0.759 13.756 34211 Z= 0.395 Chirality : 0.045 0.624 4252 Planarity : 0.006 0.132 4418 Dihedral : 6.419 59.687 4104 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.73 % Favored : 92.05 % Rotamer: Outliers : 0.05 % Allowed : 0.53 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.15), residues: 3169 helix: 0.42 (0.14), residues: 1361 sheet: -1.59 (0.24), residues: 408 loop : -1.44 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 335 HIS 0.009 0.002 HIS A 162 PHE 0.029 0.002 PHE B 57 TYR 0.034 0.003 TYR B 686 ARG 0.013 0.001 ARG A 260 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 8) link_NAG-ASN : angle 3.54479 ( 24) link_BETA1-4 : bond 0.00347 ( 8) link_BETA1-4 : angle 1.60544 ( 24) hydrogen bonds : bond 0.04770 ( 1209) hydrogen bonds : angle 6.67775 ( 3483) SS BOND : bond 0.00418 ( 16) SS BOND : angle 1.87393 ( 32) covalent geometry : bond 0.00502 (24820) covalent geometry : angle 0.75079 (34131) Misc. bond : bond 0.00125 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.9481 (mmt) cc_final: 0.8926 (mmt) REVERT: A 354 MET cc_start: 0.9253 (mmm) cc_final: 0.8180 (mmm) REVERT: A 605 MET cc_start: 0.8948 (ptp) cc_final: 0.8579 (ppp) REVERT: A 704 MET cc_start: 0.9820 (ptp) cc_final: 0.9584 (ppp) REVERT: B 495 MET cc_start: 0.9270 (mmp) cc_final: 0.9030 (tpp) REVERT: B 689 MET cc_start: 0.9694 (ptp) cc_final: 0.9477 (mpp) REVERT: B 816 MET cc_start: 0.9546 (ptp) cc_final: 0.9339 (ptp) REVERT: C 125 MET cc_start: 0.9044 (mpp) cc_final: 0.8753 (mpp) REVERT: C 298 MET cc_start: 0.9188 (mpp) cc_final: 0.8944 (mpp) REVERT: C 499 MET cc_start: 0.9390 (ttm) cc_final: 0.8698 (mtp) REVERT: C 510 MET cc_start: 0.9578 (tpt) cc_final: 0.9356 (tpp) REVERT: C 574 MET cc_start: 0.9615 (tmm) cc_final: 0.9329 (ptp) REVERT: C 760 MET cc_start: 0.7888 (ptt) cc_final: 0.7304 (pmm) REVERT: D 152 MET cc_start: 0.9009 (mtp) cc_final: 0.8582 (mmt) REVERT: D 817 MET cc_start: 0.4126 (pmm) cc_final: 0.3868 (pmm) outliers start: 1 outliers final: 1 residues processed: 109 average time/residue: 0.2923 time to fit residues: 56.5405 Evaluate side-chains 109 residues out of total 2773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.6616 > 50: distance: 14 - 89: 16.524 distance: 17 - 98: 13.868 distance: 24 - 101: 20.391 distance: 27 - 110: 32.559 distance: 54 - 59: 22.807 distance: 59 - 60: 6.078 distance: 60 - 61: 10.679 distance: 60 - 63: 31.814 distance: 61 - 62: 5.054 distance: 61 - 69: 23.846 distance: 63 - 64: 13.279 distance: 64 - 65: 31.184 distance: 64 - 66: 14.848 distance: 65 - 67: 5.464 distance: 66 - 68: 10.374 distance: 67 - 68: 11.106 distance: 69 - 70: 10.473 distance: 70 - 71: 18.922 distance: 70 - 73: 29.092 distance: 71 - 72: 19.451 distance: 71 - 74: 27.987 distance: 74 - 75: 28.418 distance: 74 - 80: 5.264 distance: 75 - 76: 21.884 distance: 75 - 78: 18.412 distance: 76 - 77: 36.722 distance: 76 - 81: 34.827 distance: 78 - 79: 24.492 distance: 79 - 80: 24.933 distance: 81 - 82: 24.711 distance: 82 - 83: 38.897 distance: 82 - 85: 46.944 distance: 83 - 84: 20.226 distance: 83 - 86: 17.240 distance: 86 - 87: 26.520 distance: 87 - 88: 18.699 distance: 87 - 90: 32.119 distance: 88 - 89: 38.148 distance: 88 - 91: 28.266 distance: 91 - 92: 24.949 distance: 91 - 97: 10.895 distance: 92 - 93: 23.018 distance: 92 - 95: 25.611 distance: 93 - 94: 23.377 distance: 93 - 98: 10.754 distance: 95 - 96: 10.446 distance: 96 - 97: 25.623 distance: 98 - 99: 7.951 distance: 99 - 100: 16.457 distance: 99 - 102: 20.760 distance: 100 - 101: 14.797 distance: 100 - 103: 15.842 distance: 103 - 104: 9.169 distance: 104 - 105: 13.051 distance: 104 - 107: 12.153 distance: 105 - 106: 35.666 distance: 105 - 110: 28.111 distance: 107 - 108: 14.791 distance: 107 - 109: 17.271 distance: 110 - 111: 25.590 distance: 111 - 112: 28.412 distance: 111 - 114: 17.326 distance: 112 - 113: 23.000 distance: 112 - 115: 9.757 distance: 115 - 116: 16.789 distance: 116 - 117: 23.524 distance: 116 - 119: 21.136 distance: 117 - 118: 14.277 distance: 117 - 123: 13.781 distance: 119 - 120: 7.918 distance: 120 - 121: 28.934 distance: 120 - 122: 14.610