Starting phenix.real_space_refine on Fri Feb 16 20:49:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mey_23807/02_2024/7mey_23807_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mey_23807/02_2024/7mey_23807.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mey_23807/02_2024/7mey_23807_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mey_23807/02_2024/7mey_23807_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mey_23807/02_2024/7mey_23807_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mey_23807/02_2024/7mey_23807.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mey_23807/02_2024/7mey_23807.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mey_23807/02_2024/7mey_23807_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mey_23807/02_2024/7mey_23807_updated.pdb" } resolution = 3.67 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: 5 Type Number sf(0) Gaussians Zn 7 6.06 5 S 85 5.16 5 C 10504 2.51 5 N 2774 2.21 5 O 3098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1765": "OE1" <-> "OE2" Residue "A TYR 1784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1806": "OD1" <-> "OD2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "B GLU 18": "OE1" <-> "OE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "D GLU 18": "OE1" <-> "OE2" Residue "D GLU 34": "OE1" <-> "OE2" 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: 16468 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 14045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1731, 14045 Classifications: {'peptide': 1731} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 61, 'TRANS': 1669} Chain breaks: 5 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "C" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 554 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 67} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 1234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1234 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 15, 'TRANS': 137} Chain: "D" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 597 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' ZN': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'Z3V': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1019 SG CYS A 136 43.419 73.004 44.885 1.00 78.04 S ATOM 1044 SG CYS A 139 41.137 74.532 42.427 1.00 84.59 S ATOM 910 SG CYS A 123 55.526 81.492 36.276 1.00 90.28 S ATOM 1104 SG CYS A 148 54.767 81.564 39.975 1.00 80.73 S ATOM 1128 SG CYS A 151 52.173 82.491 37.633 1.00 93.77 S ATOM 1316 SG CYS A 175 53.250 78.888 37.869 1.00 76.58 S ATOM 1128 SG CYS A 151 52.173 82.491 37.633 1.00 93.77 S ATOM 1330 SG CYS A 177 48.897 81.478 36.176 1.00 88.74 S ATOM 1424 SG CYS A 189 49.613 85.056 37.015 1.00108.38 S ATOM 13189 SG CYS A1703 60.349 87.379 69.325 1.00 75.46 S ATOM 13210 SG CYS A1706 60.269 90.992 68.799 1.00 74.37 S ATOM 13358 SG CYS A1727 62.436 89.560 71.398 1.00 95.12 S ATOM 9880 SG CYS A1295 60.393 74.664 93.587 1.00107.71 S ATOM 10099 SG CYS A1320 62.503 71.572 93.820 1.00121.95 S ATOM 10120 SG CYS A1323 59.815 71.827 91.304 1.00112.90 S ATOM 9280 SG CYS A1220 65.057 66.426 105.379 1.00148.10 S ATOM 9299 SG CYS A1223 68.101 65.131 107.603 1.00149.39 S ATOM 9950 SG CYS A1303 68.767 66.888 104.111 1.00131.03 S Time building chain proxies: 8.33, per 1000 atoms: 0.51 Number of scatterers: 16468 At special positions: 0 Unit cell: (116.93, 137.127, 130.749, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 7 29.99 S 85 16.00 O 3098 8.00 N 2774 7.00 C 10504 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.17 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 160 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 157 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 136 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 139 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 148 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 151 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 175 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 123 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" NE2 HIS A 118 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 151 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 177 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 189 " pdb=" ZN A2004 " pdb="ZN ZN A2004 " - pdb=" NE2 HIS A1722 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1703 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1706 " pdb="ZN ZN A2004 " - pdb=" SG CYS A1727 " pdb=" ZN A2005 " pdb="ZN ZN A2005 " - pdb=" ND1 HIS A1297 " pdb="ZN ZN A2005 " - pdb=" SG CYS A1323 " pdb="ZN ZN A2005 " - pdb=" SG CYS A1320 " pdb="ZN ZN A2005 " - pdb=" SG CYS A1295 " pdb=" ZN A2006 " pdb="ZN ZN A2006 " - pdb=" ND1 HIS A1300 " pdb="ZN ZN A2006 " - pdb=" SG CYS A1220 " pdb="ZN ZN A2006 " - pdb=" SG CYS A1223 " pdb="ZN ZN A2006 " - pdb=" SG CYS A1303 " pdb=" ZN A2007 " pdb="ZN ZN A2007 " - pdb=" NE2 HIS A1763 " pdb="ZN ZN A2007 " - pdb=" NE2 HIS A 161 " Number of angles added : 20 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3926 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 94 helices and 11 sheets defined 48.9% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.18 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 removed outlier: 3.571A pdb=" N SER A 21 " --> pdb=" O ARG A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 56 removed outlier: 3.855A pdb=" N ALA A 38 " --> pdb=" O PRO A 34 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 60 No H-bonds generated for 'chain 'A' and resid 58 through 60' Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 94 through 97 No H-bonds generated for 'chain 'A' and resid 94 through 97' Processing helix chain 'A' and resid 154 through 157 Processing helix chain 'A' and resid 190 through 193 No H-bonds generated for 'chain 'A' and resid 190 through 193' Processing helix chain 'A' and resid 217 through 240 removed outlier: 3.797A pdb=" N GLN A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 261 Processing helix chain 'A' and resid 265 through 275 Processing helix chain 'A' and resid 323 through 333 Processing helix chain 'A' and resid 343 through 348 removed outlier: 3.686A pdb=" N ILE A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 374 removed outlier: 3.548A pdb=" N GLY A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ALA A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N VAL A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLN A 372 " --> pdb=" O PHE A 368 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 404 removed outlier: 3.543A pdb=" N LEU A 403 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN A 404 " --> pdb=" O THR A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 423 removed outlier: 3.864A pdb=" N ASN A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 477 through 479 No H-bonds generated for 'chain 'A' and resid 477 through 479' Processing helix chain 'A' and resid 502 through 511 removed outlier: 3.626A pdb=" N ASP A 510 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASN A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 531 Proline residue: A 527 - end of helix Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'A' and resid 547 through 556 Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 566 through 573 Processing helix chain 'A' and resid 577 through 585 Processing helix chain 'A' and resid 588 through 603 removed outlier: 3.872A pdb=" N GLU A 602 " --> pdb=" O ASP A 598 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N PHE A 603 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 641 Processing helix chain 'A' and resid 648 through 650 No H-bonds generated for 'chain 'A' and resid 648 through 650' Processing helix chain 'A' and resid 652 through 665 removed outlier: 3.993A pdb=" N LEU A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N PHE A 665 " --> pdb=" O LEU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 709 removed outlier: 3.795A pdb=" N SER A 688 " --> pdb=" O ASN A 685 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A 693 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A 709 " --> pdb=" O VAL A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 731 Processing helix chain 'A' and resid 761 through 772 Processing helix chain 'A' and resid 775 through 781 Processing helix chain 'A' and resid 788 through 806 removed outlier: 4.715A pdb=" N PHE A 794 " --> pdb=" O LYS A 790 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N SER A 795 " --> pdb=" O ILE A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 824 Processing helix chain 'A' and resid 832 through 845 Processing helix chain 'A' and resid 851 through 861 Processing helix chain 'A' and resid 865 through 868 No H-bonds generated for 'chain 'A' and resid 865 through 868' Processing helix chain 'A' and resid 880 through 899 removed outlier: 4.224A pdb=" N SER A 884 " --> pdb=" O ASP A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 904 No H-bonds generated for 'chain 'A' and resid 902 through 904' Processing helix chain 'A' and resid 910 through 926 Processing helix chain 'A' and resid 933 through 939 Processing helix chain 'A' and resid 942 through 945 No H-bonds generated for 'chain 'A' and resid 942 through 945' Processing helix chain 'A' and resid 948 through 958 Processing helix chain 'A' and resid 977 through 982 removed outlier: 4.020A pdb=" N ALA A 981 " --> pdb=" O SER A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 990 No H-bonds generated for 'chain 'A' and resid 988 through 990' Processing helix chain 'A' and resid 996 through 1006 Processing helix chain 'A' and resid 1010 through 1012 No H-bonds generated for 'chain 'A' and resid 1010 through 1012' Processing helix chain 'A' and resid 1029 through 1031 No H-bonds generated for 'chain 'A' and resid 1029 through 1031' Processing helix chain 'A' and resid 1034 through 1036 No H-bonds generated for 'chain 'A' and resid 1034 through 1036' Processing helix chain 'A' and resid 1041 through 1057 Processing helix chain 'A' and resid 1063 through 1081 Processing helix chain 'A' and resid 1088 through 1092 removed outlier: 3.829A pdb=" N SER A1092 " --> pdb=" O ALA A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1103 Processing helix chain 'A' and resid 1112 through 1128 Processing helix chain 'A' and resid 1131 through 1141 removed outlier: 3.701A pdb=" N GLU A1135 " --> pdb=" O ASN A1131 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SER A1136 " --> pdb=" O GLU A1132 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A1137 " --> pdb=" O LEU A1133 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER A1140 " --> pdb=" O SER A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1152 removed outlier: 3.514A pdb=" N ASP A1151 " --> pdb=" O ASN A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1193 removed outlier: 3.965A pdb=" N LYS A1168 " --> pdb=" O GLU A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1255 No H-bonds generated for 'chain 'A' and resid 1252 through 1255' Processing helix chain 'A' and resid 1274 through 1285 Processing helix chain 'A' and resid 1287 through 1289 No H-bonds generated for 'chain 'A' and resid 1287 through 1289' Processing helix chain 'A' and resid 1301 through 1311 Processing helix chain 'A' and resid 1345 through 1350 Processing helix chain 'A' and resid 1355 through 1361 removed outlier: 5.492A pdb=" N LEU A1361 " --> pdb=" O THR A1357 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1383 Processing helix chain 'A' and resid 1389 through 1393 Processing helix chain 'A' and resid 1399 through 1423 removed outlier: 3.775A pdb=" N VAL A1402 " --> pdb=" O HIS A1399 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER A1403 " --> pdb=" O LYS A1400 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1432 No H-bonds generated for 'chain 'A' and resid 1430 through 1432' Processing helix chain 'A' and resid 1436 through 1456 Processing helix chain 'A' and resid 1478 through 1488 Processing helix chain 'A' and resid 1494 through 1514 removed outlier: 3.706A pdb=" N THR A1499 " --> pdb=" O ARG A1495 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1533 Processing helix chain 'A' and resid 1541 through 1550 Processing helix chain 'A' and resid 1562 through 1594 Proline residue: A1578 - end of helix Processing helix chain 'A' and resid 1609 through 1613 Processing helix chain 'A' and resid 1618 through 1629 Processing helix chain 'A' and resid 1635 through 1640 Processing helix chain 'A' and resid 1649 through 1651 No H-bonds generated for 'chain 'A' and resid 1649 through 1651' Processing helix chain 'A' and resid 1671 through 1676 removed outlier: 4.072A pdb=" N THR A1676 " --> pdb=" O THR A1673 " (cutoff:3.500A) Processing helix chain 'A' and resid 1716 through 1719 No H-bonds generated for 'chain 'A' and resid 1716 through 1719' Processing helix chain 'A' and resid 1721 through 1724 No H-bonds generated for 'chain 'A' and resid 1721 through 1724' Processing helix chain 'A' and resid 1767 through 1774 removed outlier: 3.809A pdb=" N ARG A1772 " --> pdb=" O ASN A1769 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ARG A1773 " --> pdb=" O ALA A1770 " (cutoff:3.500A) Processing helix chain 'A' and resid 1781 through 1792 Processing helix chain 'A' and resid 1795 through 1811 removed outlier: 3.575A pdb=" N MET A1804 " --> pdb=" O ILE A1800 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP A1806 " --> pdb=" O ARG A1802 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU A1807 " --> pdb=" O VAL A1803 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N PHE A1808 " --> pdb=" O MET A1804 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG A1809 " --> pdb=" O GLY A1805 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL A1810 " --> pdb=" O ASP A1806 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR A1811 " --> pdb=" O GLU A1807 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 34 Processing helix chain 'C' and resid 56 through 59 No H-bonds generated for 'chain 'C' and resid 56 through 59' Processing helix chain 'B' and resid 4 through 18 Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 124 through 131 Processing helix chain 'B' and resid 134 through 150 Processing helix chain 'D' and resid 23 through 33 Processing helix chain 'D' and resid 38 through 40 No H-bonds generated for 'chain 'D' and resid 38 through 40' Processing helix chain 'D' and resid 57 through 59 No H-bonds generated for 'chain 'D' and resid 57 through 59' Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 Processing sheet with id= B, first strand: chain 'A' and resid 379 through 382 removed outlier: 4.048A pdb=" N LYS A 356 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE A 315 " --> pdb=" O MET A 354 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N MET A 354 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 604 through 607 removed outlier: 3.518A pdb=" N VAL A 610 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 959 through 962 Processing sheet with id= E, first strand: chain 'A' and resid 1329 through 1333 removed outlier: 4.501A pdb=" N PHE A1232 " --> pdb=" O LEU A1333 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1731 through 1736 Processing sheet with id= G, first strand: chain 'A' and resid 1759 through 1761 Processing sheet with id= H, first strand: chain 'A' and resid 737 through 741 removed outlier: 6.987A pdb=" N HIS A 744 " --> pdb=" O ILE A 740 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 12 through 16 removed outlier: 3.506A pdb=" N HIS C 68 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL C 70 " --> pdb=" O ARG C 42 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 24 through 28 removed outlier: 3.516A pdb=" N LEU B 57 " --> pdb=" O TRP B 36 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 12 through 16 removed outlier: 5.677A pdb=" N SER D 65 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LYS D 6 " --> pdb=" O SER D 65 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU D 67 " --> pdb=" O LYS D 6 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG D 42 " --> pdb=" O VAL D 70 " (cutoff:3.500A) 658 hydrogen bonds defined for protein. 1755 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.50 Time building geometry restraints manager: 6.70 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: 4518 1.33 - 1.46: 3160 1.46 - 1.58: 9008 1.58 - 1.70: 0 1.70 - 1.82: 124 Bond restraints: 16810 Sorted by residual: bond pdb=" C2 Z3V D 201 " pdb=" N1 Z3V D 201 " ideal model delta sigma weight residual 1.452 1.478 -0.026 2.00e-02 2.50e+03 1.70e+00 bond pdb=" CG GLU A 996 " pdb=" CD GLU A 996 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.33e+00 bond pdb=" CD GLN A 261 " pdb=" OE1 GLN A 261 " ideal model delta sigma weight residual 1.231 1.212 0.019 1.90e-02 2.77e+03 1.03e+00 bond pdb=" C ASP A 984 " pdb=" N PRO A 985 " ideal model delta sigma weight residual 1.334 1.326 0.008 8.40e-03 1.42e+04 8.84e-01 bond pdb=" CA GLN A 261 " pdb=" CB GLN A 261 " ideal model delta sigma weight residual 1.531 1.546 -0.015 1.59e-02 3.96e+03 8.79e-01 ... (remaining 16805 not shown) Histogram of bond angle deviations from ideal: 98.64 - 105.75: 318 105.75 - 112.85: 9105 112.85 - 119.96: 5770 119.96 - 127.07: 7382 127.07 - 134.17: 168 Bond angle restraints: 22743 Sorted by residual: angle pdb=" N GLN A 261 " pdb=" CA GLN A 261 " pdb=" CB GLN A 261 " ideal model delta sigma weight residual 110.26 115.79 -5.53 1.49e+00 4.50e-01 1.38e+01 angle pdb=" C THR A 260 " pdb=" N GLN A 261 " pdb=" CA GLN A 261 " ideal model delta sigma weight residual 121.64 114.00 7.64 2.13e+00 2.20e-01 1.29e+01 angle pdb=" CA GLN A 261 " pdb=" CB GLN A 261 " pdb=" CG GLN A 261 " ideal model delta sigma weight residual 114.10 120.23 -6.13 2.00e+00 2.50e-01 9.40e+00 angle pdb=" C MET A 259 " pdb=" N THR A 260 " pdb=" CA THR A 260 " ideal model delta sigma weight residual 121.66 116.48 5.18 1.76e+00 3.23e-01 8.67e+00 angle pdb=" C LYS A1083 " pdb=" N ASP A1084 " pdb=" CA ASP A1084 " ideal model delta sigma weight residual 121.54 127.13 -5.59 1.91e+00 2.74e-01 8.56e+00 ... (remaining 22738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.99: 9702 26.99 - 53.99: 464 53.99 - 80.98: 43 80.98 - 107.97: 6 107.97 - 134.97: 1 Dihedral angle restraints: 10216 sinusoidal: 4188 harmonic: 6028 Sorted by residual: dihedral pdb=" C2 Z3V D 201 " pdb=" C3 Z3V D 201 " pdb=" N1 Z3V D 201 " pdb=" C4 Z3V D 201 " ideal model delta sinusoidal sigma weight residual 194.08 59.11 134.97 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" CA LEU A 898 " pdb=" C LEU A 898 " pdb=" N THR A 899 " pdb=" CA THR A 899 " ideal model delta harmonic sigma weight residual -180.00 -159.95 -20.05 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA GLN A1748 " pdb=" C GLN A1748 " pdb=" N PRO A1749 " pdb=" CA PRO A1749 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 10213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1495 0.027 - 0.055: 648 0.055 - 0.082: 259 0.082 - 0.110: 127 0.110 - 0.137: 27 Chirality restraints: 2556 Sorted by residual: chirality pdb=" CA ASP A 251 " pdb=" N ASP A 251 " pdb=" C ASP A 251 " pdb=" CB ASP A 251 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA ASP A1084 " pdb=" N ASP A1084 " pdb=" C ASP A1084 " pdb=" CB ASP A1084 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ARG B 11 " pdb=" N ARG B 11 " pdb=" C ARG B 11 " pdb=" CB ARG B 11 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 2553 not shown) Planarity restraints: 2911 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 996 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.43e+00 pdb=" CD GLU A 996 " -0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU A 996 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 996 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 257 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.26e+00 pdb=" C ARG A 257 " -0.031 2.00e-02 2.50e+03 pdb=" O ARG A 257 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU A 258 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A1749 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO A1750 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A1750 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1750 " 0.022 5.00e-02 4.00e+02 ... (remaining 2908 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 226 2.62 - 3.19: 15412 3.19 - 3.76: 25903 3.76 - 4.33: 35170 4.33 - 4.90: 57708 Nonbonded interactions: 134419 Sorted by model distance: nonbonded pdb=" SG CYS A 139 " pdb=" NE2 HIS A 157 " model vdw 2.049 2.880 nonbonded pdb=" OH TYR A 824 " pdb=" OD2 ASP A 836 " model vdw 2.165 2.440 nonbonded pdb=" OG1 THR A 501 " pdb=" OE1 GLN A 542 " model vdw 2.181 2.440 nonbonded pdb=" O SER A1354 " pdb=" OG1 THR A1357 " model vdw 2.201 2.440 nonbonded pdb=" OG SER A 908 " pdb=" OD2 ASP A 912 " model vdw 2.204 2.440 ... (remaining 134414 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 1 through 47 or resid 49 through 71)) selection = (chain 'D' and (resid 1 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 or resid 49 through 71)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.520 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 47.770 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 : 0.003 0.030 16810 Z= 0.188 Angle : 0.542 10.442 22743 Z= 0.277 Chirality : 0.040 0.137 2556 Planarity : 0.003 0.039 2911 Dihedral : 14.806 134.966 6290 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 0.75 (0.19), residues: 2013 helix: 1.62 (0.17), residues: 963 sheet: -0.54 (0.43), residues: 128 loop : -0.52 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 149 HIS 0.005 0.001 HIS A 160 PHE 0.013 0.001 PHE A1037 TYR 0.024 0.001 TYR A 980 ARG 0.006 0.000 ARG D 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 2.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 MET cc_start: 0.8556 (mpp) cc_final: 0.8113 (mpp) REVERT: A 1191 MET cc_start: 0.8499 (ppp) cc_final: 0.8175 (ppp) REVERT: C 63 LYS cc_start: 0.8680 (tptt) cc_final: 0.8377 (tppp) REVERT: B 13 PHE cc_start: 0.8656 (t80) cc_final: 0.8293 (t80) REVERT: B 17 LYS cc_start: 0.8948 (mtpt) cc_final: 0.8713 (mtpt) REVERT: B 39 MET cc_start: 0.8443 (tmm) cc_final: 0.7668 (tmm) REVERT: B 40 ILE cc_start: 0.9456 (mt) cc_final: 0.9061 (mt) REVERT: B 135 SER cc_start: 0.8548 (m) cc_final: 0.8192 (t) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.3034 time to fit residues: 76.6521 Evaluate side-chains 111 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 1.9990 chunk 153 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 158 optimal weight: 0.0370 chunk 61 optimal weight: 8.9990 chunk 96 optimal weight: 0.0870 chunk 117 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1374 ASN C 68 HIS ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16810 Z= 0.148 Angle : 0.531 11.735 22743 Z= 0.266 Chirality : 0.039 0.155 2556 Planarity : 0.004 0.042 2911 Dihedral : 5.032 133.755 2198 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.48 % Allowed : 6.40 % Favored : 93.11 % 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 (0.19), residues: 2013 helix: 1.60 (0.17), residues: 971 sheet: -0.58 (0.42), residues: 134 loop : -0.44 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 149 HIS 0.006 0.001 HIS A 157 PHE 0.015 0.001 PHE B 53 TYR 0.009 0.001 TYR A 980 ARG 0.005 0.000 ARG D 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7702 (p0) cc_final: 0.7267 (p0) REVERT: A 340 ILE cc_start: 0.7978 (tt) cc_final: 0.7729 (tt) REVERT: A 418 MET cc_start: 0.7566 (ttp) cc_final: 0.7360 (ttm) REVERT: B 17 LYS cc_start: 0.8946 (mtpt) cc_final: 0.8708 (mtpt) REVERT: B 95 ARG cc_start: 0.7411 (tpm170) cc_final: 0.7088 (tpm170) REVERT: B 135 SER cc_start: 0.8554 (m) cc_final: 0.8142 (t) REVERT: D 1 MET cc_start: 0.6958 (tpt) cc_final: 0.6634 (tpt) outliers start: 9 outliers final: 7 residues processed: 139 average time/residue: 0.2770 time to fit residues: 60.4702 Evaluate side-chains 119 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 52 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 198 optimal weight: 7.9990 chunk 163 optimal weight: 8.9990 chunk 182 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 147 optimal weight: 30.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.075 16810 Z= 0.585 Angle : 0.759 9.658 22743 Z= 0.393 Chirality : 0.045 0.177 2556 Planarity : 0.005 0.040 2911 Dihedral : 5.699 142.414 2198 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.56 % Allowed : 10.17 % Favored : 88.27 % 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: -0.02 (0.18), residues: 2013 helix: 0.88 (0.16), residues: 981 sheet: -1.25 (0.41), residues: 143 loop : -0.73 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 149 HIS 0.008 0.002 HIS A 160 PHE 0.024 0.002 PHE A 768 TYR 0.028 0.002 TYR A 980 ARG 0.006 0.001 ARG A1687 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7290 (p0) REVERT: A 340 ILE cc_start: 0.8214 (tt) cc_final: 0.7925 (tt) REVERT: B 95 ARG cc_start: 0.7603 (tpm170) cc_final: 0.7353 (tpm170) outliers start: 29 outliers final: 17 residues processed: 122 average time/residue: 0.2751 time to fit residues: 53.2939 Evaluate side-chains 118 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 1011 ASP Chi-restraints excluded: chain A residue 1590 LEU Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain A residue 1768 ARG Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 58 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 0.1980 chunk 138 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 chunk 184 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 174 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 16810 Z= 0.155 Angle : 0.535 11.593 22743 Z= 0.267 Chirality : 0.039 0.155 2556 Planarity : 0.004 0.041 2911 Dihedral : 5.286 137.076 2198 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.97 % Allowed : 12.43 % Favored : 86.60 % 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: 0.61 (0.19), residues: 2013 helix: 1.44 (0.17), residues: 973 sheet: -1.07 (0.40), residues: 142 loop : -0.44 (0.22), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 149 HIS 0.004 0.001 HIS A 118 PHE 0.013 0.001 PHE A1728 TYR 0.011 0.001 TYR A 386 ARG 0.003 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 ARG cc_start: 0.7558 (tpm170) cc_final: 0.7346 (tpm170) outliers start: 18 outliers final: 11 residues processed: 130 average time/residue: 0.2869 time to fit residues: 58.9725 Evaluate side-chains 122 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 58 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 1.9990 chunk 110 optimal weight: 0.0970 chunk 2 optimal weight: 6.9990 chunk 145 optimal weight: 30.0000 chunk 80 optimal weight: 0.4980 chunk 166 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 0.9990 chunk 175 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16810 Z= 0.147 Angle : 0.527 11.867 22743 Z= 0.262 Chirality : 0.039 0.154 2556 Planarity : 0.004 0.049 2911 Dihedral : 5.090 132.704 2198 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.81 % Allowed : 13.56 % Favored : 85.63 % 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: 0.66 (0.19), residues: 2013 helix: 1.49 (0.17), residues: 970 sheet: -0.95 (0.40), residues: 141 loop : -0.45 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 149 HIS 0.003 0.000 HIS A 118 PHE 0.012 0.001 PHE A1728 TYR 0.008 0.001 TYR A 394 ARG 0.003 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 122 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 ARG cc_start: 0.7573 (tpm170) cc_final: 0.7363 (tpm170) outliers start: 15 outliers final: 11 residues processed: 132 average time/residue: 0.2942 time to fit residues: 60.2236 Evaluate side-chains 119 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 1145 TYR Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 58 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 0.0770 chunk 175 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16810 Z= 0.162 Angle : 0.530 12.753 22743 Z= 0.261 Chirality : 0.039 0.272 2556 Planarity : 0.003 0.045 2911 Dihedral : 5.012 131.065 2198 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.35 % Allowed : 13.51 % Favored : 85.15 % 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: 0.67 (0.19), residues: 2013 helix: 1.51 (0.17), residues: 967 sheet: -0.99 (0.40), residues: 145 loop : -0.42 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 149 HIS 0.003 0.001 HIS A 118 PHE 0.020 0.001 PHE A 170 TYR 0.009 0.001 TYR A 394 ARG 0.007 0.000 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 1.996 Fit side-chains revert: symmetry clash REVERT: A 1355 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8296 (tt) REVERT: A 1628 MET cc_start: 0.7869 (mmt) cc_final: 0.7667 (mmt) REVERT: B 17 LYS cc_start: 0.8930 (mtpt) cc_final: 0.8724 (mttt) REVERT: B 95 ARG cc_start: 0.7629 (tpm170) cc_final: 0.7419 (tpm170) outliers start: 25 outliers final: 14 residues processed: 136 average time/residue: 0.2849 time to fit residues: 59.8604 Evaluate side-chains 126 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 1355 LEU Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1416 MET Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 58 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 164 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 194 optimal weight: 0.0970 chunk 121 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16810 Z= 0.268 Angle : 0.579 12.593 22743 Z= 0.288 Chirality : 0.040 0.218 2556 Planarity : 0.004 0.056 2911 Dihedral : 5.121 132.023 2198 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.18 % Allowed : 13.94 % Favored : 84.88 % 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: 0.58 (0.19), residues: 2013 helix: 1.39 (0.17), residues: 987 sheet: -1.08 (0.41), residues: 145 loop : -0.45 (0.22), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 149 HIS 0.004 0.001 HIS A 160 PHE 0.038 0.001 PHE B 13 TYR 0.011 0.001 TYR A 692 ARG 0.007 0.000 ARG D 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 2.019 Fit side-chains revert: symmetry clash REVERT: A 259 MET cc_start: 0.8499 (mpp) cc_final: 0.8053 (mpp) REVERT: B 14 LYS cc_start: 0.9179 (tppt) cc_final: 0.8829 (mmtt) outliers start: 22 outliers final: 18 residues processed: 126 average time/residue: 0.2781 time to fit residues: 55.4929 Evaluate side-chains 127 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 58 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 120 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 116 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 38 optimal weight: 0.0670 chunk 37 optimal weight: 1.9990 chunk 123 optimal weight: 0.0270 chunk 132 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 18 optimal weight: 0.3980 chunk 153 optimal weight: 5.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 16810 Z= 0.144 Angle : 0.560 15.369 22743 Z= 0.269 Chirality : 0.040 0.250 2556 Planarity : 0.004 0.041 2911 Dihedral : 4.967 133.018 2198 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.75 % Allowed : 14.91 % Favored : 84.34 % 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: 0.70 (0.19), residues: 2013 helix: 1.50 (0.17), residues: 974 sheet: -0.90 (0.42), residues: 139 loop : -0.40 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 149 HIS 0.003 0.001 HIS A 118 PHE 0.012 0.001 PHE B 13 TYR 0.010 0.001 TYR A 535 ARG 0.012 0.000 ARG D 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 125 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 MET cc_start: 0.8444 (mpp) cc_final: 0.8155 (mpp) REVERT: A 1191 MET cc_start: 0.8382 (ppp) cc_final: 0.8005 (ppp) REVERT: B 95 ARG cc_start: 0.7861 (tpm170) cc_final: 0.7216 (tpp-160) outliers start: 14 outliers final: 11 residues processed: 134 average time/residue: 0.2884 time to fit residues: 60.5800 Evaluate side-chains 126 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 58 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 9.9990 chunk 186 optimal weight: 7.9990 chunk 170 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 171 optimal weight: 0.0970 chunk 180 optimal weight: 6.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16810 Z= 0.247 Angle : 0.580 13.234 22743 Z= 0.286 Chirality : 0.040 0.237 2556 Planarity : 0.004 0.039 2911 Dihedral : 5.007 132.397 2198 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.13 % Allowed : 14.64 % Favored : 84.23 % 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: 0.64 (0.19), residues: 2013 helix: 1.45 (0.17), residues: 969 sheet: -0.86 (0.42), residues: 138 loop : -0.44 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP B 149 HIS 0.003 0.001 HIS A 160 PHE 0.017 0.001 PHE B 13 TYR 0.019 0.001 TYR A1784 ARG 0.007 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 MET cc_start: 0.8499 (mpp) cc_final: 0.8270 (mpp) REVERT: B 95 ARG cc_start: 0.7910 (tpm170) cc_final: 0.7327 (tpp-160) outliers start: 21 outliers final: 18 residues processed: 127 average time/residue: 0.2749 time to fit residues: 55.0647 Evaluate side-chains 127 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 511 ASN Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 58 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 119 optimal weight: 9.9990 chunk 191 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 201 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 chunk 160 optimal weight: 0.3980 chunk 16 optimal weight: 5.9990 chunk 123 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 16810 Z= 0.158 Angle : 0.572 15.059 22743 Z= 0.275 Chirality : 0.040 0.241 2556 Planarity : 0.004 0.040 2911 Dihedral : 4.944 133.233 2198 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.86 % Allowed : 15.18 % Favored : 83.96 % 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: 0.65 (0.19), residues: 2013 helix: 1.46 (0.17), residues: 968 sheet: -0.78 (0.42), residues: 139 loop : -0.44 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 149 HIS 0.003 0.001 HIS A 118 PHE 0.014 0.001 PHE B 13 TYR 0.011 0.001 TYR A1784 ARG 0.009 0.000 ARG D 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4026 Ramachandran restraints generated. 2013 Oldfield, 0 Emsley, 2013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1543 MET cc_start: 0.8948 (ptp) cc_final: 0.8720 (pmm) REVERT: B 95 ARG cc_start: 0.7947 (tpm170) cc_final: 0.7408 (tpp-160) outliers start: 16 outliers final: 16 residues processed: 128 average time/residue: 0.2806 time to fit residues: 56.8735 Evaluate side-chains 132 residues out of total 1877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 52 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 160 optimal weight: 0.1980 chunk 67 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 HIS ** 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 = 0.3245 r_free = 0.3245 target = 0.048200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.035418 restraints weight = 90780.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.036655 restraints weight = 50565.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.037481 restraints weight = 35083.117| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16810 Z= 0.193 Angle : 0.583 14.376 22743 Z= 0.282 Chirality : 0.040 0.236 2556 Planarity : 0.004 0.040 2911 Dihedral : 4.942 132.352 2198 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.97 % Allowed : 15.23 % Favored : 83.80 % 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: 0.67 (0.19), residues: 2013 helix: 1.47 (0.17), residues: 965 sheet: -0.73 (0.43), residues: 139 loop : -0.43 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 149 HIS 0.003 0.001 HIS A 118 PHE 0.016 0.001 PHE B 13 TYR 0.021 0.001 TYR A1784 ARG 0.006 0.000 ARG D 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2726.87 seconds wall clock time: 51 minutes 30.86 seconds (3090.86 seconds total)