Starting phenix.real_space_refine on Mon Feb 19 22:06:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abf_11694/02_2024/7abf_11694_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abf_11694/02_2024/7abf_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_11694/02_2024/7abf_11694.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abf_11694/02_2024/7abf_11694.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abf_11694/02_2024/7abf_11694_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7abf_11694/02_2024/7abf_11694_neut_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 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. 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-5238/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: 15.22, per 1000 atoms: 0.59 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: 11.58 Conformation dependent library (CDL) restraints added in 5.4 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: 12.48 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: 11.19 Time building geometry restraints manager: 12.30 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: 15359 35.89 - 71.78: 350 71.78 - 107.68: 56 107.68 - 143.57: 7 143.57 - 179.46: 3 Dihedral angle restraints: 15775 sinusoidal: 4851 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 15772 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 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: 7.200 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: 19.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 79.030 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 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 : 15.385 179.460 8659 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.82 % Favored : 88.10 % Rotamer: Outliers : 0.19 % Allowed : 5.71 % Favored : 94.10 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1582 HIS 0.011 0.002 HIS A 884 PHE 0.025 0.002 PHE A 316 TYR 0.020 0.002 TYR A 580 ARG 0.007 0.001 ARG A1544 *********************** 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 : 3.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 26 ASP cc_start: 0.7416 (t70) cc_final: 0.7214 (t70) REVERT: A 108 MET cc_start: 0.2699 (mmp) cc_final: 0.2278 (mmt) REVERT: A 651 TRP cc_start: 0.7959 (m-10) cc_final: 0.7675 (m-10) outliers start: 2 outliers final: 0 residues processed: 379 average time/residue: 0.3933 time to fit residues: 232.7337 Evaluate side-chains 219 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 2.816 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN A 601 GLN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 26772 Z= 0.159 Angle : 0.580 11.540 37716 Z= 0.285 Chirality : 0.042 0.578 4675 Planarity : 0.004 0.059 4463 Dihedral : 15.865 178.253 6251 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.57 % Favored : 90.40 % Rotamer: Outliers : 3.00 % Allowed : 13.06 % Favored : 83.95 % 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: -2.48 (0.14), residues: 3698 helix: 0.46 (0.13), residues: 1560 sheet: -3.23 (0.22), residues: 359 loop : -3.40 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 35 HIS 0.005 0.001 HIS A 884 PHE 0.021 0.001 PHE A 640 TYR 0.026 0.002 TYR A 256 ARG 0.006 0.001 ARG r 888 *********************** 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 263 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 232 time to evaluate : 2.578 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: A 331 TRP cc_start: 0.7107 (OUTLIER) cc_final: 0.6621 (t-100) REVERT: A 651 TRP cc_start: 0.8181 (m-10) cc_final: 0.7735 (m-10) outliers start: 31 outliers final: 17 residues processed: 252 average time/residue: 0.3311 time to fit residues: 141.3622 Evaluate side-chains 222 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 204 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 161 ILE Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1247 ILE Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain r residue 189 VAL Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain K residue 385 ARG Chi-restraints excluded: chain K residue 393 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 191 optimal weight: 0.5980 chunk 107 optimal weight: 0.0170 chunk 287 optimal weight: 4.9990 chunk 234 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 345 optimal weight: 6.9990 chunk 373 optimal weight: 7.9990 chunk 307 optimal weight: 7.9990 chunk 342 optimal weight: 5.9990 chunk 117 optimal weight: 0.6980 chunk 277 optimal weight: 2.9990 overall best weight: 1.2622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26772 Z= 0.228 Angle : 0.596 11.693 37716 Z= 0.301 Chirality : 0.042 0.256 4675 Planarity : 0.004 0.061 4463 Dihedral : 15.887 178.640 6251 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer: Outliers : 4.55 % Allowed : 13.54 % Favored : 81.91 % 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: -1.89 (0.14), residues: 3698 helix: 1.10 (0.14), residues: 1555 sheet: -2.79 (0.23), residues: 376 loop : -3.24 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A1263 HIS 0.013 0.002 HIS A1712 PHE 0.021 0.002 PHE K 347 TYR 0.027 0.002 TYR A 925 ARG 0.008 0.001 ARG I 156 *********************** 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 264 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 217 time to evaluate : 2.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 161 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8646 (mt) REVERT: A 108 MET cc_start: 0.4791 (mmp) cc_final: 0.3876 (mmp) REVERT: A 651 TRP cc_start: 0.8471 (m-10) cc_final: 0.8053 (m-10) REVERT: A 1267 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8497 (tt) REVERT: A 1730 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7137 (tmm) REVERT: r 172 PHE cc_start: 0.7611 (m-80) cc_final: 0.7328 (m-10) outliers start: 47 outliers final: 25 residues processed: 248 average time/residue: 0.3249 time to fit residues: 136.9177 Evaluate side-chains 217 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 189 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 161 ILE Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1101 PHE Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1274 PHE Chi-restraints excluded: chain A residue 1454 TRP Chi-restraints excluded: chain A residue 1730 MET Chi-restraints excluded: chain r residue 137 HIS Chi-restraints excluded: chain r residue 149 LEU Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain r residue 189 VAL Chi-restraints excluded: chain r residue 604 LEU Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain q residue 64 ASP Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain K residue 380 VAL Chi-restraints excluded: chain K residue 385 ARG Chi-restraints excluded: chain K residue 393 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 341 optimal weight: 20.0000 chunk 259 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 232 optimal weight: 7.9990 chunk 346 optimal weight: 20.0000 chunk 367 optimal weight: 10.0000 chunk 181 optimal weight: 0.9990 chunk 328 optimal weight: 40.0000 chunk 98 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 140 HIS r 238 ASN ** 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: 0.7635 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.134 26772 Z= 0.332 Angle : 0.676 13.888 37716 Z= 0.348 Chirality : 0.044 0.199 4675 Planarity : 0.005 0.083 4463 Dihedral : 16.098 177.183 6251 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.82 % Favored : 88.13 % Rotamer: Outliers : 7.16 % Allowed : 14.12 % Favored : 78.72 % 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: -1.94 (0.14), residues: 3698 helix: 0.99 (0.14), residues: 1555 sheet: -2.63 (0.24), residues: 370 loop : -3.26 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP I 35 HIS 0.010 0.002 HIS A 610 PHE 0.019 0.002 PHE A 582 TYR 0.029 0.003 TYR A 208 ARG 0.016 0.001 ARG A 635 *********************** 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 266 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 192 time to evaluate : 2.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 29 MET cc_start: 0.8508 (tpp) cc_final: 0.8295 (ttt) REVERT: I 105 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8771 (tm) REVERT: I 128 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7345 (mtp180) REVERT: A 430 TRP cc_start: 0.8591 (OUTLIER) cc_final: 0.7506 (m-10) REVERT: A 651 TRP cc_start: 0.8740 (m-10) cc_final: 0.8249 (m-10) REVERT: A 1474 MET cc_start: 0.8947 (tpp) cc_final: 0.8491 (tpp) REVERT: A 1591 MET cc_start: 0.8055 (mmt) cc_final: 0.7852 (mmm) REVERT: r 140 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.7634 (m-70) REVERT: r 175 GLN cc_start: 0.8279 (tp40) cc_final: 0.8000 (tp40) REVERT: r 323 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7693 (t80) outliers start: 74 outliers final: 35 residues processed: 250 average time/residue: 0.3061 time to fit residues: 131.9300 Evaluate side-chains 219 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 179 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 23 ASP Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 128 ARG Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 430 TRP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1101 PHE Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1274 PHE Chi-restraints excluded: chain A residue 1454 TRP Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1629 ILE Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1730 MET Chi-restraints excluded: chain r residue 137 HIS Chi-restraints excluded: chain r residue 140 HIS Chi-restraints excluded: chain r residue 149 LEU Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain r residue 189 VAL Chi-restraints excluded: chain r residue 205 THR Chi-restraints excluded: chain r residue 281 ILE Chi-restraints excluded: chain r residue 323 PHE Chi-restraints excluded: chain r residue 435 VAL Chi-restraints excluded: chain r residue 934 MET Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain q residue 39 TRP Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain K residue 393 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 305 optimal weight: 3.9990 chunk 208 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 273 optimal weight: 10.0000 chunk 151 optimal weight: 0.7980 chunk 313 optimal weight: 0.0770 chunk 253 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 329 optimal weight: 0.3980 chunk 92 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1096 HIS ** 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: 0.7543 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26772 Z= 0.155 Angle : 0.565 15.955 37716 Z= 0.280 Chirality : 0.041 0.229 4675 Planarity : 0.004 0.065 4463 Dihedral : 15.922 179.884 6251 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 5.32 % Allowed : 16.83 % Favored : 77.85 % 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: -1.44 (0.14), residues: 3698 helix: 1.45 (0.14), residues: 1568 sheet: -2.41 (0.25), residues: 370 loop : -3.05 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1263 HIS 0.016 0.001 HIS r 140 PHE 0.014 0.001 PHE A 264 TYR 0.024 0.001 TYR A 925 ARG 0.003 0.000 ARG A 420 *********************** 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 256 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 201 time to evaluate : 2.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 31 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6819 (mm-30) REVERT: A 430 TRP cc_start: 0.8475 (OUTLIER) cc_final: 0.7408 (m-10) REVERT: A 651 TRP cc_start: 0.8694 (m-10) cc_final: 0.8278 (m-10) REVERT: A 1474 MET cc_start: 0.8826 (tpp) cc_final: 0.8445 (tpp) REVERT: A 1591 MET cc_start: 0.8054 (mmt) cc_final: 0.7633 (mmt) REVERT: A 1730 MET cc_start: 0.7641 (tmm) cc_final: 0.7177 (tmm) REVERT: r 175 GLN cc_start: 0.8118 (tp40) cc_final: 0.7769 (tp40) REVERT: r 286 ASN cc_start: 0.8532 (m-40) cc_final: 0.8260 (m-40) REVERT: r 323 PHE cc_start: 0.7829 (OUTLIER) cc_final: 0.7562 (t80) REVERT: r 433 MET cc_start: 0.7213 (ppp) cc_final: 0.7010 (ptm) REVERT: K 324 LYS cc_start: 0.7379 (tptt) cc_final: 0.7101 (ptpp) REVERT: K 378 MET cc_start: 0.4588 (mmp) cc_final: 0.4220 (mmp) outliers start: 55 outliers final: 29 residues processed: 246 average time/residue: 0.3490 time to fit residues: 147.0808 Evaluate side-chains 219 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 188 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 166 GLN Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 430 TRP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1101 PHE Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1629 ILE Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain r residue 189 VAL Chi-restraints excluded: chain r residue 205 THR Chi-restraints excluded: chain r residue 323 PHE Chi-restraints excluded: chain r residue 435 VAL Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain K residue 385 ARG Chi-restraints excluded: chain K residue 393 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 123 optimal weight: 10.0000 chunk 330 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 367 optimal weight: 3.9990 chunk 305 optimal weight: 8.9990 chunk 170 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 121 optimal weight: 0.8980 chunk 193 optimal weight: 0.7980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 HIS ** A 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN ** 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: 0.7610 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26772 Z= 0.239 Angle : 0.601 16.874 37716 Z= 0.302 Chirality : 0.042 0.295 4675 Planarity : 0.004 0.071 4463 Dihedral : 15.927 179.814 6251 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.44 % Favored : 88.53 % Rotamer: Outliers : 5.61 % Allowed : 17.41 % Favored : 76.98 % 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: -1.39 (0.14), residues: 3698 helix: 1.46 (0.14), residues: 1567 sheet: -2.26 (0.26), residues: 368 loop : -3.02 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP r 904 HIS 0.007 0.001 HIS A 610 PHE 0.022 0.001 PHE A1490 TYR 0.019 0.002 TYR A 925 ARG 0.004 0.001 ARG K 358 *********************** 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 246 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 188 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 TRP cc_start: 0.8502 (OUTLIER) cc_final: 0.7405 (m-10) REVERT: A 776 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8484 (tm) REVERT: A 1730 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7099 (tmm) REVERT: r 175 GLN cc_start: 0.8271 (tp40) cc_final: 0.7929 (tp-100) REVERT: r 286 ASN cc_start: 0.8531 (m-40) cc_final: 0.8262 (m-40) REVERT: r 323 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7615 (t80) REVERT: K 324 LYS cc_start: 0.7603 (tptt) cc_final: 0.7322 (ptpp) outliers start: 58 outliers final: 40 residues processed: 233 average time/residue: 0.3283 time to fit residues: 131.4525 Evaluate side-chains 225 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 181 time to evaluate : 3.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 166 GLN Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 326 HIS Chi-restraints excluded: chain A residue 430 TRP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1101 PHE Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1274 PHE Chi-restraints excluded: chain A residue 1454 TRP Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1490 PHE Chi-restraints excluded: chain A residue 1629 ILE Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1730 MET Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain r residue 189 VAL Chi-restraints excluded: chain r residue 205 THR Chi-restraints excluded: chain r residue 304 LEU Chi-restraints excluded: chain r residue 323 PHE Chi-restraints excluded: chain r residue 435 VAL Chi-restraints excluded: chain q residue 20 THR Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain q residue 39 TRP Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain K residue 385 ARG Chi-restraints excluded: chain K residue 393 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 354 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 209 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 309 optimal weight: 10.0000 chunk 205 optimal weight: 0.0670 chunk 366 optimal weight: 20.0000 chunk 229 optimal weight: 10.0000 chunk 223 optimal weight: 5.9990 chunk 169 optimal weight: 0.9980 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 579 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: 0.7592 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26772 Z= 0.196 Angle : 0.575 16.866 37716 Z= 0.287 Chirality : 0.041 0.221 4675 Planarity : 0.004 0.072 4463 Dihedral : 15.901 179.585 6251 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 5.32 % Allowed : 17.99 % Favored : 76.69 % 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: -1.23 (0.15), residues: 3698 helix: 1.59 (0.14), residues: 1572 sheet: -2.16 (0.26), residues: 378 loop : -2.95 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1465 HIS 0.006 0.001 HIS r 245 PHE 0.020 0.001 PHE A1490 TYR 0.025 0.002 TYR Q 59 ARG 0.006 0.000 ARG K 358 *********************** 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 253 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 198 time to evaluate : 2.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 TRP cc_start: 0.8478 (OUTLIER) cc_final: 0.7409 (m-10) REVERT: A 1730 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7256 (tmm) REVERT: r 175 GLN cc_start: 0.8241 (tp40) cc_final: 0.7934 (tp-100) REVERT: r 286 ASN cc_start: 0.8250 (m-40) cc_final: 0.7991 (m-40) REVERT: r 323 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7564 (t80) REVERT: K 324 LYS cc_start: 0.7557 (tptt) cc_final: 0.7131 (ptpp) REVERT: K 378 MET cc_start: 0.4642 (mmp) cc_final: 0.4272 (mmp) outliers start: 55 outliers final: 42 residues processed: 237 average time/residue: 0.3303 time to fit residues: 133.2061 Evaluate side-chains 231 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 186 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 166 GLN Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 430 TRP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1101 PHE Chi-restraints excluded: chain A residue 1157 ILE Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1490 PHE Chi-restraints excluded: chain A residue 1629 ILE Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1730 MET Chi-restraints excluded: chain r residue 137 HIS Chi-restraints excluded: chain r residue 188 VAL Chi-restraints excluded: chain r residue 189 VAL Chi-restraints excluded: chain r residue 205 THR Chi-restraints excluded: chain r residue 248 GLN Chi-restraints excluded: chain r residue 323 PHE Chi-restraints excluded: chain r residue 419 VAL Chi-restraints excluded: chain r residue 435 VAL Chi-restraints excluded: chain r residue 934 MET Chi-restraints excluded: chain q residue 24 ILE Chi-restraints excluded: chain q residue 39 TRP Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain K residue 385 ARG Chi-restraints excluded: chain K residue 393 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 226 optimal weight: 0.0970 chunk 146 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 71 optimal weight: 0.0870 chunk 70 optimal weight: 0.4980 chunk 232 optimal weight: 9.9990 chunk 249 optimal weight: 4.9990 chunk 181 optimal weight: 0.0060 chunk 34 optimal weight: 0.0000 chunk 287 optimal weight: 2.9990 overall best weight: 0.1376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 579 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: 0.7476 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 26772 Z= 0.133 Angle : 0.542 16.730 37716 Z= 0.265 Chirality : 0.040 0.280 4675 Planarity : 0.004 0.060 4463 Dihedral : 15.702 178.062 6251 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 3.77 % Allowed : 19.44 % Favored : 76.79 % 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: -0.83 (0.15), residues: 3698 helix: 1.95 (0.14), residues: 1561 sheet: -1.73 (0.26), residues: 368 loop : -2.78 (0.15), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1465 HIS 0.004 0.001 HIS A 121 PHE 0.017 0.001 PHE A1490 TYR 0.018 0.001 TYR A 140 ARG 0.012 0.000 ARG K 344 *********************** 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 252 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 213 time to evaluate : 2.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 31 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6743 (mm-30) REVERT: A 70 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8141 (tp) REVERT: A 147 MET cc_start: 0.8935 (mmp) cc_final: 0.8730 (mmp) REVERT: A 1730 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7425 (tmm) REVERT: r 175 GLN cc_start: 0.8133 (tp40) cc_final: 0.7893 (tp-100) REVERT: r 286 ASN cc_start: 0.8421 (m-40) cc_final: 0.8136 (m-40) REVERT: r 323 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7534 (t80) REVERT: K 324 LYS cc_start: 0.7445 (tptt) cc_final: 0.6876 (ptpp) REVERT: K 378 MET cc_start: 0.4422 (mmp) cc_final: 0.4053 (mmp) outliers start: 39 outliers final: 25 residues processed: 241 average time/residue: 0.3277 time to fit residues: 134.7640 Evaluate side-chains 222 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 194 time to evaluate : 3.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1101 PHE Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1274 PHE Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1490 PHE Chi-restraints excluded: chain A residue 1629 ILE Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1730 MET Chi-restraints excluded: chain A residue 1740 LEU Chi-restraints excluded: chain r residue 248 GLN Chi-restraints excluded: chain r residue 323 PHE Chi-restraints excluded: chain r residue 875 ILE Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain K residue 385 ARG Chi-restraints excluded: chain K residue 393 HIS 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: 0.1980 chunk 341 optimal weight: 30.0000 chunk 205 optimal weight: 0.1980 chunk 148 optimal weight: 2.9990 chunk 268 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 308 optimal weight: 7.9990 chunk 322 optimal weight: 20.0000 chunk 340 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 579 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: 0.7598 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26772 Z= 0.233 Angle : 0.592 16.461 37716 Z= 0.295 Chirality : 0.042 0.251 4675 Planarity : 0.004 0.091 4463 Dihedral : 15.771 178.907 6251 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 3.58 % Allowed : 20.12 % Favored : 76.31 % 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: -0.97 (0.15), residues: 3698 helix: 1.77 (0.14), residues: 1571 sheet: -1.77 (0.26), residues: 373 loop : -2.82 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1582 HIS 0.006 0.001 HIS A 610 PHE 0.020 0.002 PHE A1490 TYR 0.019 0.002 TYR Q 59 ARG 0.003 0.001 ARG K 358 *********************** 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 229 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 192 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1730 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7208 (tmm) REVERT: r 286 ASN cc_start: 0.8287 (m-40) cc_final: 0.8021 (m-40) REVERT: r 323 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7470 (t80) outliers start: 37 outliers final: 27 residues processed: 216 average time/residue: 0.3357 time to fit residues: 125.4408 Evaluate side-chains 214 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 185 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 166 GLN Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1101 PHE Chi-restraints excluded: chain A residue 1274 PHE Chi-restraints excluded: chain A residue 1454 TRP Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1490 PHE Chi-restraints excluded: chain A residue 1629 ILE Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1730 MET Chi-restraints excluded: chain r residue 248 GLN Chi-restraints excluded: chain r residue 323 PHE Chi-restraints excluded: chain r residue 435 VAL Chi-restraints excluded: chain r residue 934 MET Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain K residue 385 ARG Chi-restraints excluded: chain K residue 393 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 224 optimal weight: 4.9990 chunk 360 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 171 optimal weight: 0.7980 chunk 250 optimal weight: 10.0000 chunk 378 optimal weight: 20.0000 chunk 348 optimal weight: 30.0000 chunk 301 optimal weight: 5.9990 chunk 31 optimal weight: 0.3980 chunk 232 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 579 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: 0.7664 moved from start: 0.4616 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= 0.276 Angle : 0.630 17.851 37716 Z= 0.319 Chirality : 0.043 0.209 4675 Planarity : 0.005 0.090 4463 Dihedral : 15.982 179.308 6251 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.93 % Favored : 88.07 % Rotamer: Outliers : 3.58 % Allowed : 20.70 % Favored : 75.73 % 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: -1.21 (0.14), residues: 3698 helix: 1.44 (0.14), residues: 1577 sheet: -1.75 (0.27), residues: 368 loop : -2.87 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP r 904 HIS 0.006 0.001 HIS A 121 PHE 0.030 0.002 PHE A 629 TYR 0.027 0.002 TYR A 832 ARG 0.004 0.001 ARG K 388 ********************** REFINEMENT MACRO_CYCLE 10 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: 37 poor density : 189 time to evaluate : 3.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1241 HIS cc_start: 0.7684 (OUTLIER) cc_final: 0.7447 (m-70) REVERT: A 1730 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7383 (tmm) REVERT: r 286 ASN cc_start: 0.8316 (m-40) cc_final: 0.8055 (m-40) REVERT: r 323 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7662 (t80) REVERT: r 433 MET cc_start: 0.7401 (ppp) cc_final: 0.7164 (ptm) REVERT: K 324 LYS cc_start: 0.7647 (tptt) cc_final: 0.7265 (ptpp) outliers start: 37 outliers final: 28 residues processed: 214 average time/residue: 0.3153 time to fit residues: 116.1853 Evaluate side-chains 216 residues out of total 3359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 185 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 49 ILE Chi-restraints excluded: chain Q residue 88 LEU Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 166 GLN Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1478 LEU Chi-restraints excluded: chain A residue 1490 PHE Chi-restraints excluded: chain A residue 1629 ILE Chi-restraints excluded: chain A residue 1726 ILE Chi-restraints excluded: chain A residue 1730 MET Chi-restraints excluded: chain r residue 137 HIS Chi-restraints excluded: chain r residue 248 GLN Chi-restraints excluded: chain r residue 323 PHE Chi-restraints excluded: chain r residue 435 VAL Chi-restraints excluded: chain r residue 934 MET Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain K residue 385 ARG Chi-restraints excluded: chain K residue 393 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 239 optimal weight: 0.7980 chunk 321 optimal weight: 0.0870 chunk 92 optimal weight: 0.0060 chunk 277 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 chunk 83 optimal weight: 0.5980 chunk 301 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 310 optimal weight: 0.0370 chunk 38 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.2052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.105842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.087858 restraints weight = 92221.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.089230 restraints weight = 53973.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.090104 restraints weight = 37151.401| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26772 Z= 0.140 Angle : 0.560 17.803 37716 Z= 0.275 Chirality : 0.040 0.199 4675 Planarity : 0.004 0.084 4463 Dihedral : 15.767 178.286 6251 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 3.19 % Allowed : 21.28 % Favored : 75.53 % 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: -0.79 (0.15), residues: 3698 helix: 1.87 (0.14), residues: 1571 sheet: -1.51 (0.27), residues: 372 loop : -2.73 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1465 HIS 0.005 0.001 HIS r 902 PHE 0.024 0.001 PHE A 640 TYR 0.046 0.001 TYR A 454 ARG 0.005 0.000 ARG K 358 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4428.64 seconds wall clock time: 81 minutes 19.02 seconds (4879.02 seconds total)