Starting phenix.real_space_refine on Thu Sep 18 21:58:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rlb_4918/09_2025/6rlb_4918.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rlb_4918/09_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_4918/09_2025/6rlb_4918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rlb_4918/09_2025/6rlb_4918.map" model { file = "/net/cci-nas-00/data/ceres_data/6rlb_4918/09_2025/6rlb_4918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rlb_4918/09_2025/6rlb_4918.cif" } 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 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'PHE:plan': 46, 'GLN:plan1': 65, 'ASN:plan1': 41, 'TYR:plan': 25, 'GLU:plan': 82, 'TRP:plan': 18, 'ASP:plan': 55, 'ARG:plan': 48, 'HIS:plan': 22} 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: {'PHE:plan': 43, 'GLN:plan1': 58, 'ASN:plan1': 39, 'TYR:plan': 24, 'GLU:plan': 69, 'TRP:plan': 17, 'ASP:plan': 51, 'ARG:plan': 46, 'HIS:plan': 19} 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: {'ASN:plan1': 13, 'GLN:plan1': 29, 'TYR:plan': 4, 'GLU:plan': 22, 'ASP:plan': 28, 'ARG:plan': 24, 'TRP:plan': 11, 'HIS:plan': 15, 'PHE:plan': 20} 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: {'ARG:plan': 19, 'TRP:plan': 12, 'GLU:plan': 20, 'GLN:plan1': 34, 'ASN:plan1': 8, 'HIS:plan': 14, 'ASP:plan': 21, 'TYR:plan': 9, 'PHE: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: {'GLU:plan': 22, 'TRP:plan': 5, 'ARG:plan': 13, 'ASN:plan1': 11, 'PHE:plan': 14, 'ASP:plan': 20, 'TYR:plan': 8, 'HIS:plan': 6, 'GLN:plan1': 9} 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: {'GLU:plan': 22, 'TRP:plan': 5, 'ARG:plan': 13, 'ASN:plan1': 11, 'PHE:plan': 14, 'ASP:plan': 20, 'TYR:plan': 8, 'HIS:plan': 6, 'GLN:plan1': 9} 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: {'GLU:plan': 5, 'ARG:plan': 5, 'GLN:plan1': 6, 'ASN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3} 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: {'GLU:plan': 5, 'ARG:plan': 5, 'GLN:plan1': 6, 'ASN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3} 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: {'ARG:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 7, 'GLN:plan1': 4, 'TYR:plan': 5, 'HIS:plan': 4, 'PHE:plan': 5, 'TRP:plan': 1} 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: {'ARG:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 7, 'GLN:plan1': 4, 'TYR:plan': 5, 'HIS:plan': 4, 'PHE:plan': 5, 'TRP:plan': 1} 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: {'ARG:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 7, 'GLN:plan1': 4, 'TYR:plan': 5, 'HIS:plan': 4, 'PHE:plan': 5, 'TRP:plan': 1} 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: {'ARG:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 7, 'GLN:plan1': 4, 'TYR:plan': 5, 'HIS:plan': 4, 'PHE:plan': 5, 'TRP:plan': 1} 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: {'ARG:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 7, 'GLN:plan1': 4, 'TYR:plan': 5, 'HIS:plan': 4, 'PHE:plan': 5, 'TRP:plan': 1} 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: {'ARG:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 7, 'GLN:plan1': 4, 'TYR:plan': 5, 'HIS:plan': 4, 'PHE:plan': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 172 Time building chain proxies: 5.81, per 1000 atoms: 0.28 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: 2.32 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.07 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: 5.10 Time building geometry restraints manager: 2.90 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: 1.490 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.700 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.560 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (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 TYR 0.000 0.000 TYR A 20 PHE 0.000 0.000 PHE A 12 TRP 0.000 0.000 TRP A 28 Details of bonding type rmsd covalent geometry : bond 0.00741 (20377) covalent geometry : angle 0.94875 (28358) hydrogen bonds : bond 0.20474 ( 1927) hydrogen bonds : angle 7.20737 ( 5643) *********************** 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 : 0.767 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0878 time to fit residues: 14.1372 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 : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 197 optimal weight: 30.0000 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 30.0000 chunk 401 optimal weight: 7.9990 chunk 155 optimal weight: 40.0000 chunk 244 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.069861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.054423 restraints weight = 295525.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.054274 restraints weight = 284611.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.054332 restraints weight = 276343.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.054308 restraints weight = 270671.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.054320 restraints weight = 270432.459| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20377 Z= 0.292 Angle : 0.730 13.055 28358 Z= 0.464 Chirality : 0.046 0.168 3919 Planarity : 0.005 0.026 4092 Dihedral : 6.258 35.320 4092 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.35 % Favored : 93.48 % 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 : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.13), residues: 4062 helix: 0.71 (0.11), residues: 1891 sheet: -0.93 (0.22), residues: 523 loop : -2.46 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 20 PHE 0.000 0.000 PHE A 12 TRP 0.000 0.000 TRP A 28 Details of bonding type rmsd covalent geometry : bond 0.00401 (20377) covalent geometry : angle 0.72975 (28358) hydrogen bonds : bond 0.06593 ( 1927) hydrogen bonds : angle 6.23682 ( 5643) *********************** 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 : 0.808 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0853 time to fit residues: 13.9075 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 : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 277 optimal weight: 10.0000 chunk 231 optimal weight: 20.0000 chunk 122 optimal weight: 40.0000 chunk 140 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 304 optimal weight: 0.8980 chunk 341 optimal weight: 0.0570 chunk 170 optimal weight: 30.0000 chunk 182 optimal weight: 50.0000 chunk 154 optimal weight: 0.8980 chunk 267 optimal weight: 20.0000 overall best weight: 6.3706 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.067954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.052399 restraints weight = 299290.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.052436 restraints weight = 287988.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.052436 restraints weight = 281392.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.052436 restraints weight = 281392.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.052436 restraints weight = 281392.855| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.6140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20377 Z= 0.225 Angle : 0.587 9.249 28358 Z= 0.372 Chirality : 0.042 0.144 3919 Planarity : 0.003 0.019 4092 Dihedral : 5.254 26.347 4092 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.46 % Favored : 92.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.13), residues: 4062 helix: 1.66 (0.11), residues: 1904 sheet: -1.25 (0.21), residues: 559 loop : -2.54 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 20 PHE 0.000 0.000 PHE A 12 TRP 0.000 0.000 TRP A 28 Details of bonding type rmsd covalent geometry : bond 0.00310 (20377) covalent geometry : angle 0.58685 (28358) hydrogen bonds : bond 0.05907 ( 1927) hydrogen bonds : angle 5.42143 ( 5643) *********************** 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 : 0.851 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0898 time to fit residues: 14.6160 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 : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 240 optimal weight: 20.0000 chunk 280 optimal weight: 8.9990 chunk 39 optimal weight: 20.0000 chunk 90 optimal weight: 7.9990 chunk 291 optimal weight: 20.0000 chunk 37 optimal weight: 0.5980 chunk 114 optimal weight: 8.9990 chunk 88 optimal weight: 30.0000 chunk 358 optimal weight: 20.0000 chunk 71 optimal weight: 7.9990 chunk 331 optimal weight: 50.0000 overall best weight: 6.9188 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.065788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.051448 restraints weight = 303229.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.051444 restraints weight = 286707.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.051444 restraints weight = 273480.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.051444 restraints weight = 273480.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.051444 restraints weight = 273480.329| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.8263 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= 0.253 Angle : 0.637 8.360 28358 Z= 0.407 Chirality : 0.043 0.149 3919 Planarity : 0.004 0.020 4092 Dihedral : 5.981 30.736 4092 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.82 % Favored : 90.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.13), residues: 4062 helix: 1.16 (0.11), residues: 1913 sheet: -1.24 (0.22), residues: 522 loop : -2.91 (0.14), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 20 PHE 0.000 0.000 PHE A 12 TRP 0.000 0.000 TRP A 28 Details of bonding type rmsd covalent geometry : bond 0.00347 (20377) covalent geometry : angle 0.63685 (28358) hydrogen bonds : bond 0.05908 ( 1927) hydrogen bonds : angle 5.97891 ( 5643) *********************** 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 : 0.800 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0864 time to fit residues: 13.9944 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 : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 157 optimal weight: 30.0000 chunk 235 optimal weight: 40.0000 chunk 181 optimal weight: 50.0000 chunk 14 optimal weight: 30.0000 chunk 126 optimal weight: 40.0000 chunk 186 optimal weight: 20.0000 chunk 356 optimal weight: 30.0000 chunk 308 optimal weight: 30.0000 chunk 47 optimal weight: 5.9990 chunk 185 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 overall best weight: 14.3994 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.063298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.048534 restraints weight = 306392.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.048654 restraints weight = 291583.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.048697 restraints weight = 277617.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.048699 restraints weight = 267720.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.048700 restraints weight = 267462.607| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.9928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 20377 Z= 0.467 Angle : 0.912 10.990 28358 Z= 0.594 Chirality : 0.047 0.212 3919 Planarity : 0.006 0.032 4092 Dihedral : 8.022 38.643 4092 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.34 % Allowed : 14.92 % Favored : 84.74 % 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 : 1.18 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.11 (0.12), residues: 4062 helix: -0.88 (0.11), residues: 1893 sheet: -1.65 (0.23), residues: 457 loop : -3.62 (0.13), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 20 PHE 0.000 0.000 PHE A 12 TRP 0.000 0.000 TRP A 28 Details of bonding type rmsd covalent geometry : bond 0.00644 (20377) covalent geometry : angle 0.91156 (28358) hydrogen bonds : bond 0.08594 ( 1927) hydrogen bonds : angle 7.96679 ( 5643) *********************** 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 : 0.551 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0869 time to fit residues: 14.0963 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 : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 342 optimal weight: 9.9990 chunk 369 optimal weight: 9.9990 chunk 183 optimal weight: 40.0000 chunk 149 optimal weight: 9.9990 chunk 77 optimal weight: 30.0000 chunk 344 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 272 optimal weight: 30.0000 chunk 381 optimal weight: 40.0000 chunk 337 optimal weight: 20.0000 chunk 229 optimal weight: 20.0000 overall best weight: 8.1788 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.064123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.049973 restraints weight = 302047.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.049699 restraints weight = 284930.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.049700 restraints weight = 271221.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 13)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.049700 restraints weight = 271116.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.049700 restraints weight = 271116.605| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 moved from start: 1.0077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 20377 Z= 0.278 Angle : 0.646 7.609 28358 Z= 0.414 Chirality : 0.043 0.148 3919 Planarity : 0.004 0.022 4092 Dihedral : 6.523 28.906 4092 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 12.80 % Favored : 87.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.13), residues: 4062 helix: 0.19 (0.11), residues: 1894 sheet: -1.76 (0.24), residues: 456 loop : -3.47 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 20 PHE 0.000 0.000 PHE A 12 TRP 0.000 0.000 TRP A 28 Details of bonding type rmsd covalent geometry : bond 0.00381 (20377) covalent geometry : angle 0.64551 (28358) hydrogen bonds : bond 0.06090 ( 1927) hydrogen bonds : angle 6.63031 ( 5643) *********************** 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 : 0.705 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0842 time to fit residues: 13.5937 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 : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 171 optimal weight: 10.0000 chunk 169 optimal weight: 20.0000 chunk 359 optimal weight: 6.9990 chunk 241 optimal weight: 20.0000 chunk 152 optimal weight: 20.0000 chunk 299 optimal weight: 7.9990 chunk 398 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 chunk 216 optimal weight: 8.9990 chunk 331 optimal weight: 7.9990 chunk 187 optimal weight: 0.0030 overall best weight: 6.3998 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.064378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.049172 restraints weight = 303745.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.049285 restraints weight = 291948.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.049341 restraints weight = 278733.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.049341 restraints weight = 271829.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.049341 restraints weight = 271829.733| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 1.0450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20377 Z= 0.221 Angle : 0.566 7.296 28358 Z= 0.360 Chirality : 0.043 0.146 3919 Planarity : 0.003 0.022 4092 Dihedral : 5.758 28.201 4092 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.42 % Favored : 86.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.13), residues: 4062 helix: 1.09 (0.12), residues: 1900 sheet: -1.82 (0.24), residues: 454 loop : -3.34 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 20 PHE 0.000 0.000 PHE A 12 TRP 0.000 0.000 TRP A 28 Details of bonding type rmsd covalent geometry : bond 0.00301 (20377) covalent geometry : angle 0.56646 (28358) hydrogen bonds : bond 0.05336 ( 1927) hydrogen bonds : angle 6.00728 ( 5643) *********************** 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 : 0.751 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0883 time to fit residues: 14.3143 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 : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 323 optimal weight: 8.9990 chunk 223 optimal weight: 20.0000 chunk 402 optimal weight: 8.9990 chunk 166 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 chunk 129 optimal weight: 50.0000 chunk 271 optimal weight: 30.0000 chunk 352 optimal weight: 9.9990 chunk 304 optimal weight: 20.0000 chunk 188 optimal weight: 0.5980 chunk 398 optimal weight: 20.0000 overall best weight: 7.1188 ------------------------------------------------------------------------------- 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 = 0.3429 r_free = 0.3429 target = 0.064159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.050303 restraints weight = 301543.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.050312 restraints weight = 288227.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.050312 restraints weight = 276384.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.050312 restraints weight = 276384.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.050312 restraints weight = 276384.245| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 1.0945 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= 0.251 Angle : 0.606 7.629 28358 Z= 0.388 Chirality : 0.043 0.148 3919 Planarity : 0.003 0.021 4092 Dihedral : 6.115 29.398 4092 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.07 % Favored : 86.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.13), residues: 4062 helix: 0.85 (0.12), residues: 1907 sheet: -1.73 (0.25), residues: 443 loop : -3.45 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 20 PHE 0.000 0.000 PHE A 12 TRP 0.000 0.000 TRP A 28 Details of bonding type rmsd covalent geometry : bond 0.00344 (20377) covalent geometry : angle 0.60630 (28358) hydrogen bonds : bond 0.05754 ( 1927) hydrogen bonds : angle 6.38216 ( 5643) *********************** 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 : 0.823 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0855 time to fit residues: 13.8689 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 : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 404 optimal weight: 40.0000 chunk 35 optimal weight: 40.0000 chunk 44 optimal weight: 0.4980 chunk 247 optimal weight: 10.0000 chunk 270 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 141 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 358 optimal weight: 0.9990 chunk 102 optimal weight: 50.0000 chunk 379 optimal weight: 4.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.064897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.050504 restraints weight = 302605.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.050314 restraints weight = 286718.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.050333 restraints weight = 273421.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.050429 restraints weight = 270773.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.050470 restraints weight = 259026.077| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 1.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20377 Z= 0.134 Angle : 0.467 6.924 28358 Z= 0.292 Chirality : 0.041 0.133 3919 Planarity : 0.002 0.021 4092 Dihedral : 5.071 26.332 4092 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.04 % Favored : 89.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.14), residues: 4062 helix: 1.97 (0.12), residues: 1904 sheet: -1.75 (0.24), residues: 482 loop : -3.19 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 20 PHE 0.000 0.000 PHE A 12 TRP 0.000 0.000 TRP A 28 Details of bonding type rmsd covalent geometry : bond 0.00180 (20377) covalent geometry : angle 0.46718 (28358) hydrogen bonds : bond 0.04360 ( 1927) hydrogen bonds : angle 5.40826 ( 5643) *********************** 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 : 0.712 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0830 time to fit residues: 13.3508 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 : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 389 optimal weight: 50.0000 chunk 224 optimal weight: 20.0000 chunk 400 optimal weight: 20.0000 chunk 280 optimal weight: 8.9990 chunk 229 optimal weight: 0.0980 chunk 270 optimal weight: 20.0000 chunk 114 optimal weight: 8.9990 chunk 6 optimal weight: 0.4980 chunk 208 optimal weight: 1.9990 chunk 175 optimal weight: 30.0000 chunk 332 optimal weight: 30.0000 overall best weight: 4.1186 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.064936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.050753 restraints weight = 297734.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.050738 restraints weight = 285670.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.050742 restraints weight = 278737.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.050742 restraints weight = 278185.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.050742 restraints weight = 278185.978| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 1.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20377 Z= 0.160 Angle : 0.476 6.795 28358 Z= 0.301 Chirality : 0.042 0.135 3919 Planarity : 0.002 0.019 4092 Dihedral : 4.981 25.225 4092 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.50 % Favored : 88.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.14), residues: 4062 helix: 2.10 (0.12), residues: 1917 sheet: -1.68 (0.24), residues: 461 loop : -3.15 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 20 PHE 0.000 0.000 PHE A 12 TRP 0.000 0.000 TRP A 28 Details of bonding type rmsd covalent geometry : bond 0.00218 (20377) covalent geometry : angle 0.47649 (28358) hydrogen bonds : bond 0.04459 ( 1927) hydrogen bonds : angle 5.36015 ( 5643) ********************** 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 : 0.796 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0857 time to fit residues: 13.7794 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 : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 199 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 382 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 212 optimal weight: 5.9990 chunk 129 optimal weight: 40.0000 chunk 133 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 367 optimal weight: 9.9990 chunk 350 optimal weight: 30.0000 chunk 84 optimal weight: 9.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.064434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.050372 restraints weight = 299064.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.050378 restraints weight = 289426.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.050378 restraints weight = 280552.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.050378 restraints weight = 280552.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.050378 restraints weight = 280552.316| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 1.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20377 Z= 0.202 Angle : 0.531 7.149 28358 Z= 0.338 Chirality : 0.042 0.140 3919 Planarity : 0.003 0.020 4092 Dihedral : 5.414 27.645 4092 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 13.02 % Favored : 86.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.14), residues: 4062 helix: 1.73 (0.12), residues: 1914 sheet: -1.73 (0.24), residues: 459 loop : -3.25 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 20 PHE 0.000 0.000 PHE A 12 TRP 0.000 0.000 TRP A 28 Details of bonding type rmsd covalent geometry : bond 0.00277 (20377) covalent geometry : angle 0.53148 (28358) hydrogen bonds : bond 0.04984 ( 1927) hydrogen bonds : angle 5.79063 ( 5643) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3788.34 seconds wall clock time: 65 minutes 7.15 seconds (3907.15 seconds total)