Starting phenix.real_space_refine (version: dev) on Thu Feb 23 15:42:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rlb_4918/02_2023/6rlb_4918.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rlb_4918/02_2023/6rlb_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rlb_4918/02_2023/6rlb_4918.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rlb_4918/02_2023/6rlb_4918.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rlb_4918/02_2023/6rlb_4918.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rlb_4918/02_2023/6rlb_4918.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 13.17, per 1000 atoms: 0.65 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 - 3.50 Amino acid : False - 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: 8.98 Conformation dependent library (CDL) restraints added in 4.6 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: 1.66 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: 9.27 Time building geometry restraints manager: 9.63 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: 101.55 - 108.11: 440 108.11 - 114.68: 11557 114.68 - 121.25: 9941 121.25 - 127.82: 6407 127.82 - 134.38: 13 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 2.520 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 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 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. 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: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.680 Check model and map are aligned: 0.290 Process input model: 59.910 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.180 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 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= 0.556 Angle : 0.948 14.081 28358 Z= 0.645 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 % 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.440 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1795 time to fit residues: 30.3478 Evaluate side-chains 79 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.461 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2666 ------------------------------------------------------------------------------- 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: 10.0000 chunk 306 optimal weight: 9.9990 chunk 170 optimal weight: 20.0000 chunk 104 optimal weight: 50.0000 chunk 207 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 317 optimal weight: 0.9980 chunk 122 optimal weight: 0.0570 chunk 193 optimal weight: 20.0000 chunk 236 optimal weight: 20.0000 chunk 367 optimal weight: 3.9990 overall best weight: 4.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 20377 Z= 0.204 Angle : 0.535 8.582 28358 Z= 0.341 Chirality : 0.042 0.142 3919 Planarity : 0.003 0.016 4092 Dihedral : 4.776 27.286 4092 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 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: 0.29 (0.13), residues: 4062 helix: 2.15 (0.11), residues: 1879 sheet: -0.57 (0.22), residues: 551 loop : -1.99 (0.15), residues: 1632 *********************** 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 fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.354 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1849 time to fit residues: 31.0861 Evaluate side-chains 79 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.440 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 204 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 306 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 101 optimal weight: 50.0000 chunk 368 optimal weight: 20.0000 chunk 398 optimal weight: 30.0000 chunk 328 optimal weight: 30.0000 chunk 365 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 chunk 295 optimal weight: 2.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.7065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 20377 Z= 0.299 Angle : 0.720 10.171 28358 Z= 0.459 Chirality : 0.045 0.191 3919 Planarity : 0.004 0.024 4092 Dihedral : 6.457 30.220 4092 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.21 % Favored : 90.45 % Rotamer Outliers : 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: -1.00 (0.13), residues: 4062 helix: 1.11 (0.11), residues: 1913 sheet: -1.11 (0.22), residues: 520 loop : -2.78 (0.14), residues: 1629 *********************** 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 fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.538 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1835 time to fit residues: 31.0550 Evaluate side-chains 79 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.477 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 364 optimal weight: 20.0000 chunk 277 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 chunk 40 optimal weight: 20.0000 chunk 175 optimal weight: 10.0000 chunk 247 optimal weight: 0.7980 chunk 369 optimal weight: 10.0000 chunk 391 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 350 optimal weight: 20.0000 chunk 105 optimal weight: 40.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.7179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 20377 Z= 0.161 Angle : 0.490 5.745 28358 Z= 0.307 Chirality : 0.042 0.146 3919 Planarity : 0.002 0.014 4092 Dihedral : 5.061 27.575 4092 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer Outliers : 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: -0.04 (0.14), residues: 4062 helix: 2.20 (0.11), residues: 1918 sheet: -1.10 (0.22), residues: 528 loop : -2.58 (0.15), residues: 1616 *********************** 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 fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.630 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1946 time to fit residues: 32.4673 Evaluate side-chains 79 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.499 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 326 optimal weight: 0.0050 chunk 222 optimal weight: 0.9990 chunk 5 optimal weight: 50.0000 chunk 291 optimal weight: 0.8980 chunk 161 optimal weight: 9.9990 chunk 334 optimal weight: 40.0000 chunk 270 optimal weight: 20.0000 chunk 0 optimal weight: 60.0000 chunk 199 optimal weight: 30.0000 chunk 351 optimal weight: 0.9980 chunk 98 optimal weight: 20.0000 overall best weight: 2.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.7400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 20377 Z= 0.111 Angle : 0.414 5.048 28358 Z= 0.257 Chirality : 0.041 0.129 3919 Planarity : 0.002 0.013 4092 Dihedral : 4.149 23.402 4092 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer Outliers : 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 (0.14), residues: 4062 helix: 3.07 (0.12), residues: 1930 sheet: -1.05 (0.22), residues: 553 loop : -2.40 (0.16), residues: 1579 *********************** 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 fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.481 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1862 time to fit residues: 31.4912 Evaluate side-chains 79 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.478 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 131 optimal weight: 10.0000 chunk 352 optimal weight: 0.8980 chunk 77 optimal weight: 20.0000 chunk 229 optimal weight: 0.0070 chunk 96 optimal weight: 30.0000 chunk 391 optimal weight: 50.0000 chunk 325 optimal weight: 40.0000 chunk 181 optimal weight: 40.0000 chunk 32 optimal weight: 0.0470 chunk 129 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 overall best weight: 1.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.7597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.001 0.015 20377 Z= 0.091 Angle : 0.379 5.193 28358 Z= 0.233 Chirality : 0.041 0.125 3919 Planarity : 0.002 0.011 4092 Dihedral : 3.803 21.444 4092 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer Outliers : 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: 1.05 (0.14), residues: 4062 helix: 3.36 (0.11), residues: 1944 sheet: -0.97 (0.22), residues: 556 loop : -2.35 (0.16), residues: 1562 *********************** 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 fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.594 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1937 time to fit residues: 33.1052 Evaluate side-chains 79 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.738 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 377 optimal weight: 0.6980 chunk 44 optimal weight: 8.9990 chunk 223 optimal weight: 20.0000 chunk 286 optimal weight: 5.9990 chunk 221 optimal weight: 20.0000 chunk 329 optimal weight: 30.0000 chunk 218 optimal weight: 10.0000 chunk 390 optimal weight: 50.0000 chunk 244 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 180 optimal weight: 40.0000 overall best weight: 7.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.8595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 20377 Z= 0.255 Angle : 0.571 9.252 28358 Z= 0.367 Chirality : 0.043 0.152 3919 Planarity : 0.003 0.015 4092 Dihedral : 5.283 27.965 4092 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.96 % Favored : 89.00 % Rotamer Outliers : 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: -0.17 (0.14), residues: 4062 helix: 2.09 (0.11), residues: 1923 sheet: -1.10 (0.22), residues: 545 loop : -2.69 (0.15), residues: 1594 *********************** 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 fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.651 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1948 time to fit residues: 32.6576 Evaluate side-chains 79 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.553 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 241 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 233 optimal weight: 40.0000 chunk 117 optimal weight: 50.0000 chunk 76 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 248 optimal weight: 8.9990 chunk 265 optimal weight: 9.9990 chunk 192 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 chunk 306 optimal weight: 0.6980 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.9019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 20377 Z= 0.188 Angle : 0.489 6.091 28358 Z= 0.309 Chirality : 0.042 0.138 3919 Planarity : 0.002 0.017 4092 Dihedral : 4.897 25.011 4092 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.11 % Favored : 90.87 % Rotamer Outliers : 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: -0.08 (0.14), residues: 4062 helix: 2.30 (0.12), residues: 1933 sheet: -1.28 (0.23), residues: 534 loop : -2.77 (0.15), residues: 1595 *********************** 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 fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.489 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1882 time to fit residues: 31.6288 Evaluate side-chains 79 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.480 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 355 optimal weight: 10.0000 chunk 373 optimal weight: 50.0000 chunk 341 optimal weight: 6.9990 chunk 363 optimal weight: 30.0000 chunk 218 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 285 optimal weight: 9.9990 chunk 111 optimal weight: 50.0000 chunk 328 optimal weight: 8.9990 chunk 344 optimal weight: 8.9990 chunk 362 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.9733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 20377 Z= 0.249 Angle : 0.581 8.282 28358 Z= 0.372 Chirality : 0.043 0.150 3919 Planarity : 0.003 0.020 4092 Dihedral : 5.661 28.334 4092 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.85 % Favored : 87.08 % Rotamer Outliers : 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: -0.88 (0.13), residues: 4062 helix: 1.49 (0.12), residues: 1926 sheet: -1.31 (0.23), residues: 503 loop : -3.06 (0.14), residues: 1633 *********************** 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 fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.679 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2209 time to fit residues: 36.9764 Evaluate side-chains 79 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.764 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 238 optimal weight: 6.9990 chunk 384 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 chunk 182 optimal weight: 50.0000 chunk 267 optimal weight: 30.0000 chunk 403 optimal weight: 8.9990 chunk 371 optimal weight: 9.9990 chunk 321 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 248 optimal weight: 0.6980 chunk 197 optimal weight: 30.0000 overall best weight: 7.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 1.0475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 20377 Z= 0.237 Angle : 0.572 8.739 28358 Z= 0.363 Chirality : 0.042 0.139 3919 Planarity : 0.003 0.021 4092 Dihedral : 5.761 29.406 4092 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.64 % Favored : 89.32 % Rotamer Outliers : 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 (0.13), residues: 4062 helix: 1.38 (0.12), residues: 1917 sheet: -1.27 (0.24), residues: 467 loop : -3.23 (0.14), residues: 1678 ********************** 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 fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.487 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1853 time to fit residues: 31.2178 Evaluate side-chains 79 residues out of total 3670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.504 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 255 optimal weight: 8.9990 chunk 342 optimal weight: 30.0000 chunk 98 optimal weight: 7.9990 chunk 296 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 89 optimal weight: 0.0570 chunk 321 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 330 optimal weight: 30.0000 chunk 40 optimal weight: 20.0000 chunk 59 optimal weight: 40.0000 overall best weight: 6.0106 ------------------------------------------------------------------------------- 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 = 0.3440 r_free = 0.3440 target = 0.064438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.049425 restraints weight = 302544.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.049530 restraints weight = 289624.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.049530 restraints weight = 274528.398| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 1.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 20377 Z= 0.214 Angle : 0.539 7.511 28358 Z= 0.342 Chirality : 0.042 0.142 3919 Planarity : 0.003 0.020 4092 Dihedral : 5.451 27.120 4092 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.95 % Favored : 86.98 % Rotamer Outliers : 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: -0.95 (0.14), residues: 4062 helix: 1.57 (0.12), residues: 1927 sheet: -1.37 (0.24), residues: 477 loop : -3.26 (0.14), residues: 1658 =============================================================================== Job complete usr+sys time: 2533.09 seconds wall clock time: 46 minutes 6.53 seconds (2766.53 seconds total)