Starting phenix.real_space_refine on Wed Mar 4 21:31:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mey_23807/03_2026/7mey_23807.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mey_23807/03_2026/7mey_23807.map 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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7mey_23807/03_2026/7mey_23807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mey_23807/03_2026/7mey_23807.map" model { file = "/net/cci-nas-00/data/ceres_data/7mey_23807/03_2026/7mey_23807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mey_23807/03_2026/7mey_23807.cif" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'GLU:plan': 4, 'ARG:plan': 5, 'HIS:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} 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: 3.18, per 1000 atoms: 0.19 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 518.3 milliseconds 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... Secondary structure from input PDB file: 101 helices and 14 sheets defined 56.9% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 removed outlier: 4.267A pdb=" N GLY A 13 " --> pdb=" O GLY A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 30 removed outlier: 4.722A pdb=" N TYR A 30 " --> pdb=" O PRO A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 57 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 61 Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 93 through 98 Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.955A pdb=" N VAL A 158 " --> pdb=" O LYS A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 Processing helix chain 'A' and resid 216 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 248 through 262 Processing helix chain 'A' and resid 264 through 276 removed outlier: 3.721A pdb=" N ARG A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 334 Processing helix chain 'A' and resid 342 through 349 removed outlier: 3.968A pdb=" N ARG A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 349 " --> pdb=" O SER A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 369 removed outlier: 3.892A pdb=" N VAL A 364 " --> pdb=" O ASP A 360 " (cutoff:3.500A) 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) Processing helix chain 'A' and resid 370 through 375 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 403 removed outlier: 3.543A pdb=" N LEU A 403 " --> pdb=" O ILE A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 424 removed outlier: 3.864A pdb=" N ASN A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 443 removed outlier: 3.678A pdb=" N VAL A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 476 through 480 Processing helix chain 'A' and resid 501 through 509 Processing helix chain 'A' and resid 510 through 512 No H-bonds generated for 'chain 'A' and resid 510 through 512' Processing helix chain 'A' and resid 514 through 532 Proline residue: A 527 - end of helix Processing helix chain 'A' and resid 535 through 546 removed outlier: 3.632A pdb=" N ILE A 546 " --> pdb=" O GLN A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 557 Processing helix chain 'A' and resid 560 through 564 Processing helix chain 'A' and resid 565 through 574 Processing helix chain 'A' and resid 576 through 586 Processing helix chain 'A' and resid 587 through 602 removed outlier: 3.872A pdb=" N GLU A 602 " --> pdb=" O ASP A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 642 removed outlier: 3.769A pdb=" N ILE A 627 " --> pdb=" O LYS A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 650 Processing helix chain 'A' and resid 651 through 664 removed outlier: 3.993A pdb=" N LEU A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 710 removed outlier: 4.348A pdb=" N TYR A 689 " --> pdb=" O ASN A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 732 removed outlier: 3.662A pdb=" N PHE A 719 " --> pdb=" O ASP A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 773 removed outlier: 3.580A pdb=" N VAL A 773 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 782 Processing helix chain 'A' and resid 787 through 807 removed outlier: 3.830A pdb=" N ILE A 791 " --> pdb=" O ASP A 787 " (cutoff:3.500A) 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) removed outlier: 3.735A pdb=" N VAL A 807 " --> pdb=" O SER A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 825 removed outlier: 4.109A pdb=" N LEU A 818 " --> pdb=" O GLY A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 846 Processing helix chain 'A' and resid 850 through 862 removed outlier: 3.625A pdb=" N ILE A 854 " --> pdb=" O ASP A 850 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TRP A 862 " --> pdb=" O ILE A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 869 Processing helix chain 'A' and resid 879 through 881 No H-bonds generated for 'chain 'A' and resid 879 through 881' Processing helix chain 'A' and resid 882 through 900 removed outlier: 3.654A pdb=" N GLU A 900 " --> pdb=" O GLN A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 905 Processing helix chain 'A' and resid 909 through 927 Processing helix chain 'A' and resid 933 through 940 Processing helix chain 'A' and resid 941 through 946 removed outlier: 3.583A pdb=" N THR A 945 " --> pdb=" O PRO A 941 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 946 " --> pdb=" O ASP A 942 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 941 through 946' Processing helix chain 'A' and resid 947 through 958 Processing helix chain 'A' and resid 977 through 983 removed outlier: 4.020A pdb=" N ALA A 981 " --> pdb=" O SER A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 991 Processing helix chain 'A' and resid 995 through 1007 Processing helix chain 'A' and resid 1009 through 1013 removed outlier: 3.715A pdb=" N ILE A1013 " --> pdb=" O LYS A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1032 removed outlier: 3.720A pdb=" N LEU A1032 " --> pdb=" O LYS A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1037 removed outlier: 4.170A pdb=" N PHE A1037 " --> pdb=" O LEU A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1058 Processing helix chain 'A' and resid 1062 through 1082 Processing helix chain 'A' and resid 1088 through 1093 removed outlier: 3.579A pdb=" N LYS A1093 " --> pdb=" O ALA A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1104 removed outlier: 4.203A pdb=" N LEU A1098 " --> pdb=" O PRO A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1129 Processing helix chain 'A' and resid 1130 through 1142 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) removed outlier: 3.580A pdb=" N GLY A1142 " --> pdb=" O ILE A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1153 removed outlier: 3.514A pdb=" N ASP A1151 " --> pdb=" O ASN A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1194 removed outlier: 3.965A pdb=" N LYS A1168 " --> pdb=" O GLU A1164 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1256 Processing helix chain 'A' and resid 1273 through 1286 Processing helix chain 'A' and resid 1287 through 1290 removed outlier: 3.548A pdb=" N LYS A1290 " --> pdb=" O GLY A1287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1287 through 1290' Processing helix chain 'A' and resid 1301 through 1312 Processing helix chain 'A' and resid 1345 through 1351 Processing helix chain 'A' and resid 1354 through 1360 Processing helix chain 'A' and resid 1366 through 1384 Processing helix chain 'A' and resid 1388 through 1394 Processing helix chain 'A' and resid 1398 through 1400 No H-bonds generated for 'chain 'A' and resid 1398 through 1400' Processing helix chain 'A' and resid 1401 through 1422 removed outlier: 3.875A pdb=" N ILE A1405 " --> pdb=" O ASP A1401 " (cutoff:3.500A) Processing helix chain 'A' and resid 1429 through 1433 Processing helix chain 'A' and resid 1435 through 1457 Processing helix chain 'A' and resid 1477 through 1489 Processing helix chain 'A' and resid 1493 through 1515 removed outlier: 3.706A pdb=" N THR A1499 " --> pdb=" O ARG A1495 " (cutoff:3.500A) Processing helix chain 'A' and resid 1522 through 1534 Processing helix chain 'A' and resid 1540 through 1551 Processing helix chain 'A' and resid 1561 through 1594 removed outlier: 3.824A pdb=" N TYR A1565 " --> pdb=" O GLU A1561 " (cutoff:3.500A) Proline residue: A1578 - end of helix Processing helix chain 'A' and resid 1609 through 1614 Processing helix chain 'A' and resid 1617 through 1630 Processing helix chain 'A' and resid 1634 through 1641 Processing helix chain 'A' and resid 1648 through 1652 removed outlier: 4.066A pdb=" N GLU A1652 " --> pdb=" O PRO A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1672 through 1677 Processing helix chain 'A' and resid 1715 through 1720 removed outlier: 3.534A pdb=" N MET A1719 " --> pdb=" O ASP A1715 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR A1720 " --> pdb=" O ARG A1716 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1715 through 1720' Processing helix chain 'A' and resid 1720 through 1725 removed outlier: 4.339A pdb=" N ASN A1724 " --> pdb=" O THR A1720 " (cutoff:3.500A) Processing helix chain 'A' and resid 1767 through 1772 removed outlier: 4.093A pdb=" N MET A1771 " --> pdb=" O GLY A1767 " (cutoff:3.500A) Processing helix chain 'A' and resid 1773 through 1775 No H-bonds generated for 'chain 'A' and resid 1773 through 1775' Processing helix chain 'A' and resid 1780 through 1793 removed outlier: 3.600A pdb=" N ASN A1793 " --> pdb=" O ARG A1789 " (cutoff:3.500A) Processing helix chain 'A' and resid 1794 through 1805 removed outlier: 4.589A pdb=" N GLY A1798 " --> pdb=" O ASN A1794 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET A1804 " --> pdb=" O ILE A1800 " (cutoff:3.500A) Processing helix chain 'A' and resid 1806 through 1812 removed outlier: 3.537A pdb=" N ARG A1809 " --> pdb=" O ASP A1806 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 35 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'B' and resid 4 through 19 Processing helix chain 'B' and resid 101 through 113 Processing helix chain 'B' and resid 123 through 132 Processing helix chain 'B' and resid 133 through 151 removed outlier: 4.362A pdb=" N TYR B 137 " --> pdb=" O HIS B 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 34 Processing helix chain 'D' and resid 37 through 41 Processing helix chain 'D' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 136 Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 358 removed outlier: 5.693A pdb=" N MET A 354 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE A 315 " --> pdb=" O MET A 354 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS A 356 " --> pdb=" O VAL A 313 " (cutoff:3.500A) Processing sheet with id=AA3, 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=AA4, 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=AA5, first strand: chain 'A' and resid 931 through 932 Processing sheet with id=AA6, first strand: chain 'A' and resid 1291 through 1294 Processing sheet with id=AA7, first strand: chain 'A' and resid 1291 through 1294 removed outlier: 4.501A pdb=" N PHE A1232 " --> pdb=" O LEU A1333 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1318 through 1319 Processing sheet with id=AA9, first strand: chain 'A' and resid 1603 through 1604 Processing sheet with id=AB1, first strand: chain 'A' and resid 1709 through 1710 Processing sheet with id=AB2, first strand: chain 'A' and resid 1759 through 1761 Processing sheet with id=AB3, first strand: chain 'C' and resid 12 through 16 removed outlier: 9.165A pdb=" N LEU C 67 " --> pdb=" O GLN C 2 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE C 4 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU C 69 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LYS C 6 " --> pdb=" O LEU C 69 " (cutoff:3.500A) 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=AB4, 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=AB5, first strand: chain 'D' and resid 12 through 16 removed outlier: 4.106A pdb=" N SER D 65 " --> pdb=" O GLN D 2 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG D 42 " --> pdb=" O VAL D 70 " (cutoff:3.500A) 800 hydrogen bonds defined for protein. 2253 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: 3.45 Time building geometry restraints manager: 1.45 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 1.453 1.478 -0.025 2.00e-02 2.50e+03 1.57e+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: 0.00 - 2.09: 22499 2.09 - 4.18: 201 4.18 - 6.27: 35 6.27 - 8.35: 6 8.35 - 10.44: 2 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 - 33.10: 9962 33.10 - 66.21: 228 66.21 - 99.31: 25 99.31 - 132.41: 0 132.41 - 165.51: 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 -106.40 59.11 -165.51 1 3.00e+01 1.11e-03 2.10e+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: 219 2.62 - 3.19: 15283 3.19 - 3.76: 25815 3.76 - 4.33: 34886 4.33 - 4.90: 57664 Nonbonded interactions: 133867 Sorted by model distance: nonbonded pdb=" SG CYS A 139 " pdb=" NE2 HIS A 157 " model vdw 2.049 3.480 nonbonded pdb=" OH TYR A 824 " pdb=" OD2 ASP A 836 " model vdw 2.165 3.040 nonbonded pdb=" OG1 THR A 501 " pdb=" OE1 GLN A 542 " model vdw 2.181 3.040 nonbonded pdb=" O SER A1354 " pdb=" OG1 THR A1357 " model vdw 2.201 3.040 nonbonded pdb=" OG SER A 908 " pdb=" OD2 ASP A 912 " model vdw 2.204 3.040 ... (remaining 133862 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.790 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.380 ------------------------------------------------------------------------------- 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 : 0.004 0.271 16839 Z= 0.262 Angle : 0.554 12.237 22763 Z= 0.278 Chirality : 0.040 0.137 2556 Planarity : 0.003 0.039 2911 Dihedral : 14.816 165.514 6290 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.74 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.006 0.000 ARG D 42 TYR 0.024 0.001 TYR A 980 PHE 0.013 0.001 PHE A1037 TRP 0.013 0.001 TRP B 149 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00288 (16810) covalent geometry : angle 0.54183 (22743) hydrogen bonds : bond 0.16846 ( 796) hydrogen bonds : angle 6.23581 ( 2253) metal coordination : bond 0.06097 ( 26) metal coordination : angle 3.90773 ( 20) Misc. bond : bond 0.16073 ( 3) *********************** 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 to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.548 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: 0.8176 (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: 0.1317 time to fit residues: 33.2265 Evaluate side-chains 111 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 98 optimal weight: 0.1980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN A 620 ASN ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 HIS ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN D 68 HIS ** F 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.049103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.036121 restraints weight = 88912.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.037395 restraints weight = 49353.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.038235 restraints weight = 34106.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.038814 restraints weight = 26844.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.039208 restraints weight = 22841.097| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 16839 Z= 0.130 Angle : 0.576 11.330 22763 Z= 0.290 Chirality : 0.040 0.145 2556 Planarity : 0.004 0.052 2911 Dihedral : 5.036 147.270 2198 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.48 % Allowed : 5.97 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.19), residues: 2013 helix: 1.69 (0.17), residues: 990 sheet: -0.60 (0.41), residues: 141 loop : -0.52 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 54 TYR 0.013 0.001 TYR A 980 PHE 0.014 0.001 PHE B 53 TRP 0.026 0.001 TRP B 149 HIS 0.008 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00288 (16810) covalent geometry : angle 0.56805 (22743) hydrogen bonds : bond 0.04021 ( 796) hydrogen bonds : angle 5.03131 ( 2253) metal coordination : bond 0.01857 ( 26) metal coordination : angle 3.28614 ( 20) Misc. bond : bond 0.00393 ( 3) *********************** 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 132 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 ILE cc_start: 0.8551 (tt) cc_final: 0.8255 (tt) REVERT: A 1191 MET cc_start: 0.9054 (ppp) cc_final: 0.8623 (ppp) REVERT: A 1543 MET cc_start: 0.9362 (mtt) cc_final: 0.9062 (ptp) REVERT: A 1691 MET cc_start: 0.7069 (mpp) cc_final: 0.6860 (pmm) REVERT: A 1771 MET cc_start: 0.8837 (tpt) cc_final: 0.8575 (tpt) REVERT: B 13 PHE cc_start: 0.9311 (t80) cc_final: 0.8955 (t80) REVERT: B 17 LYS cc_start: 0.9359 (mtpt) cc_final: 0.8986 (mtpt) REVERT: D 1 MET cc_start: 0.8219 (tpt) cc_final: 0.7850 (tpt) REVERT: D 63 LYS cc_start: 0.9352 (tppt) cc_final: 0.8928 (tppt) REVERT: D 64 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8815 (mt-10) REVERT: D 74 ARG cc_start: 0.6768 (mmp80) cc_final: 0.6562 (mmp80) outliers start: 9 outliers final: 5 residues processed: 127 average time/residue: 0.1217 time to fit residues: 24.7012 Evaluate side-chains 116 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 842 LEU 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 64 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 154 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 121 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN ** A 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 HIS B 114 ASN ** F 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.047191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.034376 restraints weight = 91658.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.035575 restraints weight = 51265.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.036362 restraints weight = 35695.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.036921 restraints weight = 28209.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.037260 restraints weight = 24070.203| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16839 Z= 0.233 Angle : 0.604 9.782 22763 Z= 0.309 Chirality : 0.042 0.162 2556 Planarity : 0.004 0.055 2911 Dihedral : 5.079 138.739 2198 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.18 % Allowed : 8.61 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.19), residues: 2013 helix: 1.59 (0.16), residues: 989 sheet: -0.92 (0.40), residues: 148 loop : -0.53 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 54 TYR 0.018 0.002 TYR A 980 PHE 0.015 0.001 PHE A1728 TRP 0.010 0.001 TRP B 149 HIS 0.005 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00512 (16810) covalent geometry : angle 0.59937 (22743) hydrogen bonds : bond 0.03809 ( 796) hydrogen bonds : angle 4.95621 ( 2253) metal coordination : bond 0.02037 ( 26) metal coordination : angle 2.66846 ( 20) Misc. bond : bond 0.00045 ( 3) *********************** 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 136 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 ILE cc_start: 0.8659 (tt) cc_final: 0.8346 (tt) REVERT: A 1191 MET cc_start: 0.9130 (ppp) cc_final: 0.8849 (ppp) REVERT: B 13 PHE cc_start: 0.9414 (t80) cc_final: 0.9127 (t80) REVERT: B 17 LYS cc_start: 0.9423 (mtpt) cc_final: 0.9111 (mtpt) REVERT: B 39 MET cc_start: 0.8380 (tmm) cc_final: 0.8167 (tmm) REVERT: B 95 ARG cc_start: 0.7585 (tpm170) cc_final: 0.7315 (tpp-160) REVERT: D 18 GLU cc_start: 0.8912 (tp30) cc_final: 0.8507 (tp30) REVERT: D 54 ARG cc_start: 0.8939 (mtm-85) cc_final: 0.8521 (mtm-85) REVERT: D 63 LYS cc_start: 0.9322 (tppt) cc_final: 0.8916 (tppt) REVERT: D 64 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8857 (mp0) outliers start: 22 outliers final: 15 residues processed: 125 average time/residue: 0.1222 time to fit residues: 23.9065 Evaluate side-chains 120 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 1011 ASP Chi-restraints excluded: chain A residue 1076 ASP Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 135 SER 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 Chi-restraints excluded: chain D residue 64 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 63 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 43 optimal weight: 0.3980 chunk 3 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1605 ASN ** A1752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 HIS ** F 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.048195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.035273 restraints weight = 89737.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.036502 restraints weight = 50042.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.037312 restraints weight = 34822.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.037880 restraints weight = 27481.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.038257 restraints weight = 23463.733| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16839 Z= 0.124 Angle : 0.541 11.284 22763 Z= 0.270 Chirality : 0.040 0.148 2556 Planarity : 0.004 0.052 2911 Dihedral : 4.944 135.681 2198 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.08 % Allowed : 10.01 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 2013 helix: 1.76 (0.17), residues: 984 sheet: -0.74 (0.41), residues: 142 loop : -0.49 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 54 TYR 0.009 0.001 TYR A 394 PHE 0.014 0.001 PHE A1728 TRP 0.010 0.001 TRP A 594 HIS 0.003 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00275 (16810) covalent geometry : angle 0.53597 (22743) hydrogen bonds : bond 0.03354 ( 796) hydrogen bonds : angle 4.66898 ( 2253) metal coordination : bond 0.01308 ( 26) metal coordination : angle 2.56544 ( 20) Misc. bond : bond 0.00005 ( 3) *********************** 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 to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 ILE cc_start: 0.8576 (tt) cc_final: 0.8286 (tt) REVERT: A 1191 MET cc_start: 0.9103 (ppp) cc_final: 0.8840 (ppp) REVERT: A 1543 MET cc_start: 0.9377 (mtt) cc_final: 0.9151 (ptp) REVERT: A 1628 MET cc_start: 0.8752 (mmt) cc_final: 0.8401 (mmt) REVERT: B 17 LYS cc_start: 0.9422 (mtpt) cc_final: 0.9034 (mttt) REVERT: B 95 ARG cc_start: 0.7623 (tpm170) cc_final: 0.7404 (tpp-160) REVERT: D 18 GLU cc_start: 0.8963 (tp30) cc_final: 0.8532 (tp30) REVERT: D 54 ARG cc_start: 0.8936 (mtm-85) cc_final: 0.8416 (mtm-85) REVERT: D 58 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8369 (p0) REVERT: D 63 LYS cc_start: 0.9351 (tppt) cc_final: 0.8930 (tppt) REVERT: D 64 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8820 (mp0) outliers start: 20 outliers final: 9 residues processed: 130 average time/residue: 0.1158 time to fit residues: 23.7734 Evaluate side-chains 122 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 1145 TYR 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 14 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 64 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 45 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 166 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 173 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN ** D 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.046405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.033634 restraints weight = 92151.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.034781 restraints weight = 51985.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.035554 restraints weight = 36453.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.036090 restraints weight = 28942.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.036422 restraints weight = 24768.918| |-----------------------------------------------------------------------------| r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 16839 Z= 0.270 Angle : 0.628 10.698 22763 Z= 0.321 Chirality : 0.042 0.140 2556 Planarity : 0.004 0.059 2911 Dihedral : 5.097 132.854 2198 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.56 % Allowed : 11.52 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.19), residues: 2013 helix: 1.52 (0.16), residues: 997 sheet: -0.82 (0.42), residues: 137 loop : -0.60 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 11 TYR 0.014 0.002 TYR A 980 PHE 0.017 0.002 PHE A 170 TRP 0.033 0.002 TRP B 149 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00592 (16810) covalent geometry : angle 0.62333 (22743) hydrogen bonds : bond 0.03694 ( 796) hydrogen bonds : angle 4.87619 ( 2253) metal coordination : bond 0.02188 ( 26) metal coordination : angle 2.58685 ( 20) Misc. bond : bond 0.00029 ( 3) *********************** 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 to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 ILE cc_start: 0.8734 (tt) cc_final: 0.8444 (tt) REVERT: A 842 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9119 (mm) REVERT: A 1543 MET cc_start: 0.9355 (mtt) cc_final: 0.9095 (mtp) REVERT: B 39 MET cc_start: 0.8403 (tmm) cc_final: 0.8068 (tmm) REVERT: D 18 GLU cc_start: 0.9001 (tp30) cc_final: 0.8587 (tp30) REVERT: D 54 ARG cc_start: 0.8932 (mtm-85) cc_final: 0.8520 (mtm-85) REVERT: D 58 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8343 (p0) REVERT: D 63 LYS cc_start: 0.9368 (tppt) cc_final: 0.8915 (tppt) REVERT: D 64 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8859 (mp0) outliers start: 29 outliers final: 14 residues processed: 122 average time/residue: 0.1299 time to fit residues: 24.8516 Evaluate side-chains 121 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 1011 ASP Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain B residue 11 ARG 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 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 Chi-restraints excluded: chain D residue 64 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 164 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 131 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 181 optimal weight: 0.0030 chunk 142 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 115 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1752 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 = 0.3242 r_free = 0.3242 target = 0.048285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.035420 restraints weight = 89086.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.036659 restraints weight = 49487.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.037496 restraints weight = 34325.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.038055 restraints weight = 27100.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.038425 restraints weight = 23139.167| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 16839 Z= 0.104 Angle : 0.543 12.981 22763 Z= 0.269 Chirality : 0.039 0.147 2556 Planarity : 0.004 0.049 2911 Dihedral : 4.819 124.783 2198 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.97 % Allowed : 12.27 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.19), residues: 2013 helix: 1.82 (0.17), residues: 979 sheet: -0.81 (0.42), residues: 137 loop : -0.52 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 95 TYR 0.010 0.001 TYR A 535 PHE 0.012 0.001 PHE A1728 TRP 0.016 0.001 TRP B 149 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00232 (16810) covalent geometry : angle 0.53753 (22743) hydrogen bonds : bond 0.03229 ( 796) hydrogen bonds : angle 4.51578 ( 2253) metal coordination : bond 0.01024 ( 26) metal coordination : angle 2.66049 ( 20) Misc. bond : bond 0.00016 ( 3) *********************** 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 147 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 ILE cc_start: 0.8603 (tt) cc_final: 0.8331 (tt) REVERT: A 842 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9061 (mm) REVERT: A 996 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8259 (pp20) REVERT: A 1355 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8398 (tt) REVERT: A 1628 MET cc_start: 0.8713 (mmt) cc_final: 0.8373 (mmt) REVERT: B 39 MET cc_start: 0.8296 (tmm) cc_final: 0.7943 (tmm) REVERT: D 18 GLU cc_start: 0.8995 (tp30) cc_final: 0.8616 (tp30) REVERT: D 34 GLU cc_start: 0.9318 (mm-30) cc_final: 0.9104 (mm-30) REVERT: D 50 LEU cc_start: 0.8425 (mp) cc_final: 0.8175 (mp) REVERT: D 54 ARG cc_start: 0.8941 (mtm-85) cc_final: 0.8541 (mtm-85) REVERT: D 58 ASP cc_start: 0.8561 (m-30) cc_final: 0.8340 (p0) REVERT: D 63 LYS cc_start: 0.9360 (tppt) cc_final: 0.9136 (tppt) outliers start: 18 outliers final: 8 residues processed: 142 average time/residue: 0.1260 time to fit residues: 27.6525 Evaluate side-chains 124 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 996 GLU Chi-restraints excluded: chain A residue 1355 LEU Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 32 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 141 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1752 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 = 0.3232 r_free = 0.3232 target = 0.047886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.035066 restraints weight = 89828.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.036293 restraints weight = 49755.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.037122 restraints weight = 34421.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.037676 restraints weight = 27121.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.038021 restraints weight = 23133.692| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16839 Z= 0.123 Angle : 0.548 12.555 22763 Z= 0.271 Chirality : 0.040 0.167 2556 Planarity : 0.004 0.067 2911 Dihedral : 4.739 122.839 2198 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.86 % Allowed : 13.83 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.19), residues: 2013 helix: 1.80 (0.17), residues: 984 sheet: -0.76 (0.43), residues: 136 loop : -0.55 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 54 TYR 0.009 0.001 TYR A 394 PHE 0.021 0.001 PHE A 170 TRP 0.042 0.001 TRP B 149 HIS 0.003 0.001 HIS A1240 Details of bonding type rmsd covalent geometry : bond 0.00279 (16810) covalent geometry : angle 0.54281 (22743) hydrogen bonds : bond 0.03178 ( 796) hydrogen bonds : angle 4.48805 ( 2253) metal coordination : bond 0.01091 ( 26) metal coordination : angle 2.51428 ( 20) Misc. bond : bond 0.00010 ( 3) *********************** 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 139 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 ILE cc_start: 0.8652 (tt) cc_final: 0.8386 (tt) REVERT: A 418 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8359 (ttm) REVERT: A 842 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9025 (mm) REVERT: A 996 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8173 (pp20) REVERT: B 10 MET cc_start: 0.8983 (mtp) cc_final: 0.8576 (tpp) REVERT: B 14 LYS cc_start: 0.9416 (ttmt) cc_final: 0.9126 (mmtp) REVERT: B 17 LYS cc_start: 0.9336 (mtpt) cc_final: 0.9127 (mttt) REVERT: D 18 GLU cc_start: 0.8993 (tp30) cc_final: 0.8619 (tp30) REVERT: D 34 GLU cc_start: 0.9345 (mm-30) cc_final: 0.9138 (mm-30) REVERT: D 50 LEU cc_start: 0.8454 (mp) cc_final: 0.8190 (mp) REVERT: D 54 ARG cc_start: 0.8905 (mtm-85) cc_final: 0.8362 (mtm-85) REVERT: D 63 LYS cc_start: 0.9288 (tppt) cc_final: 0.9033 (tppt) outliers start: 16 outliers final: 8 residues processed: 132 average time/residue: 0.1235 time to fit residues: 25.8737 Evaluate side-chains 130 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 418 MET 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 996 GLU Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain D residue 32 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 36 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 174 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1752 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 = 0.3211 r_free = 0.3211 target = 0.047340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.034539 restraints weight = 90213.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.035732 restraints weight = 50103.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.036552 restraints weight = 34818.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.037099 restraints weight = 27452.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.037469 restraints weight = 23432.003| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 16839 Z= 0.159 Angle : 0.563 12.959 22763 Z= 0.281 Chirality : 0.040 0.149 2556 Planarity : 0.004 0.051 2911 Dihedral : 4.707 115.071 2198 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.86 % Allowed : 13.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.19), residues: 2013 helix: 1.76 (0.17), residues: 985 sheet: -0.81 (0.43), residues: 140 loop : -0.55 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 32 TYR 0.010 0.001 TYR A 394 PHE 0.015 0.001 PHE B 13 TRP 0.028 0.001 TRP B 149 HIS 0.003 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00358 (16810) covalent geometry : angle 0.55920 (22743) hydrogen bonds : bond 0.03242 ( 796) hydrogen bonds : angle 4.53255 ( 2253) metal coordination : bond 0.01323 ( 26) metal coordination : angle 2.30209 ( 20) Misc. bond : bond 0.00011 ( 3) *********************** 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 136 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.8925 (ttp) cc_final: 0.8680 (mtm) REVERT: A 340 ILE cc_start: 0.8679 (tt) cc_final: 0.8428 (tt) REVERT: A 842 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9000 (mm) REVERT: A 996 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8130 (pp20) REVERT: A 1628 MET cc_start: 0.8764 (mmt) cc_final: 0.8456 (mmt) REVERT: B 10 MET cc_start: 0.9004 (mtp) cc_final: 0.8479 (tpp) REVERT: B 14 LYS cc_start: 0.9409 (ttmt) cc_final: 0.9122 (mmtt) REVERT: B 49 GLU cc_start: 0.8963 (tt0) cc_final: 0.8640 (tt0) REVERT: B 150 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8807 (mm-30) REVERT: D 50 LEU cc_start: 0.8552 (mp) cc_final: 0.8249 (mp) REVERT: D 54 ARG cc_start: 0.8578 (mtm-85) cc_final: 0.8330 (mtm-85) REVERT: D 63 LYS cc_start: 0.9310 (tppt) cc_final: 0.9045 (tppt) outliers start: 16 outliers final: 12 residues processed: 130 average time/residue: 0.1163 time to fit residues: 24.5929 Evaluate side-chains 130 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 522 GLN 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 915 MET Chi-restraints excluded: chain A residue 996 GLU Chi-restraints excluded: chain A residue 1151 ASP Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 32 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 23 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 174 optimal weight: 6.9990 chunk 29 optimal weight: 0.0570 chunk 65 optimal weight: 2.9990 chunk 126 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 110 optimal weight: 0.0770 chunk 84 optimal weight: 0.8980 chunk 63 optimal weight: 0.4980 chunk 155 optimal weight: 2.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN A 620 ASN ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.048681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.035776 restraints weight = 88391.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.037031 restraints weight = 48449.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.037877 restraints weight = 33442.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.038463 restraints weight = 26252.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.038844 restraints weight = 22298.693| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 16839 Z= 0.102 Angle : 0.570 17.049 22763 Z= 0.276 Chirality : 0.040 0.213 2556 Planarity : 0.004 0.049 2911 Dihedral : 4.417 88.442 2198 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.59 % Allowed : 14.32 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.19), residues: 2013 helix: 1.79 (0.17), residues: 983 sheet: -0.71 (0.43), residues: 137 loop : -0.50 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 54 TYR 0.008 0.001 TYR A 535 PHE 0.015 0.001 PHE B 13 TRP 0.024 0.001 TRP B 149 HIS 0.004 0.001 HIS A1240 Details of bonding type rmsd covalent geometry : bond 0.00227 (16810) covalent geometry : angle 0.56541 (22743) hydrogen bonds : bond 0.03063 ( 796) hydrogen bonds : angle 4.36520 ( 2253) metal coordination : bond 0.00907 ( 26) metal coordination : angle 2.59348 ( 20) Misc. bond : bond 0.00046 ( 3) *********************** 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 141 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.593 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 340 ILE cc_start: 0.8623 (tt) cc_final: 0.8380 (tt) REVERT: A 417 MET cc_start: 0.8288 (mmp) cc_final: 0.8043 (mmp) REVERT: A 842 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9079 (mm) REVERT: A 1628 MET cc_start: 0.8714 (mmt) cc_final: 0.8382 (mmt) REVERT: B 49 GLU cc_start: 0.8980 (tt0) cc_final: 0.8634 (tt0) REVERT: B 150 GLU cc_start: 0.9044 (tm-30) cc_final: 0.8810 (mm-30) REVERT: D 18 GLU cc_start: 0.8967 (tp30) cc_final: 0.8500 (tp30) REVERT: D 50 LEU cc_start: 0.8401 (mp) cc_final: 0.8130 (mp) REVERT: D 54 ARG cc_start: 0.8666 (mtm-85) cc_final: 0.8348 (mtm-85) REVERT: D 63 LYS cc_start: 0.9306 (tppt) cc_final: 0.9035 (tppt) outliers start: 11 outliers final: 6 residues processed: 140 average time/residue: 0.1224 time to fit residues: 27.0674 Evaluate side-chains 128 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLN 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 C residue 64 GLU Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain D residue 32 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 161 optimal weight: 0.0980 chunk 120 optimal weight: 7.9990 chunk 198 optimal weight: 0.0870 chunk 96 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 115 optimal weight: 10.0000 chunk 182 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1224 GLN ** A1752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.048783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.035895 restraints weight = 88117.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.037160 restraints weight = 48550.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.038006 restraints weight = 33453.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.038593 restraints weight = 26271.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.038984 restraints weight = 22271.994| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 16839 Z= 0.103 Angle : 0.582 15.813 22763 Z= 0.278 Chirality : 0.040 0.164 2556 Planarity : 0.004 0.084 2911 Dihedral : 4.291 72.643 2198 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.43 % Allowed : 14.48 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.19), residues: 2013 helix: 1.76 (0.17), residues: 984 sheet: -0.71 (0.43), residues: 138 loop : -0.46 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 54 TYR 0.021 0.001 TYR A1784 PHE 0.054 0.001 PHE B 13 TRP 0.022 0.001 TRP B 149 HIS 0.003 0.001 HIS A1240 Details of bonding type rmsd covalent geometry : bond 0.00237 (16810) covalent geometry : angle 0.57754 (22743) hydrogen bonds : bond 0.03016 ( 796) hydrogen bonds : angle 4.33019 ( 2253) metal coordination : bond 0.00870 ( 26) metal coordination : angle 2.46823 ( 20) Misc. bond : bond 0.00043 ( 3) ********************** 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 131 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 ILE cc_start: 0.8616 (tt) cc_final: 0.8373 (tt) REVERT: A 417 MET cc_start: 0.8293 (mmp) cc_final: 0.8057 (mmp) REVERT: A 842 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9053 (mm) REVERT: A 1628 MET cc_start: 0.8711 (mmt) cc_final: 0.8383 (mmt) REVERT: B 49 GLU cc_start: 0.9006 (tt0) cc_final: 0.8690 (tt0) REVERT: B 150 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8786 (mm-30) REVERT: D 18 GLU cc_start: 0.8956 (tp30) cc_final: 0.8500 (tp30) REVERT: D 50 LEU cc_start: 0.8356 (mp) cc_final: 0.8096 (mp) REVERT: D 54 ARG cc_start: 0.8656 (mtm-85) cc_final: 0.8408 (mtm-85) REVERT: D 63 LYS cc_start: 0.9313 (tppt) cc_final: 0.9021 (tppt) outliers start: 8 outliers final: 5 residues processed: 129 average time/residue: 0.1143 time to fit residues: 23.9058 Evaluate side-chains 125 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain B residue 11 ARG Chi-restraints excluded: chain B residue 135 SER Chi-restraints excluded: chain D residue 32 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 67 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 191 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 182 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1752 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 = 0.3244 r_free = 0.3244 target = 0.048337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.035509 restraints weight = 89367.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.036746 restraints weight = 49420.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.037589 restraints weight = 34059.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.038156 restraints weight = 26754.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.038541 restraints weight = 22801.500| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16839 Z= 0.121 Angle : 0.583 15.517 22763 Z= 0.283 Chirality : 0.040 0.175 2556 Planarity : 0.004 0.066 2911 Dihedral : 4.233 65.771 2198 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.48 % Allowed : 14.59 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.19), residues: 2013 helix: 1.78 (0.17), residues: 985 sheet: -0.70 (0.43), residues: 138 loop : -0.45 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 54 TYR 0.015 0.001 TYR A1784 PHE 0.046 0.001 PHE B 13 TRP 0.053 0.001 TRP B 149 HIS 0.003 0.001 HIS A1240 Details of bonding type rmsd covalent geometry : bond 0.00278 (16810) covalent geometry : angle 0.57901 (22743) hydrogen bonds : bond 0.03080 ( 796) hydrogen bonds : angle 4.36584 ( 2253) metal coordination : bond 0.00970 ( 26) metal coordination : angle 2.26810 ( 20) Misc. bond : bond 0.00038 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2724.91 seconds wall clock time: 48 minutes 1.36 seconds (2881.36 seconds total)