Starting phenix.real_space_refine (version: dev) on Sun Dec 18 15:15:13 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abf_11694/12_2022/7abf_11694_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abf_11694/12_2022/7abf_11694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abf_11694/12_2022/7abf_11694.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abf_11694/12_2022/7abf_11694.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abf_11694/12_2022/7abf_11694_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abf_11694/12_2022/7abf_11694_neut_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "I ARG 108": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A ARG 444": "NH1" <-> "NH2" Residue "A ARG 663": "NH1" <-> "NH2" Residue "A ARG 1086": "NH1" <-> "NH2" Residue "A ARG 1100": "NH1" <-> "NH2" Residue "A ARG 1195": "NH1" <-> "NH2" Residue "A ARG 1298": "NH1" <-> "NH2" Residue "A ARG 1414": "NH1" <-> "NH2" Residue "A ARG 1471": "NH1" <-> "NH2" Residue "A ARG 1748": "NH1" <-> "NH2" Residue "r ARG 645": "NH1" <-> "NH2" Residue "r ARG 785": "NH1" <-> "NH2" Residue "r ARG 888": "NH1" <-> "NH2" Residue "K ARG 385": "NH1" <-> "NH2" Residue "K ARG 388": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 25904 Number of models: 1 Model: "" Number of chains: 17 Chain: "Q" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 850 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 6, 'TRANS': 131} Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 371 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 172 Chain: "I" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1151 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 6, 'TRANS': 169} Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 389 Unresolved non-hydrogen dihedrals: 254 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 17, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 181 Chain: "A" Number of atoms: 10522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1656, 10522 Classifications: {'peptide': 1656} Incomplete info: {'truncation_to_alanine': 958} Link IDs: {'PTRANS': 91, 'TRANS': 1564} Chain breaks: 2 Unresolved non-hydrogen bonds: 3415 Unresolved non-hydrogen angles: 4325 Unresolved non-hydrogen dihedrals: 2744 Unresolved non-hydrogen chiralities: 297 Planarities with less than four sites: {'GLN:plan1': 56, 'HIS:plan': 25, 'TYR:plan': 26, 'ASN:plan1': 72, 'TRP:plan': 9, 'ASP:plan': 94, 'PHE:plan': 24, 'GLU:plan': 90, 'ARG:plan': 80} Unresolved non-hydrogen planarities: 2014 Chain: "r" Number of atoms: 5120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 844, 5120 Classifications: {'peptide': 844} Incomplete info: {'truncation_to_alanine': 477} Link IDs: {'PTRANS': 49, 'TRANS': 794} Unresolved non-hydrogen bonds: 1585 Unresolved non-hydrogen angles: 2002 Unresolved non-hydrogen dihedrals: 1263 Unresolved non-hydrogen chiralities: 150 Planarities with less than four sites: {'GLN:plan1': 23, 'HIS:plan': 7, 'TYR:plan': 8, 'ASN:plan1': 19, 'TRP:plan': 3, 'ASP:plan': 55, 'PHE:plan': 18, 'GLU:plan': 54, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 891 Chain: "N" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 295 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'TRANS': 55} Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 5, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 92 Chain: "q" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 523 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 72} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "R" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "5" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1220 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p_pur': 18, 'rna3p_pyr': 29} Link IDs: {'rna2p': 11, 'rna3p': 46} Chain: "6" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1392 Classifications: {'RNA': 65} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 31, 'rna3p_pyr': 21} Link IDs: {'rna2p': 12, 'rna3p': 52} Chain breaks: 1 Chain: "X" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 182 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 1, 'TRANS': 34} Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "v" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 275 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'TRANS': 54} Chain breaks: 1 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 92 Chain: "G" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 1604 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 262} Link IDs: {'PTRANS': 13, 'TRANS': 306} Unresolved non-hydrogen bonds: 968 Unresolved non-hydrogen angles: 1264 Unresolved non-hydrogen dihedrals: 823 Unresolved non-hydrogen chiralities: 98 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 20, 'TYR:plan': 8, 'ASN:plan1': 11, 'TRP:plan': 11, 'HIS:plan': 17, 'PHE:plan': 8, 'GLU:plan': 10, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 551 Chain: "Z" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 622 Classifications: {'RNA': 29} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 13, 'rna3p_pyr': 8} Link IDs: {'rna2p': 8, 'rna3p': 20} Chain: "K" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 799 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 2, 'TRANS': 120} Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 322 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 19, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 175 Chain: "A4" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1235 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 231} Link IDs: {'PTRANS': 2, 'TRANS': 243} Chain breaks: 2 Unresolved non-hydrogen bonds: 904 Unresolved non-hydrogen angles: 1121 Unresolved non-hydrogen dihedrals: 750 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 18, 'PHE:plan': 8, 'GLU:plan': 37, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 551 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.97, per 1000 atoms: 0.62 Number of scatterers: 25904 At special positions: 0 Unit cell: (168.2, 160.08, 168.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 161 15.00 Mg 1 11.99 O 5054 8.00 N 4756 7.00 C 15892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.62 Conformation dependent library (CDL) restraints added in 4.6 seconds 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7116 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 24 sheets defined 39.2% alpha, 6.2% beta 39 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 10.45 Creating SS restraints... Processing helix chain 'Q' and resid 13 through 15 No H-bonds generated for 'chain 'Q' and resid 13 through 15' Processing helix chain 'Q' and resid 19 through 33 Processing helix chain 'Q' and resid 44 through 64 Proline residue: Q 48 - end of helix removed outlier: 3.518A pdb=" N ILE Q 60 " --> pdb=" O THR Q 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 80 removed outlier: 5.309A pdb=" N ILE Q 79 " --> pdb=" O TYR Q 75 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 93 Processing helix chain 'I' and resid 23 through 30 Processing helix chain 'I' and resid 46 through 52 Processing helix chain 'I' and resid 69 through 80 Processing helix chain 'I' and resid 84 through 91 Processing helix chain 'I' and resid 98 through 109 Processing helix chain 'I' and resid 113 through 123 Proline residue: I 122 - end of helix Processing helix chain 'I' and resid 144 through 152 Processing helix chain 'I' and resid 168 through 174 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.951A pdb=" N LEU A 92 " --> pdb=" O TYR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 102 No H-bonds generated for 'chain 'A' and resid 99 through 102' Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 137 through 157 Processing helix chain 'A' and resid 232 through 242 removed outlier: 3.501A pdb=" N LEU A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 317 through 320 No H-bonds generated for 'chain 'A' and resid 317 through 320' Processing helix chain 'A' and resid 375 through 378 No H-bonds generated for 'chain 'A' and resid 375 through 378' Processing helix chain 'A' and resid 399 through 406 removed outlier: 3.811A pdb=" N LEU A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TRP A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 489 through 510 Processing helix chain 'A' and resid 544 through 565 Processing helix chain 'A' and resid 573 through 586 Processing helix chain 'A' and resid 597 through 616 removed outlier: 3.646A pdb=" N LYS A 609 " --> pdb=" O LYS A 606 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR A 613 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR A 614 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 660 Proline residue: A 646 - end of helix removed outlier: 4.043A pdb=" N ALA A 657 " --> pdb=" O GLY A 653 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG A 658 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 695 Processing helix chain 'A' and resid 708 through 722 Processing helix chain 'A' and resid 733 through 762 removed outlier: 3.500A pdb=" N ILE A 761 " --> pdb=" O ASN A 757 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG A 762 " --> pdb=" O ARG A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 796 Processing helix chain 'A' and resid 803 through 820 Processing helix chain 'A' and resid 835 through 850 Processing helix chain 'A' and resid 860 through 872 Processing helix chain 'A' and resid 874 through 887 Processing helix chain 'A' and resid 913 through 933 Processing helix chain 'A' and resid 947 through 960 Processing helix chain 'A' and resid 990 through 1000 Processing helix chain 'A' and resid 1003 through 1014 removed outlier: 3.812A pdb=" N ASN A1014 " --> pdb=" O THR A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1052 Processing helix chain 'A' and resid 1056 through 1062 Processing helix chain 'A' and resid 1077 through 1081 Processing helix chain 'A' and resid 1103 through 1116 Processing helix chain 'A' and resid 1144 through 1160 removed outlier: 3.910A pdb=" N ASN A1148 " --> pdb=" O LYS A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1248 Processing helix chain 'A' and resid 1256 through 1270 Processing helix chain 'A' and resid 1276 through 1280 removed outlier: 3.718A pdb=" N ASN A1280 " --> pdb=" O GLU A1276 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1276 through 1280' Processing helix chain 'A' and resid 1282 through 1299 removed outlier: 4.728A pdb=" N ARG A1298 " --> pdb=" O LYS A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1317 removed outlier: 3.876A pdb=" N TYR A1317 " --> pdb=" O VAL A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1339 No H-bonds generated for 'chain 'A' and resid 1337 through 1339' Processing helix chain 'A' and resid 1368 through 1371 Processing helix chain 'A' and resid 1375 through 1399 removed outlier: 4.353A pdb=" N ALA A1387 " --> pdb=" O GLN A1383 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU A1388 " --> pdb=" O ARG A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1405 through 1409 Processing helix chain 'A' and resid 1419 through 1422 No H-bonds generated for 'chain 'A' and resid 1419 through 1422' Processing helix chain 'A' and resid 1427 through 1431 Processing helix chain 'A' and resid 1437 through 1444 removed outlier: 4.659A pdb=" N GLN A1444 " --> pdb=" O THR A1440 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1477 Processing helix chain 'A' and resid 1480 through 1484 Processing helix chain 'A' and resid 1529 through 1537 Processing helix chain 'A' and resid 1539 through 1542 No H-bonds generated for 'chain 'A' and resid 1539 through 1542' Processing helix chain 'A' and resid 1567 through 1576 Processing helix chain 'A' and resid 1581 through 1599 Processing helix chain 'A' and resid 1671 through 1673 No H-bonds generated for 'chain 'A' and resid 1671 through 1673' Processing helix chain 'A' and resid 1676 through 1689 Processing helix chain 'A' and resid 1723 through 1734 Processing helix chain 'A' and resid 1738 through 1751 Processing helix chain 'r' and resid 116 through 123 Processing helix chain 'r' and resid 143 through 153 Processing helix chain 'r' and resid 173 through 177 Processing helix chain 'r' and resid 209 through 220 removed outlier: 4.498A pdb=" N ARG r 220 " --> pdb=" O THR r 216 " (cutoff:3.500A) Processing helix chain 'r' and resid 237 through 249 removed outlier: 4.300A pdb=" N LYS r 244 " --> pdb=" O GLU r 240 " (cutoff:3.500A) Processing helix chain 'r' and resid 261 through 264 No H-bonds generated for 'chain 'r' and resid 261 through 264' Processing helix chain 'r' and resid 271 through 292 Processing helix chain 'r' and resid 320 through 331 Processing helix chain 'r' and resid 336 through 339 No H-bonds generated for 'chain 'r' and resid 336 through 339' Processing helix chain 'r' and resid 368 through 372 Processing helix chain 'r' and resid 374 through 385 Processing helix chain 'r' and resid 391 through 399 removed outlier: 4.479A pdb=" N GLU r 398 " --> pdb=" O ARG r 394 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU r 399 " --> pdb=" O THR r 395 " (cutoff:3.500A) Processing helix chain 'r' and resid 407 through 409 No H-bonds generated for 'chain 'r' and resid 407 through 409' Processing helix chain 'r' and resid 412 through 423 Processing helix chain 'r' and resid 431 through 434 No H-bonds generated for 'chain 'r' and resid 431 through 434' Processing helix chain 'r' and resid 441 through 452 removed outlier: 5.107A pdb=" N LYS r 446 " --> pdb=" O LYS r 442 " (cutoff:3.500A) Proline residue: r 447 - end of helix Processing helix chain 'r' and resid 460 through 465 Processing helix chain 'r' and resid 600 through 613 Processing helix chain 'r' and resid 634 through 646 Processing helix chain 'r' and resid 694 through 701 Processing helix chain 'r' and resid 711 through 720 Processing helix chain 'r' and resid 726 through 730 Processing helix chain 'r' and resid 737 through 739 No H-bonds generated for 'chain 'r' and resid 737 through 739' Processing helix chain 'r' and resid 756 through 761 Processing helix chain 'r' and resid 763 through 774 Processing helix chain 'r' and resid 805 through 807 No H-bonds generated for 'chain 'r' and resid 805 through 807' Processing helix chain 'r' and resid 809 through 821 Processing helix chain 'r' and resid 840 through 853 Processing helix chain 'r' and resid 883 through 890 removed outlier: 3.536A pdb=" N HIS r 890 " --> pdb=" O ASP r 886 " (cutoff:3.500A) Processing helix chain 'r' and resid 927 through 941 removed outlier: 4.114A pdb=" N ALA r 930 " --> pdb=" O PRO r 927 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS r 941 " --> pdb=" O ARG r 938 " (cutoff:3.500A) Processing helix chain 'r' and resid 949 through 952 No H-bonds generated for 'chain 'r' and resid 949 through 952' Processing helix chain 'N' and resid 93 through 99 removed outlier: 4.058A pdb=" N HIS N 98 " --> pdb=" O ASN N 94 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE N 99 " --> pdb=" O PHE N 95 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 108 Processing helix chain 'N' and resid 118 through 131 removed outlier: 3.587A pdb=" N VAL N 122 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL N 128 " --> pdb=" O LYS N 124 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 35 Processing helix chain 'q' and resid 57 through 60 No H-bonds generated for 'chain 'q' and resid 57 through 60' Processing helix chain 'R' and resid 219 through 224 Processing helix chain 'X' and resid 25 through 47 Processing helix chain 'X' and resid 54 through 57 No H-bonds generated for 'chain 'X' and resid 54 through 57' Processing helix chain 'v' and resid 138 through 158 Processing helix chain 'v' and resid 283 through 312 Processing helix chain 'K' and resid 272 through 313 removed outlier: 3.563A pdb=" N GLU K 277 " --> pdb=" O GLU K 273 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS K 280 " --> pdb=" O TYR K 276 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG K 291 " --> pdb=" O ILE K 287 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU K 297 " --> pdb=" O ASP K 293 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU K 298 " --> pdb=" O ARG K 294 " (cutoff:3.500A) Processing helix chain 'A4' and resid 700 through 720 Processing helix chain 'A4' and resid 857 through 890 Processing helix chain 'A4' and resid 897 through 909 Processing helix chain 'A4' and resid 918 through 927 removed outlier: 5.120A pdb=" N LYSA4 927 " --> pdb=" O ARGA4 923 " (cutoff:3.500A) Processing helix chain 'A4' and resid 931 through 934 removed outlier: 3.694A pdb=" N GLYA4 934 " --> pdb=" O TRPA4 931 " (cutoff:3.500A) No H-bonds generated for 'chain 'A4' and resid 931 through 934' Processing helix chain 'A4' and resid 939 through 966 Processing helix chain 'A4' and resid 977 through 986 removed outlier: 4.404A pdb=" N LYSA4 982 " --> pdb=" O LYSA4 978 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILEA4 983 " --> pdb=" O GLUA4 979 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLUA4 986 " --> pdb=" O LYSA4 982 " (cutoff:3.500A) Processing helix chain 'A4' and resid 988 through 991 No H-bonds generated for 'chain 'A4' and resid 988 through 991' Processing helix chain 'A4' and resid 997 through 1025 Processing helix chain 'A4' and resid 1031 through 1039 removed outlier: 3.522A pdb=" N LYSA41034 " --> pdb=" O TYRA41031 " (cutoff:3.500A) Processing helix chain 'A4' and resid 1041 through 1050 Processing helix chain 'A4' and resid 1055 through 1059 Processing helix chain 'A4' and resid 1064 through 1079 Processing sheet with id= A, first strand: chain 'I' and resid 129 through 133 Processing sheet with id= B, first strand: chain 'A' and resid 118 through 120 Processing sheet with id= C, first strand: chain 'A' and resid 896 through 898 Processing sheet with id= D, first strand: chain 'A' and resid 1174 through 1178 removed outlier: 3.770A pdb=" N CYS A 973 " --> pdb=" O PHE A1101 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A1101 " --> pdb=" O CYS A 973 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 975 " --> pdb=" O PHE A1099 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG A1100 " --> pdb=" O ILE A1085 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE A1085 " --> pdb=" O ARG A1100 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1186 through 1188 Processing sheet with id= F, first strand: chain 'A' and resid 1341 through 1345 removed outlier: 3.813A pdb=" N LYS A1344 " --> pdb=" O THR A1351 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR A1351 " --> pdb=" O LYS A1344 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1659 through 1662 removed outlier: 3.854A pdb=" N PHE A1632 " --> pdb=" O THR A1608 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR A1608 " --> pdb=" O PHE A1632 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1665 through 1667 Processing sheet with id= I, first strand: chain 'r' and resid 130 through 133 removed outlier: 3.857A pdb=" N TYR r 198 " --> pdb=" O LEU r 190 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU r 190 " --> pdb=" O TYR r 198 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE r 200 " --> pdb=" O VAL r 188 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'r' and resid 226 through 230 removed outlier: 7.019A pdb=" N THR r 254 " --> pdb=" O LEU r 227 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ILE r 229 " --> pdb=" O THR r 254 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N CYS r 256 " --> pdb=" O ILE r 229 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'r' and resid 348 through 350 Processing sheet with id= L, first strand: chain 'r' and resid 480 through 482 removed outlier: 3.725A pdb=" N LYS r 480 " --> pdb=" O PHE r 493 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY r 494 " --> pdb=" O VAL r 550 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL r 550 " --> pdb=" O GLY r 494 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN r 548 " --> pdb=" O VAL r 496 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'r' and resid 523 through 526 removed outlier: 3.518A pdb=" N THR r 566 " --> pdb=" O LYS r 508 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR r 564 " --> pdb=" O LEU r 510 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'r' and resid 663 through 666 removed outlier: 3.549A pdb=" N CYS r 663 " --> pdb=" O MET r 828 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'r' and resid 674 through 677 removed outlier: 4.125A pdb=" N CYS r 674 " --> pdb=" O MET r 687 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET r 687 " --> pdb=" O CYS r 674 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP r 793 " --> pdb=" O THR r 686 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE r 688 " --> pdb=" O ILE r 791 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ILE r 791 " --> pdb=" O ILE r 688 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N GLU r 690 " --> pdb=" O PHE r 789 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N PHE r 789 " --> pdb=" O GLU r 690 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'r' and resid 831 through 838 removed outlier: 3.557A pdb=" N ILE r 875 " --> pdb=" O TYR r 832 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU r 868 " --> pdb=" O ILE r 863 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE r 874 " --> pdb=" O VAL r 857 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL r 857 " --> pdb=" O PHE r 874 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'r' and resid 475 through 478 removed outlier: 3.711A pdb=" N SER r 498 " --> pdb=" O MET r 475 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N HIS r 477 " --> pdb=" O VAL r 496 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL r 496 " --> pdb=" O HIS r 477 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'q' and resid 4 through 6 Processing sheet with id= S, first strand: chain 'q' and resid 42 through 45 Processing sheet with id= T, first strand: chain 'G' and resid 194 through 196 Processing sheet with id= U, first strand: chain 'G' and resid 210 through 212 Processing sheet with id= V, first strand: chain 'G' and resid 251 through 254 Processing sheet with id= W, first strand: chain 'G' and resid 291 through 296 removed outlier: 6.807A pdb=" N CYS G 306 " --> pdb=" O TYR G 292 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU G 294 " --> pdb=" O VAL G 304 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL G 304 " --> pdb=" O LEU G 294 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 416 through 419 removed outlier: 6.720A pdb=" N GLY G 430 " --> pdb=" O ASN G 417 " (cutoff:3.500A) 1055 hydrogen bonds defined for protein. 2943 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 93 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 12.05 Time building geometry restraints manager: 12.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6635 1.33 - 1.45: 5596 1.45 - 1.57: 14157 1.57 - 1.69: 311 1.69 - 1.81: 73 Bond restraints: 26772 Sorted by residual: bond pdb=" C GLY r 141 " pdb=" N LYS r 142 " ideal model delta sigma weight residual 1.333 1.406 -0.073 1.34e-02 5.57e+03 2.97e+01 bond pdb=" C GLY r 141 " pdb=" O GLY r 141 " ideal model delta sigma weight residual 1.235 1.287 -0.052 1.35e-02 5.49e+03 1.49e+01 bond pdb=" N LYS K 390 " pdb=" CA LYS K 390 " ideal model delta sigma weight residual 1.458 1.489 -0.031 9.00e-03 1.23e+04 1.15e+01 bond pdb=" N VAL G 379 " pdb=" CA VAL G 379 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.21e-02 6.83e+03 8.74e+00 bond pdb=" N VAL K 380 " pdb=" CA VAL K 380 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.69e+00 ... (remaining 26767 not shown) Histogram of bond angle deviations from ideal: 98.39 - 106.81: 1743 106.81 - 115.23: 15806 115.23 - 123.65: 18853 123.65 - 132.07: 1237 132.07 - 140.49: 77 Bond angle restraints: 37716 Sorted by residual: angle pdb=" C GLY r 141 " pdb=" N LYS r 142 " pdb=" CA LYS r 142 " ideal model delta sigma weight residual 122.17 103.76 18.41 1.54e+00 4.22e-01 1.43e+02 angle pdb=" PA GTP r1500 " pdb=" O3A GTP r1500 " pdb=" PB GTP r1500 " ideal model delta sigma weight residual 120.50 140.49 -19.99 3.00e+00 1.11e-01 4.44e+01 angle pdb=" CA GLY r 141 " pdb=" C GLY r 141 " pdb=" O GLY r 141 " ideal model delta sigma weight residual 120.57 109.05 11.52 1.74e+00 3.30e-01 4.39e+01 angle pdb=" PB GTP r1500 " pdb=" O3B GTP r1500 " pdb=" PG GTP r1500 " ideal model delta sigma weight residual 120.50 136.20 -15.70 3.00e+00 1.11e-01 2.74e+01 angle pdb=" CA GLY r 141 " pdb=" C GLY r 141 " pdb=" N LYS r 142 " ideal model delta sigma weight residual 116.69 124.80 -8.11 2.04e+00 2.40e-01 1.58e+01 ... (remaining 37711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 15077 35.89 - 71.78: 132 71.78 - 107.68: 18 107.68 - 143.57: 1 143.57 - 179.46: 3 Dihedral angle restraints: 15231 sinusoidal: 4307 harmonic: 10924 Sorted by residual: dihedral pdb=" O4' C 5 23 " pdb=" C1' C 5 23 " pdb=" N1 C 5 23 " pdb=" C2 C 5 23 " ideal model delta sinusoidal sigma weight residual 200.00 45.55 154.45 1 1.50e+01 4.44e-03 8.12e+01 dihedral pdb=" O4' C 6 37 " pdb=" C1' C 6 37 " pdb=" N1 C 6 37 " pdb=" C2 C 6 37 " ideal model delta sinusoidal sigma weight residual -128.00 51.46 -179.46 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" C5' GTP r1500 " pdb=" O5' GTP r1500 " pdb=" PA GTP r1500 " pdb=" O3A GTP r1500 " ideal model delta sinusoidal sigma weight residual 69.27 -168.03 -122.70 1 2.00e+01 2.50e-03 3.70e+01 ... (remaining 15228 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.006: 4672 1.006 - 2.011: 0 2.011 - 3.017: 0 3.017 - 4.023: 0 4.023 - 5.028: 3 Chirality restraints: 4675 Sorted by residual: chirality pdb=" C4 IHP A3001 " pdb=" C3 IHP A3001 " pdb=" C5 IHP A3001 " pdb=" O14 IHP A3001 " both_signs ideal model delta sigma weight residual False 2.48 -2.55 5.03 2.00e-01 2.50e+01 6.32e+02 chirality pdb=" C2 IHP A3001 " pdb=" C1 IHP A3001 " pdb=" C3 IHP A3001 " pdb=" O12 IHP A3001 " both_signs ideal model delta sigma weight residual False -2.52 2.29 -4.81 2.00e-01 2.50e+01 5.78e+02 chirality pdb=" C1 IHP A3001 " pdb=" C2 IHP A3001 " pdb=" C6 IHP A3001 " pdb=" O11 IHP A3001 " both_signs ideal model delta sigma weight residual False 2.32 -2.47 4.78 2.00e-01 2.50e+01 5.72e+02 ... (remaining 4672 not shown) Planarity restraints: 4463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 167 " -0.045 5.00e-02 4.00e+02 6.75e-02 7.28e+00 pdb=" N PRO A 168 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 168 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 168 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 108 " -0.036 5.00e-02 4.00e+02 5.45e-02 4.76e+00 pdb=" N PRO A 109 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 109 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 109 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 946 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO A 947 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 947 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 947 " 0.030 5.00e-02 4.00e+02 ... (remaining 4460 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 45 2.38 - 3.01: 14259 3.01 - 3.64: 39636 3.64 - 4.27: 51856 4.27 - 4.90: 82404 Nonbonded interactions: 188200 Sorted by model distance: nonbonded pdb=" N1 G 5 24 " pdb=" N3 G 5 57 " model vdw 1.747 2.600 nonbonded pdb=" N2 G 5 24 " pdb=" O2' G 5 57 " model vdw 1.860 2.520 nonbonded pdb=" O GLY r 141 " pdb=" CD2 PHE r 228 " model vdw 1.972 3.340 nonbonded pdb=" N GLN r 313 " pdb=" N2 GTP r1500 " model vdw 1.980 2.560 nonbonded pdb=" C6 G 5 24 " pdb=" N3 G 5 57 " model vdw 2.052 3.340 ... (remaining 188195 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 161 5.49 5 Mg 1 5.21 5 S 40 5.16 5 C 15892 2.51 5 N 4756 2.21 5 O 5054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 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: 0.040 Extract box with map and model: 14.970 Check model and map are aligned: 0.450 Convert atoms to be neutral: 0.220 Process input model: 78.240 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 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 : 0.004 0.073 26772 Z= 0.254 Angle : 0.692 19.992 37716 Z= 0.348 Chirality : 0.130 5.028 4675 Planarity : 0.004 0.067 4463 Dihedral : 11.140 179.460 8115 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.82 % Favored : 88.10 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.12), residues: 3698 helix: -0.81 (0.12), residues: 1536 sheet: -3.66 (0.22), residues: 349 loop : -3.87 (0.13), residues: 1813 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 377 time to evaluate : 2.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 379 average time/residue: 0.3735 time to fit residues: 222.8730 Evaluate side-chains 218 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 2.702 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 320 optimal weight: 0.0010 chunk 288 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 153 optimal weight: 0.2980 chunk 297 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 221 optimal weight: 0.0770 chunk 345 optimal weight: 6.9990 overall best weight: 0.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 54 HIS A 336 ASN A 601 GLN A1586 HIS r 137 HIS r 208 HIS ** r 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.078 26772 Z= 0.158 Angle : 0.571 11.240 37716 Z= 0.281 Chirality : 0.042 0.461 4675 Planarity : 0.004 0.060 4463 Dihedral : 10.853 177.930 5707 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.60 % Favored : 90.37 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.13), residues: 3698 helix: 0.40 (0.13), residues: 1559 sheet: -3.26 (0.22), residues: 357 loop : -3.45 (0.14), residues: 1782 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 234 time to evaluate : 2.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 15 residues processed: 254 average time/residue: 0.3188 time to fit residues: 138.3319 Evaluate side-chains 224 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 209 time to evaluate : 2.661 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2625 time to fit residues: 10.4816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 191 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 287 optimal weight: 0.4980 chunk 234 optimal weight: 0.5980 chunk 95 optimal weight: 0.0020 chunk 345 optimal weight: 7.9990 chunk 373 optimal weight: 6.9990 chunk 307 optimal weight: 10.0000 chunk 342 optimal weight: 5.9990 chunk 117 optimal weight: 0.0570 chunk 277 optimal weight: 2.9990 overall best weight: 0.8308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1586 HIS r 140 HIS r 208 HIS r 238 ASN ** r 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 903 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 26772 Z= 0.172 Angle : 0.555 10.528 37716 Z= 0.275 Chirality : 0.041 0.251 4675 Planarity : 0.004 0.060 4463 Dihedral : 10.768 179.212 5707 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.14), residues: 3698 helix: 1.11 (0.13), residues: 1562 sheet: -2.81 (0.24), residues: 353 loop : -3.22 (0.14), residues: 1783 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 223 time to evaluate : 3.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 238 average time/residue: 0.3233 time to fit residues: 131.8456 Evaluate side-chains 211 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 200 time to evaluate : 2.692 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.2278 time to fit residues: 8.1932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 341 optimal weight: 9.9990 chunk 259 optimal weight: 0.2980 chunk 179 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 164 optimal weight: 7.9990 chunk 232 optimal weight: 7.9990 chunk 346 optimal weight: 9.9990 chunk 367 optimal weight: 20.0000 chunk 181 optimal weight: 4.9990 chunk 328 optimal weight: 40.0000 chunk 98 optimal weight: 0.5980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 54 HIS A 105 ASN ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 26772 Z= 0.296 Angle : 0.654 13.261 37716 Z= 0.336 Chirality : 0.044 0.198 4675 Planarity : 0.005 0.065 4463 Dihedral : 11.177 177.772 5707 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.63 % Favored : 88.32 % Rotamer Outliers : 4.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.14), residues: 3698 helix: 1.10 (0.14), residues: 1558 sheet: -2.64 (0.24), residues: 369 loop : -3.23 (0.14), residues: 1771 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 201 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 22 residues processed: 234 average time/residue: 0.3161 time to fit residues: 129.3262 Evaluate side-chains 205 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 183 time to evaluate : 2.964 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2561 time to fit residues: 14.0118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 305 optimal weight: 8.9990 chunk 208 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 273 optimal weight: 8.9990 chunk 151 optimal weight: 0.9980 chunk 313 optimal weight: 8.9990 chunk 253 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 329 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 26772 Z= 0.262 Angle : 0.617 11.425 37716 Z= 0.312 Chirality : 0.043 0.231 4675 Planarity : 0.004 0.067 4463 Dihedral : 11.189 178.862 5707 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Rotamer Outliers : 3.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.14), residues: 3698 helix: 1.25 (0.14), residues: 1560 sheet: -2.45 (0.25), residues: 377 loop : -3.14 (0.14), residues: 1761 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 203 time to evaluate : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 13 residues processed: 231 average time/residue: 0.3060 time to fit residues: 122.5258 Evaluate side-chains 195 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 182 time to evaluate : 2.547 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2234 time to fit residues: 8.9045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 123 optimal weight: 9.9990 chunk 330 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 215 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 367 optimal weight: 6.9990 chunk 305 optimal weight: 5.9990 chunk 170 optimal weight: 0.0470 chunk 30 optimal weight: 0.0370 chunk 121 optimal weight: 0.9990 chunk 193 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 GLN A1096 HIS ** r 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 286 ASN ** r 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 328 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 26772 Z= 0.154 Angle : 0.563 11.884 37716 Z= 0.279 Chirality : 0.041 0.190 4675 Planarity : 0.004 0.071 4463 Dihedral : 11.002 179.345 5707 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.15), residues: 3698 helix: 1.59 (0.14), residues: 1563 sheet: -2.27 (0.25), residues: 376 loop : -2.97 (0.14), residues: 1759 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 203 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 216 average time/residue: 0.3259 time to fit residues: 122.3108 Evaluate side-chains 199 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 188 time to evaluate : 2.712 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2606 time to fit residues: 8.9707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 354 optimal weight: 0.1980 chunk 41 optimal weight: 0.9990 chunk 209 optimal weight: 9.9990 chunk 268 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 309 optimal weight: 9.9990 chunk 205 optimal weight: 0.6980 chunk 366 optimal weight: 20.0000 chunk 229 optimal weight: 9.9990 chunk 223 optimal weight: 0.4980 chunk 169 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: r 175 GLN ** r 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 26772 Z= 0.142 Angle : 0.551 15.545 37716 Z= 0.269 Chirality : 0.040 0.201 4675 Planarity : 0.004 0.061 4463 Dihedral : 10.831 178.411 5707 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.15), residues: 3698 helix: 1.84 (0.14), residues: 1558 sheet: -1.99 (0.26), residues: 375 loop : -2.83 (0.14), residues: 1765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 209 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 220 average time/residue: 0.3176 time to fit residues: 120.3697 Evaluate side-chains 199 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 192 time to evaluate : 2.343 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2630 time to fit residues: 6.7114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 226 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 232 optimal weight: 7.9990 chunk 249 optimal weight: 6.9990 chunk 181 optimal weight: 0.0970 chunk 34 optimal weight: 0.9990 chunk 287 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 HIS ** r 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 26772 Z= 0.249 Angle : 0.610 17.842 37716 Z= 0.305 Chirality : 0.042 0.293 4675 Planarity : 0.004 0.069 4463 Dihedral : 11.054 179.694 5707 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.14 % Favored : 88.86 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.15), residues: 3698 helix: 1.60 (0.14), residues: 1573 sheet: -1.83 (0.26), residues: 372 loop : -2.95 (0.14), residues: 1753 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 191 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 206 average time/residue: 0.3202 time to fit residues: 115.6735 Evaluate side-chains 197 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 184 time to evaluate : 2.696 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2591 time to fit residues: 9.7535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 333 optimal weight: 30.0000 chunk 350 optimal weight: 3.9990 chunk 320 optimal weight: 30.0000 chunk 341 optimal weight: 20.0000 chunk 205 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 268 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 308 optimal weight: 7.9990 chunk 322 optimal weight: 10.0000 chunk 340 optimal weight: 20.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** r 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.090 26772 Z= 0.346 Angle : 0.699 17.478 37716 Z= 0.358 Chirality : 0.045 0.269 4675 Planarity : 0.005 0.077 4463 Dihedral : 11.599 179.900 5707 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.98 % Favored : 86.97 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.14), residues: 3698 helix: 1.02 (0.13), residues: 1580 sheet: -1.97 (0.26), residues: 365 loop : -3.06 (0.14), residues: 1753 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 2.755 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 197 average time/residue: 0.3204 time to fit residues: 109.6829 Evaluate side-chains 185 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 174 time to evaluate : 2.720 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2425 time to fit residues: 8.5260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.4066 > 50: distance: 72 - 75: 5.069 distance: 75 - 76: 7.126 distance: 76 - 77: 3.842 distance: 76 - 79: 8.499 distance: 77 - 78: 5.165 distance: 77 - 80: 18.434 distance: 80 - 81: 9.947 distance: 81 - 82: 10.345 distance: 81 - 84: 5.270 distance: 82 - 83: 7.485 distance: 82 - 85: 11.057 distance: 85 - 86: 12.262 distance: 86 - 87: 13.274 distance: 87 - 88: 14.279 distance: 87 - 90: 8.899 distance: 90 - 91: 3.324 distance: 91 - 92: 5.502 distance: 91 - 94: 7.586 distance: 92 - 93: 30.481 distance: 92 - 95: 10.575 distance: 95 - 96: 27.889 distance: 96 - 97: 17.153 distance: 96 - 99: 27.661 distance: 97 - 98: 14.641 distance: 101 - 102: 24.944 distance: 101 - 104: 8.656 distance: 102 - 103: 31.481 distance: 102 - 105: 18.881 distance: 103 - 132: 12.458 distance: 106 - 107: 16.075 distance: 106 - 109: 14.834 distance: 107 - 108: 6.547 distance: 107 - 116: 15.294 distance: 109 - 110: 14.440 distance: 110 - 111: 8.099 distance: 110 - 112: 13.556 distance: 111 - 113: 19.487 distance: 112 - 114: 25.042 distance: 113 - 115: 12.717 distance: 114 - 115: 19.497 distance: 116 - 117: 4.197 distance: 117 - 118: 9.188 distance: 117 - 120: 11.960 distance: 118 - 119: 4.286 distance: 118 - 123: 9.358 distance: 120 - 121: 8.328 distance: 120 - 122: 10.090 distance: 123 - 124: 4.061 distance: 124 - 125: 20.231 distance: 124 - 127: 18.215 distance: 125 - 126: 13.957 distance: 125 - 132: 6.378 distance: 127 - 128: 15.739 distance: 128 - 129: 14.535 distance: 129 - 130: 6.730 distance: 129 - 131: 9.572 distance: 132 - 133: 6.634 distance: 133 - 134: 8.482 distance: 133 - 136: 11.228 distance: 134 - 135: 15.153 distance: 134 - 137: 5.021