Starting phenix.real_space_refine on Tue Jun 17 23:37:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rlb_4918/06_2025/6rlb_4918.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rlb_4918/06_2025/6rlb_4918.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/6rlb_4918/06_2025/6rlb_4918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rlb_4918/06_2025/6rlb_4918.map" model { file = "/net/cci-nas-00/data/ceres_data/6rlb_4918/06_2025/6rlb_4918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rlb_4918/06_2025/6rlb_4918.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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 12163 2.51 5 N 4122 2.21 5 O 4122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20407 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 969, 4805 Classifications: {'peptide': 969} Incomplete info: {'truncation_to_alanine': 877} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 937} Chain breaks: 2 Unresolved chain link angles: 31 Unresolved non-hydrogen bonds: 3285 Unresolved non-hydrogen angles: 4191 Unresolved non-hydrogen dihedrals: 2747 Unresolved non-hydrogen chiralities: 283 Planarities with less than four sites: {'GLN:plan1': 65, 'HIS:plan': 22, 'TYR:plan': 25, 'ASN:plan1': 41, 'TRP:plan': 18, 'ASP:plan': 55, 'PHE:plan': 46, 'GLU:plan': 82, 'ARG:plan': 48} Unresolved non-hydrogen planarities: 1839 Chain: "B" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 889, 4405 Classifications: {'peptide': 889} Incomplete info: {'truncation_to_alanine': 802} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 858} Chain breaks: 1 Unresolved chain link angles: 30 Unresolved non-hydrogen bonds: 3005 Unresolved non-hydrogen angles: 3836 Unresolved non-hydrogen dihedrals: 2519 Unresolved non-hydrogen chiralities: 257 Planarities with less than four sites: {'GLN:plan1': 58, 'HIS:plan': 19, 'TYR:plan': 24, 'ASN:plan1': 39, 'TRP:plan': 17, 'ASP:plan': 51, 'PHE:plan': 43, 'GLU:plan': 69, 'ARG:plan': 46} Unresolved non-hydrogen planarities: 1682 Chain: "C" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 2443 Classifications: {'peptide': 494} Incomplete info: {'truncation_to_alanine': 437} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 465} Chain breaks: 5 Unresolved chain link angles: 28 Unresolved non-hydrogen bonds: 1483 Unresolved non-hydrogen angles: 1919 Unresolved non-hydrogen dihedrals: 1234 Unresolved non-hydrogen chiralities: 155 Planarities with less than four sites: {'GLN:plan1': 29, 'HIS:plan': 15, 'TYR:plan': 4, 'ASN:plan1': 13, 'TRP:plan': 11, 'ASP:plan': 28, 'PHE:plan': 20, 'GLU:plan': 22, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 769 Chain: "D" Number of atoms: 2200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 2200 Classifications: {'peptide': 446} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 377} Link IDs: {'PTRANS': 30, 'TRANS': 415} Chain breaks: 2 Unresolved chain link angles: 30 Unresolved non-hydrogen bonds: 1353 Unresolved non-hydrogen angles: 1765 Unresolved non-hydrogen dihedrals: 1148 Unresolved non-hydrogen chiralities: 127 Planarities with less than four sites: {'GLN:plan1': 34, 'ASP:plan': 21, 'TYR:plan': 9, 'ASN:plan1': 8, 'TRP:plan': 12, 'HIS:plan': 14, 'PHE:plan': 19, 'GLU:plan': 20, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 754 Chain: "E" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 1542 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 18, 'TRANS': 293} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1010 Unresolved non-hydrogen angles: 1280 Unresolved non-hydrogen dihedrals: 857 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 6, 'TYR:plan': 8, 'ASN:plan1': 11, 'TRP:plan': 5, 'ASP:plan': 20, 'PHE:plan': 14, 'GLU:plan': 22, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 497 Chain: "F" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 1532 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 275} Link IDs: {'PTRANS': 18, 'TRANS': 291} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1003 Unresolved non-hydrogen angles: 1272 Unresolved non-hydrogen dihedrals: 851 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 6, 'TYR:plan': 8, 'ASN:plan1': 11, 'TRP:plan': 5, 'ASP:plan': 20, 'PHE:plan': 14, 'GLU:plan': 22, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 497 Chain: "G" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 462 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 5, 'TRANS': 87} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 139 Chain: "H" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 462 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 5, 'TRANS': 87} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 139 Chain: "I" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 426 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 83} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 172 Chain: "J" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 426 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 83} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 172 Chain: "K" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 426 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 83} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 172 Chain: "L" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 426 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 83} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 172 Chain: "M" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 426 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 83} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 172 Chain: "N" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 426 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 83} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 172 Time building chain proxies: 13.97, per 1000 atoms: 0.68 Number of scatterers: 20407 At special positions: 0 Unit cell: (195.99, 122.32, 221.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 4122 8.00 N 4122 7.00 C 12163 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.29 Conformation dependent library (CDL) restraints added in 4.0 seconds 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7838 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 28 sheets defined 51.6% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 Processing helix chain 'A' and resid 35 through 45 Processing helix chain 'A' and resid 105 through 123 removed outlier: 3.862A pdb=" N ALA A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) Proline residue: A 118 - end of helix Processing helix chain 'A' and resid 130 through 150 Processing helix chain 'A' and resid 192 through 210 removed outlier: 4.011A pdb=" N ILE A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N GLU A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'A' and resid 216 through 235 removed outlier: 3.593A pdb=" N VAL A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP A 235 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 269 removed outlier: 3.654A pdb=" N THR A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 309 removed outlier: 4.478A pdb=" N GLN A 307 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 347 removed outlier: 3.605A pdb=" N LYS A 326 " --> pdb=" O GLU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 351 through 367 removed outlier: 3.504A pdb=" N CYS A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) Proline residue: A 364 - end of helix Processing helix chain 'A' and resid 378 through 409 removed outlier: 3.689A pdb=" N ALA A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 430 through 437 Processing helix chain 'A' and resid 437 through 461 Processing helix chain 'A' and resid 481 through 507 removed outlier: 3.503A pdb=" N ALA A 505 " --> pdb=" O LYS A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 550 removed outlier: 3.519A pdb=" N CYS A 515 " --> pdb=" O PRO A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 592 removed outlier: 3.501A pdb=" N LEU A 579 " --> pdb=" O TYR A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 632 Processing helix chain 'A' and resid 636 through 656 Processing helix chain 'A' and resid 656 through 661 Processing helix chain 'A' and resid 662 through 667 Processing helix chain 'A' and resid 668 through 707 Processing helix chain 'A' and resid 714 through 734 removed outlier: 3.823A pdb=" N TRP A 718 " --> pdb=" O GLN A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 768 removed outlier: 3.672A pdb=" N MET A 742 " --> pdb=" O GLN A 738 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 808 Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 827 through 832 Processing helix chain 'A' and resid 834 through 861 removed outlier: 4.307A pdb=" N THR A 838 " --> pdb=" O SER A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 876 removed outlier: 4.569A pdb=" N LEU A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS A 875 " --> pdb=" O LEU A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 897 removed outlier: 3.555A pdb=" N PHE A 886 " --> pdb=" O TRP A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 957 Processing helix chain 'A' and resid 963 through 967 removed outlier: 3.685A pdb=" N GLY A 967 " --> pdb=" O GLU A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 984 Proline residue: A 981 - end of helix Processing helix chain 'A' and resid 985 through 1001 removed outlier: 4.586A pdb=" N LEU A 996 " --> pdb=" O ASP A 992 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1033 removed outlier: 4.613A pdb=" N ASP A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 22 Processing helix chain 'B' and resid 35 through 45 Processing helix chain 'B' and resid 105 through 115 Processing helix chain 'B' and resid 115 through 123 Processing helix chain 'B' and resid 130 through 150 Processing helix chain 'B' and resid 192 through 211 removed outlier: 3.795A pdb=" N ASN B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 235 removed outlier: 5.105A pdb=" N ASP B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLU B 225 " --> pdb=" O VAL B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 269 removed outlier: 3.545A pdb=" N MET B 248 " --> pdb=" O PRO B 244 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 309 removed outlier: 3.538A pdb=" N VAL B 280 " --> pdb=" O PRO B 276 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 295 " --> pdb=" O CYS B 291 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY B 303 " --> pdb=" O ASN B 299 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN B 304 " --> pdb=" O HIS B 300 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN B 307 " --> pdb=" O GLY B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 347 removed outlier: 4.050A pdb=" N LYS B 326 " --> pdb=" O GLU B 322 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 367 removed outlier: 3.939A pdb=" N ARG B 360 " --> pdb=" O ILE B 356 " (cutoff:3.500A) Proline residue: B 364 - end of helix Processing helix chain 'B' and resid 374 through 376 No H-bonds generated for 'chain 'B' and resid 374 through 376' Processing helix chain 'B' and resid 377 through 409 removed outlier: 4.153A pdb=" N TRP B 381 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 413 through 424 Processing helix chain 'B' and resid 424 through 429 Processing helix chain 'B' and resid 430 through 437 Processing helix chain 'B' and resid 437 through 461 Processing helix chain 'B' and resid 467 through 472 Processing helix chain 'B' and resid 474 through 479 removed outlier: 4.309A pdb=" N ASN B 478 " --> pdb=" O SER B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 508 removed outlier: 3.717A pdb=" N SER B 508 " --> pdb=" O GLU B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 550 Processing helix chain 'B' and resid 574 through 592 removed outlier: 3.949A pdb=" N ARG B 578 " --> pdb=" O HIS B 574 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 631 removed outlier: 3.564A pdb=" N LYS B 609 " --> pdb=" O ASN B 605 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN B 613 " --> pdb=" O LYS B 609 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ILE B 616 " --> pdb=" O LYS B 612 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN B 619 " --> pdb=" O ILE B 615 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN B 629 " --> pdb=" O ASN B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 636 through 655 removed outlier: 4.033A pdb=" N SER B 642 " --> pdb=" O MET B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'B' and resid 662 through 667 removed outlier: 3.892A pdb=" N ASP B 666 " --> pdb=" O GLN B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 707 Processing helix chain 'B' and resid 710 through 734 removed outlier: 3.763A pdb=" N GLN B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N GLN B 716 " --> pdb=" O LEU B 712 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ARG B 717 " --> pdb=" O ARG B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 768 Processing helix chain 'B' and resid 769 through 772 removed outlier: 3.845A pdb=" N LEU B 772 " --> pdb=" O ASN B 769 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 769 through 772' Processing helix chain 'B' and resid 791 through 808 Processing helix chain 'B' and resid 822 through 832 removed outlier: 5.837A pdb=" N MET B 828 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE B 829 " --> pdb=" O PHE B 825 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASP B 830 " --> pdb=" O SER B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 861 removed outlier: 4.370A pdb=" N THR B 838 " --> pdb=" O SER B 834 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE B 861 " --> pdb=" O HIS B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 876 Processing helix chain 'B' and resid 878 through 897 Processing helix chain 'B' and resid 912 through 936 removed outlier: 4.100A pdb=" N LYS B 936 " --> pdb=" O LEU B 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 584 Processing helix chain 'C' and resid 585 through 607 removed outlier: 5.214A pdb=" N PHE C 591 " --> pdb=" O ARG C 587 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 787 Processing helix chain 'C' and resid 789 through 793 Processing helix chain 'C' and resid 1035 through 1039 Processing helix chain 'C' and resid 1042 through 1055 Processing helix chain 'D' and resid 104 through 128 removed outlier: 3.918A pdb=" N ARG D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN D 124 " --> pdb=" O ILE D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 161 Processing helix chain 'D' and resid 248 through 250 No H-bonds generated for 'chain 'D' and resid 248 through 250' Processing helix chain 'D' and resid 300 through 304 removed outlier: 3.606A pdb=" N GLY D 304 " --> pdb=" O ILE D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 534 removed outlier: 3.600A pdb=" N ASP D 526 " --> pdb=" O ARG D 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 17 Processing helix chain 'E' and resid 43 through 52 Processing helix chain 'E' and resid 92 through 98 Processing helix chain 'E' and resid 102 through 106 Processing helix chain 'E' and resid 119 through 145 Proline residue: E 125 - end of helix removed outlier: 3.848A pdb=" N ILE E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N MET E 143 " --> pdb=" O ASP E 139 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU E 145 " --> pdb=" O VAL E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 161 Processing helix chain 'E' and resid 187 through 194 removed outlier: 4.235A pdb=" N GLN E 192 " --> pdb=" O ASP E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 214 Processing helix chain 'E' and resid 225 through 235 Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 286 through 297 Processing helix chain 'E' and resid 319 through 339 Processing helix chain 'F' and resid 5 through 17 Processing helix chain 'F' and resid 43 through 52 Processing helix chain 'F' and resid 92 through 98 Processing helix chain 'F' and resid 102 through 107 removed outlier: 5.237A pdb=" N ARG F 107 " --> pdb=" O ASP F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 145 Proline residue: F 125 - end of helix removed outlier: 3.928A pdb=" N ILE F 142 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N MET F 143 " --> pdb=" O ASP F 139 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU F 145 " --> pdb=" O VAL F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 161 Processing helix chain 'F' and resid 187 through 194 removed outlier: 4.373A pdb=" N GLN F 192 " --> pdb=" O ASP F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 214 Processing helix chain 'F' and resid 225 through 235 Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 286 through 297 Processing helix chain 'F' and resid 319 through 339 Processing helix chain 'G' and resid 605 through 614 Processing helix chain 'G' and resid 636 through 662 Processing helix chain 'H' and resid 512 through 521 Processing helix chain 'H' and resid 543 through 569 Processing helix chain 'I' and resid 14 through 32 Processing helix chain 'I' and resid 34 through 51 Processing helix chain 'J' and resid 14 through 32 Processing helix chain 'J' and resid 34 through 51 Processing helix chain 'K' and resid 14 through 32 Processing helix chain 'K' and resid 34 through 51 Processing helix chain 'L' and resid 14 through 32 Processing helix chain 'L' and resid 34 through 51 Processing helix chain 'M' and resid 14 through 32 Processing helix chain 'M' and resid 34 through 51 Processing helix chain 'N' and resid 14 through 32 Processing helix chain 'N' and resid 34 through 51 Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 63 removed outlier: 5.199A pdb=" N ARG A 55 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LYS A 74 " --> pdb=" O ARG A 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 558 through 560 removed outlier: 3.571A pdb=" N SER A 558 " --> pdb=" O LYS A 572 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 785 through 789 removed outlier: 6.532A pdb=" N ILE A 775 " --> pdb=" O ASN A 909 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ASN A 911 " --> pdb=" O ILE A 775 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE A 777 " --> pdb=" O ASN A 911 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 59 through 63 removed outlier: 5.196A pdb=" N ARG B 55 " --> pdb=" O LYS B 74 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LYS B 74 " --> pdb=" O ARG B 55 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 785 through 789 removed outlier: 6.232A pdb=" N ILE B 775 " --> pdb=" O ASN B 909 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ASN B 911 " --> pdb=" O ILE B 775 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE B 777 " --> pdb=" O ASN B 911 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 528 through 534 removed outlier: 7.612A pdb=" N HIS N 55 " --> pdb=" O THR M 67 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR M 67 " --> pdb=" O HIS N 55 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE N 57 " --> pdb=" O TYR M 65 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N TYR M 65 " --> pdb=" O ILE N 57 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLY N 59 " --> pdb=" O GLY M 63 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLY M 63 " --> pdb=" O GLY N 59 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY N 63 " --> pdb=" O GLY M 59 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLY M 59 " --> pdb=" O GLY N 63 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N TYR N 65 " --> pdb=" O ILE M 57 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ILE M 57 " --> pdb=" O TYR N 65 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N THR N 67 " --> pdb=" O HIS M 55 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N HIS M 55 " --> pdb=" O THR N 67 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N HIS M 72 " --> pdb=" O LYS M 87 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR M 77 " --> pdb=" O ILE M 8 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ILE M 8 " --> pdb=" O TYR M 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 60 through 66 removed outlier: 7.364A pdb=" N HIS M 55 " --> pdb=" O THR N 67 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N THR N 67 " --> pdb=" O HIS M 55 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ILE M 57 " --> pdb=" O TYR N 65 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N TYR N 65 " --> pdb=" O ILE M 57 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLY M 59 " --> pdb=" O GLY N 63 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY N 63 " --> pdb=" O GLY M 59 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLY M 63 " --> pdb=" O GLY N 59 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLY N 59 " --> pdb=" O GLY M 63 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N TYR M 65 " --> pdb=" O ILE N 57 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE N 57 " --> pdb=" O TYR M 65 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR M 67 " --> pdb=" O HIS N 55 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N HIS N 55 " --> pdb=" O THR M 67 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LYS N 87 " --> pdb=" O GLU N 69 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N HIS N 72 " --> pdb=" O LYS N 87 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TYR N 77 " --> pdb=" O ILE N 8 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ILE N 8 " --> pdb=" O TYR N 77 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 540 through 545 removed outlier: 7.528A pdb=" N HIS L 55 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL K 66 " --> pdb=" O HIS L 55 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE L 57 " --> pdb=" O SER K 64 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER K 64 " --> pdb=" O ILE L 57 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY L 59 " --> pdb=" O PHE K 62 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE K 62 " --> pdb=" O GLY L 59 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASN L 61 " --> pdb=" O ARG K 60 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N THR L 67 " --> pdb=" O TRP K 54 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N TRP K 54 " --> pdb=" O THR L 67 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N HIS K 72 " --> pdb=" O LYS K 87 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR K 77 " --> pdb=" O ILE K 8 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE K 8 " --> pdb=" O TYR K 77 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 72 through 78 removed outlier: 7.758A pdb=" N TRP K 54 " --> pdb=" O THR L 67 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N THR L 67 " --> pdb=" O TRP K 54 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASN L 61 " --> pdb=" O ARG K 60 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE K 62 " --> pdb=" O GLY L 59 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY L 59 " --> pdb=" O PHE K 62 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER K 64 " --> pdb=" O ILE L 57 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE L 57 " --> pdb=" O SER K 64 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL K 66 " --> pdb=" O HIS L 55 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N HIS L 55 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N HIS L 72 " --> pdb=" O LYS L 87 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TYR L 77 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE L 8 " --> pdb=" O TYR L 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 551 through 557 removed outlier: 3.535A pdb=" N VAL J 66 " --> pdb=" O VAL C 554 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N HIS J 55 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL I 66 " --> pdb=" O HIS J 55 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE J 57 " --> pdb=" O SER I 64 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N SER I 64 " --> pdb=" O ILE J 57 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLY J 59 " --> pdb=" O PHE I 62 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE I 62 " --> pdb=" O GLY J 59 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ASN J 61 " --> pdb=" O ARG I 60 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR J 67 " --> pdb=" O TRP I 54 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N TRP I 54 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N HIS I 72 " --> pdb=" O LYS I 87 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR I 77 " --> pdb=" O ILE I 8 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE I 8 " --> pdb=" O TYR I 77 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 82 through 88 removed outlier: 7.576A pdb=" N TRP I 54 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR J 67 " --> pdb=" O TRP I 54 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ASN J 61 " --> pdb=" O ARG I 60 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE I 62 " --> pdb=" O GLY J 59 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLY J 59 " --> pdb=" O PHE I 62 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N SER I 64 " --> pdb=" O ILE J 57 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE J 57 " --> pdb=" O SER I 64 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL I 66 " --> pdb=" O HIS J 55 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N HIS J 55 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N HIS J 72 " --> pdb=" O LYS J 87 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TYR J 77 " --> pdb=" O ILE J 8 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE J 8 " --> pdb=" O TYR J 77 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 630 through 631 removed outlier: 3.667A pdb=" N PHE C1018 " --> pdb=" O GLU C1010 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA C1004 " --> pdb=" O ALA C1024 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 643 through 649 removed outlier: 5.683A pdb=" N VAL C 644 " --> pdb=" O ASP C 662 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASP C 662 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER C 646 " --> pdb=" O VAL C 660 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR C 676 " --> pdb=" O CYS C 695 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 699 through 704 removed outlier: 4.173A pdb=" N CYS C 701 " --> pdb=" O GLY C 715 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 765 through 771 removed outlier: 7.060A pdb=" N LEU C 802 " --> pdb=" O GLN C 766 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL C 768 " --> pdb=" O ALA C 800 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA C 800 " --> pdb=" O VAL C 768 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N HIS C 798 " --> pdb=" O PRO C 770 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 865 through 868 removed outlier: 3.598A pdb=" N ILE C 885 " --> pdb=" O PHE C 900 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 914 through 917 Processing sheet with id=AB9, first strand: chain 'C' and resid 957 through 962 removed outlier: 6.393A pdb=" N GLN C 973 " --> pdb=" O THR C 958 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LEU C 960 " --> pdb=" O LEU C 971 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU C 971 " --> pdb=" O LEU C 960 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TRP C 962 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL C 969 " --> pdb=" O TRP C 962 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP C 974 " --> pdb=" O ASN C 978 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASN C 978 " --> pdb=" O ASP C 974 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 151 through 153 removed outlier: 4.068A pdb=" N THR D 151 " --> pdb=" O VAL D 509 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY D 153 " --> pdb=" O VAL D 507 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N CYS D 487 " --> pdb=" O GLY D 501 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 163 through 169 removed outlier: 5.499A pdb=" N VAL D 164 " --> pdb=" O ARG D 182 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ARG D 182 " --> pdb=" O VAL D 164 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 220 through 225 removed outlier: 4.639A pdb=" N LEU D 223 " --> pdb=" O ALA D 234 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA D 234 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE D 225 " --> pdb=" O HIS D 232 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N HIS D 232 " --> pdb=" O PHE D 225 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL D 244 " --> pdb=" O TRP D 256 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 272 through 276 removed outlier: 3.938A pdb=" N LEU D 296 " --> pdb=" O SER D 288 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 337 through 342 removed outlier: 4.368A pdb=" N ALA D 339 " --> pdb=" O GLY D 353 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 350 " --> pdb=" O CYS D 362 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE D 386 " --> pdb=" O LYS D 361 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 395 through 399 removed outlier: 3.673A pdb=" N THR D 429 " --> pdb=" O LEU D 419 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 438 through 442 Processing sheet with id=AC8, first strand: chain 'E' and resid 67 through 71 removed outlier: 3.562A pdb=" N THR E 67 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE E 33 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL E 112 " --> pdb=" O PHE E 33 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE E 35 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL E 114 " --> pdb=" O PHE E 35 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE E 37 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ASP E 116 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 9.347A pdb=" N VAL E 182 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU E 111 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ILE E 184 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU E 113 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N SER E 186 " --> pdb=" O LEU E 113 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU E 115 " --> pdb=" O SER E 186 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER E 216 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET E 218 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY E 185 " --> pdb=" O MET E 218 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 65 through 71 removed outlier: 6.208A pdb=" N VAL F 34 " --> pdb=" O TRP F 85 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N LEU F 87 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE F 36 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER F 110 " --> pdb=" O PHE F 33 " (cutoff:3.500A) removed outlier: 10.102A pdb=" N VAL F 182 " --> pdb=" O PHE F 109 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU F 111 " --> pdb=" O VAL F 182 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N ILE F 184 " --> pdb=" O LEU F 111 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU F 113 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N SER F 186 " --> pdb=" O LEU F 113 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU F 115 " --> pdb=" O SER F 186 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER F 216 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY F 185 " --> pdb=" O MET F 218 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 630 through 633 removed outlier: 3.828A pdb=" N LYS G 632 " --> pdb=" O VAL G 623 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE G 669 " --> pdb=" O ARG H 580 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE H 576 " --> pdb=" O ARG G 673 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA H 589 " --> pdb=" O LEU H 596 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU H 596 " --> pdb=" O ALA H 589 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE H 597 " --> pdb=" O ILE H 528 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE H 528 " --> pdb=" O ILE H 597 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE H 599 " --> pdb=" O GLN H 526 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS H 539 " --> pdb=" O VAL H 530 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASN H 532 " --> pdb=" O PRO H 537 " (cutoff:3.500A) 1939 hydrogen bonds defined for protein. 5643 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: 9.59 Time building geometry restraints manager: 7.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.26: 4093 1.26 - 1.35: 4050 1.35 - 1.43: 108 1.43 - 1.51: 4397 1.51 - 1.60: 7729 Bond restraints: 20377 Sorted by residual: bond pdb=" N ALA L 6 " pdb=" CA ALA L 6 " ideal model delta sigma weight residual 1.456 1.553 -0.096 1.23e-02 6.61e+03 6.12e+01 bond pdb=" C GLY L 89 " pdb=" O GLY L 89 " ideal model delta sigma weight residual 1.231 1.383 -0.152 2.00e-02 2.50e+03 5.80e+01 bond pdb=" C GLY N 89 " pdb=" O GLY N 89 " ideal model delta sigma weight residual 1.231 1.382 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N ALA N 6 " pdb=" CA ALA N 6 " ideal model delta sigma weight residual 1.456 1.553 -0.097 1.29e-02 6.01e+03 5.66e+01 bond pdb=" C GLY J 89 " pdb=" O GLY J 89 " ideal model delta sigma weight residual 1.231 1.381 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 20372 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 27957 2.82 - 5.63: 367 5.63 - 8.45: 26 8.45 - 11.26: 4 11.26 - 14.08: 4 Bond angle restraints: 28358 Sorted by residual: angle pdb=" CA GLY J 89 " pdb=" C GLY J 89 " pdb=" O GLY J 89 " ideal model delta sigma weight residual 120.80 134.38 -13.58 2.10e+00 2.27e-01 4.18e+01 angle pdb=" CA GLY L 89 " pdb=" C GLY L 89 " pdb=" O GLY L 89 " ideal model delta sigma weight residual 120.80 134.30 -13.50 2.10e+00 2.27e-01 4.13e+01 angle pdb=" CA GLY N 89 " pdb=" C GLY N 89 " pdb=" O GLY N 89 " ideal model delta sigma weight residual 120.80 134.17 -13.37 2.10e+00 2.27e-01 4.05e+01 angle pdb=" N PRO F 298 " pdb=" CA PRO F 298 " pdb=" C PRO F 298 " ideal model delta sigma weight residual 110.70 117.97 -7.27 1.22e+00 6.72e-01 3.55e+01 angle pdb=" N PRO E 298 " pdb=" CA PRO E 298 " pdb=" C PRO E 298 " ideal model delta sigma weight residual 110.70 117.95 -7.25 1.22e+00 6.72e-01 3.54e+01 ... (remaining 28353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 4.37: 10727 4.37 - 8.75: 940 8.75 - 13.12: 192 13.12 - 17.50: 49 17.50 - 21.87: 22 Dihedral angle restraints: 11930 sinusoidal: 0 harmonic: 11930 Sorted by residual: dihedral pdb=" CA PHE B 877 " pdb=" C PHE B 877 " pdb=" N THR B 878 " pdb=" CA THR B 878 " ideal model delta harmonic sigma weight residual 180.00 158.13 21.87 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA PHE D 386 " pdb=" C PHE D 386 " pdb=" N THR D 387 " pdb=" CA THR D 387 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA GLN D 493 " pdb=" C GLN D 493 " pdb=" N GLN D 494 " pdb=" CA GLN D 494 " ideal model delta harmonic sigma weight residual -180.00 -160.47 -19.53 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 11927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2804 0.049 - 0.098: 595 0.098 - 0.147: 420 0.147 - 0.196: 92 0.196 - 0.245: 8 Chirality restraints: 3919 Sorted by residual: chirality pdb=" CA PHE L 46 " pdb=" N PHE L 46 " pdb=" C PHE L 46 " pdb=" CB PHE L 46 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA PHE J 46 " pdb=" N PHE J 46 " pdb=" C PHE J 46 " pdb=" CB PHE J 46 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA PHE L 73 " pdb=" N PHE L 73 " pdb=" C PHE L 73 " pdb=" CB PHE L 73 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 3916 not shown) Planarity restraints: 4092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 297 " -0.027 2.00e-02 2.50e+03 5.49e-02 3.01e+01 pdb=" C PHE E 297 " 0.095 2.00e-02 2.50e+03 pdb=" O PHE E 297 " -0.035 2.00e-02 2.50e+03 pdb=" N PRO E 298 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE F 297 " 0.027 2.00e-02 2.50e+03 5.43e-02 2.95e+01 pdb=" C PHE F 297 " -0.094 2.00e-02 2.50e+03 pdb=" O PHE F 297 " 0.035 2.00e-02 2.50e+03 pdb=" N PRO F 298 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS J 71 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.69e+00 pdb=" C LYS J 71 " -0.051 2.00e-02 2.50e+03 pdb=" O LYS J 71 " 0.019 2.00e-02 2.50e+03 pdb=" N HIS J 72 " 0.017 2.00e-02 2.50e+03 ... (remaining 4089 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 109 2.65 - 3.21: 20286 3.21 - 3.77: 28562 3.77 - 4.34: 31168 4.34 - 4.90: 50601 Nonbonded interactions: 130726 Sorted by model distance: nonbonded pdb=" O TRP C 555 " pdb=" CB VAL C 565 " model vdw 2.082 3.470 nonbonded pdb=" O GLN D 494 " pdb=" N GLN D 496 " model vdw 2.368 3.120 nonbonded pdb=" O ASN A 771 " pdb=" CA LEU A 772 " model vdw 2.426 2.776 nonbonded pdb=" N ALA C 577 " pdb=" N VAL C 578 " model vdw 2.454 2.560 nonbonded pdb=" O TRP A 306 " pdb=" O VAL A 310 " model vdw 2.464 3.040 ... (remaining 130721 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 10 through 937) selection = (chain 'B' and (resid 10 through 462 or resid 480 through 937)) } ncs_group { reference = (chain 'E' and (resid 4 through 300 or resid 310 through 343)) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 56.570 Find NCS groups from input model: 0.940 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: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 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 : 0.007 0.152 20377 Z= 0.536 Angle : 0.949 14.081 28358 Z= 0.646 Chirality : 0.058 0.245 3919 Planarity : 0.005 0.055 4092 Dihedral : 4.704 21.871 4092 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.04 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.15 % 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: -1.08 (0.12), residues: 4062 helix: 0.46 (0.11), residues: 1895 sheet: -0.87 (0.20), residues: 582 loop : -2.09 (0.14), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 PHE 0.000 0.000 PHE A 12 TYR 0.000 0.000 TYR A 20 Details of bonding type rmsd hydrogen bonds : bond 0.20474 ( 1927) hydrogen bonds : angle 7.20737 ( 5643) covalent geometry : bond 0.00741 (20377) covalent geometry : angle 0.94875 (28358) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 2.118 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1704 time to fit residues: 28.9856 Evaluate side-chains 79 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 341 optimal weight: 0.8980 chunk 306 optimal weight: 9.9990 chunk 170 optimal weight: 7.9990 chunk 104 optimal weight: 50.0000 chunk 207 optimal weight: 8.9990 chunk 163 optimal weight: 6.9990 chunk 317 optimal weight: 0.9990 chunk 122 optimal weight: 0.0770 chunk 193 optimal weight: 9.9990 chunk 236 optimal weight: 20.0000 chunk 367 optimal weight: 3.9990 overall best weight: 2.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.075498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.061003 restraints weight = 319050.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.061003 restraints weight = 304593.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.061003 restraints weight = 304593.144| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5845 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 20377 Z= 0.151 Angle : 0.476 6.005 28358 Z= 0.301 Chirality : 0.042 0.138 3919 Planarity : 0.003 0.014 4092 Dihedral : 4.212 23.872 4092 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 0.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.15 % 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: 0.76 (0.13), residues: 4062 helix: 2.61 (0.11), residues: 1889 sheet: -0.55 (0.22), residues: 562 loop : -1.81 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 PHE 0.000 0.000 PHE A 12 TYR 0.000 0.000 TYR A 20 Details of bonding type rmsd hydrogen bonds : bond 0.04498 ( 1927) hydrogen bonds : angle 4.81187 ( 5643) covalent geometry : bond 0.00203 (20377) covalent geometry : angle 0.47638 (28358) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 3.235 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2436 time to fit residues: 42.4727 Evaluate side-chains 79 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 116 optimal weight: 30.0000 chunk 261 optimal weight: 20.0000 chunk 8 optimal weight: 50.0000 chunk 338 optimal weight: 30.0000 chunk 348 optimal weight: 5.9990 chunk 308 optimal weight: 0.7980 chunk 334 optimal weight: 1.9990 chunk 360 optimal weight: 8.9990 chunk 291 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 364 optimal weight: 30.0000 overall best weight: 7.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.067721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.052976 restraints weight = 296185.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.052986 restraints weight = 279679.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.052986 restraints weight = 278540.833| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.6191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20377 Z= 0.304 Angle : 0.714 11.300 28358 Z= 0.458 Chirality : 0.045 0.169 3919 Planarity : 0.004 0.025 4092 Dihedral : 6.175 30.381 4092 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.58 % Favored : 92.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.64 (0.13), residues: 4062 helix: 1.34 (0.11), residues: 1896 sheet: -0.95 (0.22), residues: 531 loop : -2.48 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 PHE 0.000 0.000 PHE A 12 TYR 0.000 0.000 TYR A 20 Details of bonding type rmsd hydrogen bonds : bond 0.06905 ( 1927) hydrogen bonds : angle 6.05003 ( 5643) covalent geometry : bond 0.00414 (20377) covalent geometry : angle 0.71397 (28358) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 2.122 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1893 time to fit residues: 31.6848 Evaluate side-chains 79 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 110 optimal weight: 50.0000 chunk 16 optimal weight: 7.9990 chunk 137 optimal weight: 30.0000 chunk 61 optimal weight: 20.0000 chunk 201 optimal weight: 9.9990 chunk 185 optimal weight: 6.9990 chunk 138 optimal weight: 30.0000 chunk 46 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 155 optimal weight: 30.0000 chunk 29 optimal weight: 20.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.065931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.051377 restraints weight = 306047.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.051377 restraints weight = 291237.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.051377 restraints weight = 291237.286| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.8072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20377 Z= 0.291 Angle : 0.659 8.587 28358 Z= 0.422 Chirality : 0.044 0.152 3919 Planarity : 0.004 0.023 4092 Dihedral : 6.189 27.112 4092 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.31 % Favored : 90.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.15 % 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: -1.21 (0.13), residues: 4062 helix: 0.99 (0.11), residues: 1901 sheet: -1.30 (0.22), residues: 544 loop : -2.93 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 PHE 0.000 0.000 PHE A 12 TYR 0.000 0.000 TYR A 20 Details of bonding type rmsd hydrogen bonds : bond 0.05790 ( 1927) hydrogen bonds : angle 6.16993 ( 5643) covalent geometry : bond 0.00389 (20377) covalent geometry : angle 0.65885 (28358) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 2.202 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1911 time to fit residues: 32.1010 Evaluate side-chains 79 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 399 optimal weight: 30.0000 chunk 174 optimal weight: 20.0000 chunk 300 optimal weight: 30.0000 chunk 319 optimal weight: 50.0000 chunk 21 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 212 optimal weight: 9.9990 chunk 268 optimal weight: 9.9990 chunk 334 optimal weight: 6.9990 chunk 35 optimal weight: 30.0000 chunk 98 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.065720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.051248 restraints weight = 308764.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.051132 restraints weight = 294756.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.051132 restraints weight = 282465.732| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.8594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20377 Z= 0.198 Angle : 0.537 6.513 28358 Z= 0.339 Chirality : 0.042 0.136 3919 Planarity : 0.003 0.020 4092 Dihedral : 5.320 27.254 4092 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.18 % Favored : 90.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.15 % 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: -0.64 (0.14), residues: 4062 helix: 1.75 (0.12), residues: 1911 sheet: -1.46 (0.22), residues: 557 loop : -2.90 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 PHE 0.000 0.000 PHE A 12 TYR 0.000 0.000 TYR A 20 Details of bonding type rmsd hydrogen bonds : bond 0.05120 ( 1927) hydrogen bonds : angle 5.43019 ( 5643) covalent geometry : bond 0.00271 (20377) covalent geometry : angle 0.53667 (28358) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 2.183 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1800 time to fit residues: 30.2597 Evaluate side-chains 79 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 91 optimal weight: 2.9990 chunk 404 optimal weight: 30.0000 chunk 111 optimal weight: 50.0000 chunk 192 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 329 optimal weight: 0.9990 chunk 126 optimal weight: 50.0000 chunk 51 optimal weight: 20.0000 chunk 255 optimal weight: 9.9990 chunk 355 optimal weight: 0.8980 chunk 318 optimal weight: 50.0000 overall best weight: 4.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.065584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.050558 restraints weight = 307778.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.050665 restraints weight = 295311.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.050665 restraints weight = 283618.200| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.9098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20377 Z= 0.183 Angle : 0.509 5.942 28358 Z= 0.322 Chirality : 0.042 0.134 3919 Planarity : 0.003 0.019 4092 Dihedral : 5.157 25.392 4092 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.15 % 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 (0.14), residues: 4062 helix: 1.95 (0.12), residues: 1919 sheet: -1.50 (0.22), residues: 532 loop : -2.92 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 PHE 0.000 0.000 PHE A 12 TYR 0.000 0.000 TYR A 20 Details of bonding type rmsd hydrogen bonds : bond 0.04684 ( 1927) hydrogen bonds : angle 5.31599 ( 5643) covalent geometry : bond 0.00251 (20377) covalent geometry : angle 0.50899 (28358) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 2.451 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1852 time to fit residues: 31.2942 Evaluate side-chains 79 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 155 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 400 optimal weight: 40.0000 chunk 347 optimal weight: 20.0000 chunk 309 optimal weight: 8.9990 chunk 371 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 339 optimal weight: 9.9990 chunk 297 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.064148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.049279 restraints weight = 301925.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.049312 restraints weight = 289127.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.049318 restraints weight = 276038.777| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 1.0054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 20377 Z= 0.308 Angle : 0.683 7.844 28358 Z= 0.440 Chirality : 0.044 0.146 3919 Planarity : 0.004 0.022 4092 Dihedral : 6.389 29.554 4092 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.80 % Favored : 87.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.15 % 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: -1.67 (0.13), residues: 4062 helix: 0.73 (0.11), residues: 1908 sheet: -1.53 (0.24), residues: 462 loop : -3.28 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 PHE 0.000 0.000 PHE A 12 TYR 0.000 0.000 TYR A 20 Details of bonding type rmsd hydrogen bonds : bond 0.06450 ( 1927) hydrogen bonds : angle 6.55561 ( 5643) covalent geometry : bond 0.00424 (20377) covalent geometry : angle 0.68342 (28358) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 2.475 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1872 time to fit residues: 31.7656 Evaluate side-chains 79 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 369 optimal weight: 5.9990 chunk 245 optimal weight: 20.0000 chunk 69 optimal weight: 0.9980 chunk 276 optimal weight: 20.0000 chunk 162 optimal weight: 20.0000 chunk 211 optimal weight: 20.0000 chunk 75 optimal weight: 30.0000 chunk 30 optimal weight: 30.0000 chunk 315 optimal weight: 0.4980 chunk 19 optimal weight: 20.0000 chunk 6 optimal weight: 40.0000 overall best weight: 9.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.063897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.049479 restraints weight = 299533.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.049479 restraints weight = 287787.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.049479 restraints weight = 287786.101| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 1.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 20377 Z= 0.313 Angle : 0.672 7.693 28358 Z= 0.432 Chirality : 0.044 0.150 3919 Planarity : 0.004 0.023 4092 Dihedral : 6.592 33.195 4092 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.39 % Favored : 86.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.15 % Twisted Proline : 1.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.13), residues: 4062 helix: 0.45 (0.11), residues: 1903 sheet: -1.73 (0.24), residues: 450 loop : -3.43 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 PHE 0.000 0.000 PHE A 12 TYR 0.000 0.000 TYR A 20 Details of bonding type rmsd hydrogen bonds : bond 0.06192 ( 1927) hydrogen bonds : angle 6.67755 ( 5643) covalent geometry : bond 0.00424 (20377) covalent geometry : angle 0.67223 (28358) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 2.087 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1808 time to fit residues: 30.4193 Evaluate side-chains 79 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 262 optimal weight: 0.7980 chunk 390 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 366 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 280 optimal weight: 10.0000 chunk 393 optimal weight: 40.0000 chunk 147 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.064608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.050329 restraints weight = 298982.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.050370 restraints weight = 287415.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.050416 restraints weight = 277740.497| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 1.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20377 Z= 0.199 Angle : 0.535 7.132 28358 Z= 0.339 Chirality : 0.042 0.137 3919 Planarity : 0.003 0.021 4092 Dihedral : 5.608 28.312 4092 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.72 % Favored : 88.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.15 % 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: -1.20 (0.13), residues: 4062 helix: 1.37 (0.12), residues: 1903 sheet: -1.58 (0.25), residues: 441 loop : -3.28 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 PHE 0.000 0.000 PHE A 12 TYR 0.000 0.000 TYR A 20 Details of bonding type rmsd hydrogen bonds : bond 0.05090 ( 1927) hydrogen bonds : angle 5.86665 ( 5643) covalent geometry : bond 0.00272 (20377) covalent geometry : angle 0.53532 (28358) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 2.170 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1918 time to fit residues: 32.1641 Evaluate side-chains 79 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 360 optimal weight: 7.9990 chunk 349 optimal weight: 20.0000 chunk 246 optimal weight: 7.9990 chunk 401 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 chunk 62 optimal weight: 20.0000 chunk 142 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 326 optimal weight: 30.0000 chunk 204 optimal weight: 0.4980 chunk 79 optimal weight: 8.9990 overall best weight: 4.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.064758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.050465 restraints weight = 296862.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.050452 restraints weight = 285000.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.050452 restraints weight = 279221.123| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 1.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 20377 Z= 0.172 Angle : 0.503 7.216 28358 Z= 0.317 Chirality : 0.042 0.137 3919 Planarity : 0.002 0.022 4092 Dihedral : 5.268 27.736 4092 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.24 % Favored : 87.72 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.15 % 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: -0.87 (0.14), residues: 4062 helix: 1.75 (0.12), residues: 1912 sheet: -1.65 (0.25), residues: 457 loop : -3.21 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 PHE 0.000 0.000 PHE A 12 TYR 0.000 0.000 TYR A 20 Details of bonding type rmsd hydrogen bonds : bond 0.04703 ( 1927) hydrogen bonds : angle 5.54422 ( 5643) covalent geometry : bond 0.00235 (20377) covalent geometry : angle 0.50277 (28358) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 2.400 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1823 time to fit residues: 30.9976 Evaluate side-chains 79 residues out of total 3670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 80 optimal weight: 20.0000 chunk 314 optimal weight: 0.9980 chunk 149 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 198 optimal weight: 9.9990 chunk 404 optimal weight: 40.0000 chunk 26 optimal weight: 0.0670 chunk 394 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 223 optimal weight: 9.9990 overall best weight: 5.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.064609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.050483 restraints weight = 299429.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.050483 restraints weight = 285338.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.050483 restraints weight = 285338.219| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 1.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20377 Z= 0.186 Angle : 0.513 6.937 28358 Z= 0.325 Chirality : 0.042 0.135 3919 Planarity : 0.003 0.021 4092 Dihedral : 5.302 29.670 4092 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.21 % Favored : 87.72 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.78 % Cis-general : 0.15 % 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: -0.86 (0.14), residues: 4062 helix: 1.76 (0.12), residues: 1919 sheet: -1.71 (0.25), residues: 457 loop : -3.20 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 28 PHE 0.000 0.000 PHE A 12 TYR 0.000 0.000 TYR A 20 Details of bonding type rmsd hydrogen bonds : bond 0.04843 ( 1927) hydrogen bonds : angle 5.61773 ( 5643) covalent geometry : bond 0.00255 (20377) covalent geometry : angle 0.51281 (28358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6980.74 seconds wall clock time: 122 minutes 22.40 seconds (7342.40 seconds total)