Starting phenix.real_space_refine on Fri Jun 13 20:46:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rhz_19179/06_2025/8rhz_19179.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rhz_19179/06_2025/8rhz_19179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rhz_19179/06_2025/8rhz_19179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rhz_19179/06_2025/8rhz_19179.map" model { file = "/net/cci-nas-00/data/ceres_data/8rhz_19179/06_2025/8rhz_19179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rhz_19179/06_2025/8rhz_19179.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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 6 6.06 5 S 59 5.16 5 C 9732 2.51 5 N 2776 2.21 5 O 2650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15223 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1131, 7067 Classifications: {'peptide': 1131} Incomplete info: {'truncation_to_alanine': 592} Link IDs: {'PTRANS': 54, 'TRANS': 1076} Chain breaks: 28 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 2106 Unresolved non-hydrogen angles: 2672 Unresolved non-hydrogen dihedrals: 1662 Unresolved non-hydrogen chiralities: 197 Planarities with less than four sites: {'GLN:plan1': 54, 'ASP:plan': 37, 'TYR:plan': 11, 'ASN:plan1': 20, 'TRP:plan': 2, 'HIS:plan': 19, 'PHE:plan': 14, 'GLU:plan': 82, 'ARG:plan': 58} Unresolved non-hydrogen planarities: 1258 Chain: "C" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 556 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain breaks: 2 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 84 Chain: "B" Number of atoms: 7038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1148, 7038 Classifications: {'peptide': 1148} Incomplete info: {'truncation_to_alanine': 641} Link IDs: {'PTRANS': 56, 'TRANS': 1091} Chain breaks: 27 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 2293 Unresolved non-hydrogen angles: 2910 Unresolved non-hydrogen dihedrals: 1822 Unresolved non-hydrogen chiralities: 211 Planarities with less than four sites: {'GLN:plan1': 61, 'ASP:plan': 39, 'TYR:plan': 13, 'ASN:plan1': 23, 'TRP:plan': 3, 'HIS:plan': 20, 'PHE:plan': 18, 'GLU:plan': 83, 'ARG:plan': 60} Unresolved non-hydrogen planarities: 1371 Chain: "D" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 556 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain breaks: 2 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 84 Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7201 SG CYS C 42 96.767 75.724 95.695 1.00224.45 S ATOM 7220 SG CYS C 45 95.039 78.933 97.321 1.00234.72 S ATOM 7442 SG CYS C 83 94.619 78.172 93.705 1.00221.50 S ATOM 7371 SG CYS C 75 104.339 69.574 88.000 1.00205.63 S ATOM 7515 SG CYS C 94 104.822 73.443 88.309 1.00237.02 S ATOM 7261 SG CYS C 53 90.793 78.777 94.668 1.00222.77 S ATOM 7280 SG CYS C 56 87.086 79.055 95.518 1.00219.14 S ATOM 7321 SG CYS C 68 88.825 75.559 95.013 1.00221.55 S ATOM 14795 SG CYS D 42 96.256 73.710 36.495 1.00237.61 S ATOM 14814 SG CYS D 45 92.703 74.550 34.887 1.00249.16 S ATOM 15036 SG CYS D 83 93.382 75.259 38.473 1.00228.86 S ATOM 14965 SG CYS D 75 104.165 68.117 44.278 1.00229.53 S ATOM 15109 SG CYS D 94 100.528 66.696 44.060 1.00245.79 S ATOM 14855 SG CYS D 53 91.851 78.789 37.415 1.00237.18 S ATOM 14874 SG CYS D 56 90.664 82.286 36.467 1.00236.66 S ATOM 14915 SG CYS D 68 94.485 81.469 36.950 1.00228.78 S Time building chain proxies: 12.41, per 1000 atoms: 0.82 Number of scatterers: 15223 At special positions: 0 Unit cell: (172.794, 183.008, 131.085, 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 6 29.99 S 59 16.00 O 2650 8.00 N 2776 7.00 C 9732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.59 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 201 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 42 " pdb="ZN ZN C 201 " - pdb=" ND1 HIS C 80 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 83 " pdb="ZN ZN C 201 " - pdb=" SG CYS C 45 " pdb=" ZN C 202 " pdb="ZN ZN C 202 " - pdb=" ND1 HIS C 77 " pdb="ZN ZN C 202 " - pdb=" SG CYS C 75 " pdb="ZN ZN C 202 " - pdb=" SG CYS C 94 " pdb=" ZN C 203 " pdb="ZN ZN C 203 " - pdb=" ND1 HIS C 82 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 53 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 68 " pdb="ZN ZN C 203 " - pdb=" SG CYS C 56 " pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" ND1 HIS D 80 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 42 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 45 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 83 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" ND1 HIS D 77 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 75 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 94 " pdb=" ZN D 203 " pdb="ZN ZN D 203 " - pdb=" ND1 HIS D 82 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 56 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 68 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 53 " Number of angles added : 12 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4678 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 11 sheets defined 72.6% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 68 through 76 Processing helix chain 'A' and resid 110 through 132 Processing helix chain 'A' and resid 135 through 154 Processing helix chain 'A' and resid 158 through 166 Processing helix chain 'A' and resid 166 through 175 removed outlier: 4.196A pdb=" N LEU A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 197 removed outlier: 4.396A pdb=" N HIS A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 211 Processing helix chain 'A' and resid 219 through 234 Processing helix chain 'A' and resid 252 through 270 Processing helix chain 'A' and resid 295 through 317 Processing helix chain 'A' and resid 496 through 508 Processing helix chain 'A' and resid 510 through 522 Proline residue: A 516 - end of helix Processing helix chain 'A' and resid 540 through 552 Processing helix chain 'A' and resid 560 through 566 Processing helix chain 'A' and resid 566 through 572 removed outlier: 3.547A pdb=" N THR A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 991 Processing helix chain 'A' and resid 991 through 1003 Processing helix chain 'A' and resid 1008 through 1024 removed outlier: 3.531A pdb=" N ASP A1024 " --> pdb=" O THR A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1044 Processing helix chain 'A' and resid 1050 through 1068 removed outlier: 3.735A pdb=" N SER A1066 " --> pdb=" O HIS A1062 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N MET A1067 " --> pdb=" O ARG A1063 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N HIS A1068 " --> pdb=" O LEU A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1079 removed outlier: 4.597A pdb=" N ALA A1072 " --> pdb=" O HIS A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1084 Processing helix chain 'A' and resid 1099 through 1106 Processing helix chain 'A' and resid 1111 through 1141 Processing helix chain 'A' and resid 1148 through 1158 Processing helix chain 'A' and resid 1303 through 1330 Processing helix chain 'A' and resid 1332 through 1334 No H-bonds generated for 'chain 'A' and resid 1332 through 1334' Processing helix chain 'A' and resid 1335 through 1357 Proline residue: A1341 - end of helix Processing helix chain 'A' and resid 1360 through 1384 removed outlier: 4.573A pdb=" N SER A1377 " --> pdb=" O GLU A1373 " (cutoff:3.500A) Proline residue: A1378 - end of helix Processing helix chain 'A' and resid 1392 through 1405 Processing helix chain 'A' and resid 1406 through 1410 removed outlier: 4.104A pdb=" N ARG A1409 " --> pdb=" O GLU A1406 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A1410 " --> pdb=" O THR A1407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1406 through 1410' Processing helix chain 'A' and resid 1413 through 1431 removed outlier: 3.930A pdb=" N SER A1417 " --> pdb=" O SER A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1491 Processing helix chain 'A' and resid 1496 through 1517 Processing helix chain 'A' and resid 1519 through 1536 removed outlier: 3.950A pdb=" N MET A1523 " --> pdb=" O ARG A1519 " (cutoff:3.500A) Processing helix chain 'A' and resid 1538 through 1563 Processing helix chain 'A' and resid 1564 through 1582 removed outlier: 3.633A pdb=" N VAL A1568 " --> pdb=" O GLY A1564 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU A1569 " --> pdb=" O ALA A1565 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLU A1579 " --> pdb=" O GLN A1575 " (cutoff:3.500A) Proline residue: A1580 - end of helix Processing helix chain 'A' and resid 1583 through 1585 No H-bonds generated for 'chain 'A' and resid 1583 through 1585' Processing helix chain 'A' and resid 1589 through 1608 removed outlier: 4.226A pdb=" N HIS A1599 " --> pdb=" O HIS A1595 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR A1600 " --> pdb=" O PHE A1596 " (cutoff:3.500A) Processing helix chain 'A' and resid 1611 through 1622 removed outlier: 3.880A pdb=" N GLY A1615 " --> pdb=" O SER A1611 " (cutoff:3.500A) Processing helix chain 'A' and resid 1628 through 1667 removed outlier: 3.756A pdb=" N LEU A1632 " --> pdb=" O ARG A1628 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A1638 " --> pdb=" O LEU A1634 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A1666 " --> pdb=" O GLN A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1715 through 1719 Processing helix chain 'A' and resid 1721 through 1739 Processing helix chain 'A' and resid 1773 through 1783 Processing helix chain 'A' and resid 1789 through 1798 Processing helix chain 'A' and resid 1800 through 1813 Proline residue: A1810 - end of helix removed outlier: 3.652A pdb=" N SER A1813 " --> pdb=" O VAL A1809 " (cutoff:3.500A) Processing helix chain 'A' and resid 1865 through 1883 Processing helix chain 'A' and resid 1889 through 1902 Processing helix chain 'A' and resid 1922 through 1936 Processing helix chain 'A' and resid 2298 through 2316 Processing helix chain 'A' and resid 2327 through 2354 Processing helix chain 'A' and resid 2362 through 2387 removed outlier: 3.517A pdb=" N LEU A2387 " --> pdb=" O LEU A2383 " (cutoff:3.500A) Processing helix chain 'A' and resid 2404 through 2430 Processing helix chain 'C' and resid 53 through 59 removed outlier: 3.942A pdb=" N ASN C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 91 Processing helix chain 'B' and resid 68 through 76 Processing helix chain 'B' and resid 110 through 132 Processing helix chain 'B' and resid 135 through 154 Processing helix chain 'B' and resid 157 through 166 Processing helix chain 'B' and resid 167 through 177 Processing helix chain 'B' and resid 179 through 197 Processing helix chain 'B' and resid 197 through 210 Processing helix chain 'B' and resid 219 through 234 Processing helix chain 'B' and resid 252 through 273 Processing helix chain 'B' and resid 295 through 318 Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'B' and resid 496 through 509 Processing helix chain 'B' and resid 510 through 522 Proline residue: B 516 - end of helix Processing helix chain 'B' and resid 540 through 553 Processing helix chain 'B' and resid 560 through 566 Processing helix chain 'B' and resid 983 through 991 Processing helix chain 'B' and resid 991 through 1003 Processing helix chain 'B' and resid 1009 through 1024 removed outlier: 3.795A pdb=" N ASP B1024 " --> pdb=" O THR B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1025 through 1031 removed outlier: 4.325A pdb=" N ALA B1028 " --> pdb=" O PHE B1025 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B1030 " --> pdb=" O GLU B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1044 removed outlier: 4.216A pdb=" N GLU B1038 " --> pdb=" O HIS B1034 " (cutoff:3.500A) Proline residue: B1039 - end of helix removed outlier: 3.951A pdb=" N LEU B1044 " --> pdb=" O CYS B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1068 Processing helix chain 'B' and resid 1068 through 1078 Processing helix chain 'B' and resid 1079 through 1087 Processing helix chain 'B' and resid 1099 through 1106 Processing helix chain 'B' and resid 1111 through 1138 Processing helix chain 'B' and resid 1148 through 1158 Processing helix chain 'B' and resid 1303 through 1332 removed outlier: 3.912A pdb=" N GLU B1331 " --> pdb=" O ARG B1327 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP B1332 " --> pdb=" O ASP B1328 " (cutoff:3.500A) Processing helix chain 'B' and resid 1335 through 1358 Proline residue: B1341 - end of helix Processing helix chain 'B' and resid 1360 through 1384 removed outlier: 4.563A pdb=" N SER B1377 " --> pdb=" O GLU B1373 " (cutoff:3.500A) Proline residue: B1378 - end of helix Processing helix chain 'B' and resid 1392 through 1405 Processing helix chain 'B' and resid 1413 through 1431 removed outlier: 3.608A pdb=" N SER B1417 " --> pdb=" O SER B1413 " (cutoff:3.500A) Processing helix chain 'B' and resid 1468 through 1491 Processing helix chain 'B' and resid 1496 through 1517 Processing helix chain 'B' and resid 1519 through 1536 removed outlier: 3.704A pdb=" N MET B1523 " --> pdb=" O ARG B1519 " (cutoff:3.500A) Processing helix chain 'B' and resid 1538 through 1563 Processing helix chain 'B' and resid 1564 through 1577 removed outlier: 4.112A pdb=" N GLY B1572 " --> pdb=" O VAL B1568 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B1573 " --> pdb=" O GLU B1569 " (cutoff:3.500A) Processing helix chain 'B' and resid 1581 through 1585 Processing helix chain 'B' and resid 1589 through 1608 removed outlier: 3.905A pdb=" N HIS B1599 " --> pdb=" O HIS B1595 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR B1600 " --> pdb=" O PHE B1596 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP B1603 " --> pdb=" O HIS B1599 " (cutoff:3.500A) Processing helix chain 'B' and resid 1611 through 1622 removed outlier: 3.959A pdb=" N GLY B1615 " --> pdb=" O SER B1611 " (cutoff:3.500A) Processing helix chain 'B' and resid 1623 through 1625 No H-bonds generated for 'chain 'B' and resid 1623 through 1625' Processing helix chain 'B' and resid 1628 through 1668 removed outlier: 3.793A pdb=" N SER B1638 " --> pdb=" O LEU B1634 " (cutoff:3.500A) Processing helix chain 'B' and resid 1715 through 1720 Processing helix chain 'B' and resid 1721 through 1739 Processing helix chain 'B' and resid 1773 through 1782 Processing helix chain 'B' and resid 1790 through 1798 Processing helix chain 'B' and resid 1800 through 1813 Proline residue: B1810 - end of helix Processing helix chain 'B' and resid 1864 through 1884 Processing helix chain 'B' and resid 1885 through 1887 No H-bonds generated for 'chain 'B' and resid 1885 through 1887' Processing helix chain 'B' and resid 1890 through 1902 Processing helix chain 'B' and resid 1922 through 1937 Processing helix chain 'B' and resid 2294 through 2316 Processing helix chain 'B' and resid 2327 through 2355 Processing helix chain 'B' and resid 2362 through 2387 Processing helix chain 'B' and resid 2404 through 2430 Processing helix chain 'D' and resid 53 through 59 removed outlier: 3.942A pdb=" N ASN D 59 " --> pdb=" O GLU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 25 removed outlier: 6.930A pdb=" N ARG A 41 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU A 25 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU A 39 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1694 through 1700 removed outlier: 3.871A pdb=" N ALA A1694 " --> pdb=" O LYS C 25 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLU A1761 " --> pdb=" O LYS C 25 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N TRP C 27 " --> pdb=" O ARG A1759 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ARG A1759 " --> pdb=" O TRP C 27 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ALA C 29 " --> pdb=" O LEU A1757 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU A1757 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ALA C 31 " --> pdb=" O THR A1755 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR A1755 " --> pdb=" O ALA C 31 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1787 through 1788 Processing sheet with id=AA4, first strand: chain 'A' and resid 1939 through 1941 Processing sheet with id=AA5, first strand: chain 'C' and resid 70 through 72 Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AA7, first strand: chain 'B' and resid 1694 through 1700 removed outlier: 5.928A pdb=" N ALA B1694 " --> pdb=" O TRP D 27 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ALA D 29 " --> pdb=" O ALA B1694 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N SER B1696 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ALA D 31 " --> pdb=" O SER B1696 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU B1698 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TRP D 33 " --> pdb=" O LEU B1698 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU B1700 " --> pdb=" O TRP D 33 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1694 through 1700 removed outlier: 5.928A pdb=" N ALA B1694 " --> pdb=" O TRP D 27 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ALA D 29 " --> pdb=" O ALA B1694 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N SER B1696 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ALA D 31 " --> pdb=" O SER B1696 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU B1698 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TRP D 33 " --> pdb=" O LEU B1698 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU B1700 " --> pdb=" O TRP D 33 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLU B1761 " --> pdb=" O LYS D 25 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TRP D 27 " --> pdb=" O ARG B1759 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ARG B1759 " --> pdb=" O TRP D 27 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1788 through 1789 Processing sheet with id=AB1, first strand: chain 'B' and resid 1888 through 1889 Processing sheet with id=AB2, first strand: chain 'D' and resid 70 through 72 1329 hydrogen bonds defined for protein. 3927 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.66 Time building geometry restraints manager: 5.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5180 1.35 - 1.47: 3960 1.47 - 1.59: 6280 1.59 - 1.72: 0 1.72 - 1.84: 76 Bond restraints: 15496 Sorted by residual: bond pdb=" C SER A1708 " pdb=" N PRO A1709 " ideal model delta sigma weight residual 1.334 1.317 0.017 8.40e-03 1.42e+04 3.96e+00 bond pdb=" CB TRP A1325 " pdb=" CG TRP A1325 " ideal model delta sigma weight residual 1.498 1.443 0.055 3.10e-02 1.04e+03 3.16e+00 bond pdb=" C LEU B1336 " pdb=" O LEU B1336 " ideal model delta sigma weight residual 1.237 1.254 -0.017 1.19e-02 7.06e+03 2.09e+00 bond pdb=" CB TRP B1325 " pdb=" CG TRP B1325 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.03e+00 bond pdb=" CB TRP B1705 " pdb=" CG TRP B1705 " ideal model delta sigma weight residual 1.498 1.455 0.043 3.10e-02 1.04e+03 1.95e+00 ... (remaining 15491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 21075 2.27 - 4.53: 238 4.53 - 6.80: 23 6.80 - 9.06: 0 9.06 - 11.33: 1 Bond angle restraints: 21337 Sorted by residual: angle pdb=" N GLU B 24 " pdb=" CA GLU B 24 " pdb=" C GLU B 24 " ideal model delta sigma weight residual 108.52 113.68 -5.16 1.52e+00 4.33e-01 1.15e+01 angle pdb=" N PRO B 252 " pdb=" CA PRO B 252 " pdb=" C PRO B 252 " ideal model delta sigma weight residual 110.40 115.52 -5.12 1.61e+00 3.86e-01 1.01e+01 angle pdb=" N PRO A1709 " pdb=" CA PRO A1709 " pdb=" C PRO A1709 " ideal model delta sigma weight residual 114.68 111.43 3.25 1.04e+00 9.25e-01 9.74e+00 angle pdb=" C PHE B1357 " pdb=" N LEU B1358 " pdb=" CA LEU B1358 " ideal model delta sigma weight residual 121.80 115.29 6.51 2.44e+00 1.68e-01 7.13e+00 angle pdb=" C PHE A1357 " pdb=" CA PHE A1357 " pdb=" CB PHE A1357 " ideal model delta sigma weight residual 111.46 107.57 3.89 1.71e+00 3.42e-01 5.18e+00 ... (remaining 21332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8445 17.98 - 35.97: 378 35.97 - 53.95: 101 53.95 - 71.93: 10 71.93 - 89.91: 8 Dihedral angle restraints: 8942 sinusoidal: 1849 harmonic: 7093 Sorted by residual: dihedral pdb=" CA THR A 992 " pdb=" C THR A 992 " pdb=" N GLN A 993 " pdb=" CA GLN A 993 " ideal model delta harmonic sigma weight residual 180.00 161.88 18.12 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA GLU A 232 " pdb=" C GLU A 232 " pdb=" N THR A 233 " pdb=" CA THR A 233 " ideal model delta harmonic sigma weight residual -180.00 -163.53 -16.47 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA HIS B1068 " pdb=" C HIS B1068 " pdb=" N LYS B1069 " pdb=" CA LYS B1069 " ideal model delta harmonic sigma weight residual 180.00 163.54 16.46 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 8939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1777 0.037 - 0.073: 655 0.073 - 0.110: 171 0.110 - 0.146: 37 0.146 - 0.183: 4 Chirality restraints: 2644 Sorted by residual: chirality pdb=" CB ILE C 44 " pdb=" CA ILE C 44 " pdb=" CG1 ILE C 44 " pdb=" CG2 ILE C 44 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.38e-01 chirality pdb=" CB ILE D 44 " pdb=" CA ILE D 44 " pdb=" CG1 ILE D 44 " pdb=" CG2 ILE D 44 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.06e-01 chirality pdb=" CA VAL D 93 " pdb=" N VAL D 93 " pdb=" C VAL D 93 " pdb=" CB VAL D 93 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.41e-01 ... (remaining 2641 not shown) Planarity restraints: 2785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 251 " -0.038 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO B 252 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 252 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 252 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1579 " -0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO A1580 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A1580 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1580 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1629 " 0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO A1630 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A1630 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1630 " 0.028 5.00e-02 4.00e+02 ... (remaining 2782 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 17 2.41 - 3.03: 10240 3.03 - 3.66: 22071 3.66 - 4.28: 29226 4.28 - 4.90: 47428 Nonbonded interactions: 108982 Sorted by model distance: nonbonded pdb=" OD2 ASP C 97 " pdb="ZN ZN C 202 " model vdw 1.789 2.230 nonbonded pdb=" OD2 ASP D 97 " pdb="ZN ZN D 202 " model vdw 1.969 2.230 nonbonded pdb=" O SER B1789 " pdb=" OG1 THR B1792 " model vdw 2.212 3.040 nonbonded pdb=" O TYR D 106 " pdb=" ND1 HIS D 108 " model vdw 2.247 3.120 nonbonded pdb=" O TYR C 106 " pdb=" ND1 HIS C 108 " model vdw 2.247 3.120 ... (remaining 108977 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 75 or (resid 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 206 or (resid 207 through 229 and \ (name N or name CA or name C or name O or name CB )) or resid 230 through 242 or \ (resid 243 through 244 and (name N or name CA or name C or name O or name CB )) \ or resid 245 through 255 or (resid 256 and (name N or name CA or name C or name \ O or name CB )) or resid 257 or (resid 258 and (name N or name CA or name C or \ name O or name CB )) or resid 259 through 263 or (resid 264 and (name N or name \ CA or name C or name O or name CB )) or resid 265 or (resid 266 through 295 and \ (name N or name CA or name C or name O or name CB )) or resid 296 through 314 or \ (resid 315 through 317 and (name N or name CA or name C or name O or name CB )) \ or resid 318 through 335 or (resid 336 through 337 and (name N or name CA or na \ me C or name O or name CB )) or resid 338 through 477 or (resid 478 and (name N \ or name CA or name C or name O or name CB )) or resid 479 through 542 or (resid \ 543 through 545 and (name N or name CA or name C or name O or name CB )) or resi \ d 546 through 571 or (resid 572 through 1031 and (name N or name CA or name C or \ name O or name CB )) or resid 1032 or (resid 1033 through 1078 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1079 through 1115 or (resid 11 \ 16 through 1122 and (name N or name CA or name C or name O or name CB )) or resi \ d 1123 through 1125 or (resid 1126 through 1127 and (name N or name CA or name C \ or name O or name CB )) or resid 1128 through 1130 or (resid 1131 and (name N o \ r name CA or name C or name O or name CB )) or resid 1132 or (resid 1133 through \ 1136 and (name N or name CA or name C or name O or name CB )) or resid 1137 thr \ ough 1154 or (resid 1155 through 1302 and (name N or name CA or name C or name O \ or name CB )) or resid 1303 through 1304 or (resid 1305 and (name N or name CA \ or name C or name O or name CB )) or resid 1306 through 1308 or (resid 1309 and \ (name N or name CA or name C or name O or name CB )) or resid 1310 through 1313 \ or (resid 1314 and (name N or name CA or name C or name O or name CB )) or resid \ 1315 through 1318 or (resid 1319 through 1320 and (name N or name CA or name C \ or name O or name CB )) or resid 1321 through 1328 or (resid 1329 through 1331 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1332 through 13 \ 45 or (resid 1346 and (name N or name CA or name C or name O or name CB )) or re \ sid 1347 through 1350 or (resid 1351 and (name N or name CA or name C or name O \ or name CB )) or resid 1352 through 1357 or (resid 1358 and (name N or name CA o \ r name C or name O or name CB )) or resid 1359 through 1380 or (resid 1381 and ( \ name N or name CA or name C or name O or name CB )) or resid 1382 through 1430 o \ r (resid 1431 through 1469 and (name N or name CA or name C or name O or name CB \ )) or resid 1470 or (resid 1471 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1472 through 1478 or (resid 1479 and (name N or name CA or na \ me C or name O or name CB )) or resid 1480 through 1553 or (resid 1554 and (name \ N or name CA or name C or name O or name CB )) or resid 1555 through 1574 or (r \ esid 1575 and (name N or name CA or name C or name O or name CB )) or resid 1576 \ through 1584 or (resid 1585 and (name N or name CA or name C or name O or name \ CB )) or resid 1586 through 1612 or (resid 1613 through 1614 and (name N or name \ CA or name C or name O or name CB )) or resid 1615 through 1652 or (resid 1653 \ and (name N or name CA or name C or name O or name CB )) or resid 1654 through 1 \ 656 or (resid 1657 and (name N or name CA or name C or name O or name CB )) or r \ esid 1658 through 1702 or (resid 1703 through 1704 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1705 through 1756 or (resid 1757 and (name \ N or name CA or name C or name O or name CB )) or resid 1758 through 1780 or (re \ sid 1781 and (name N or name CA or name C or name O or name CB )) or resid 1782 \ through 1798 or (resid 1799 through 1800 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1801 through 1892 or (resid 1893 and (name N or name \ CA or name C or name O or name CB )) or resid 1894 through 1900 or (resid 1901 t \ hrough 1921 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 22 through 1932 or (resid 1933 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1934 through 1937 or (resid 1938 through 1945 and (name N or na \ me CA or name C or name O or name CB )) or resid 1946 through 2430)) selection = (chain 'B' and (resid 10 through 61 or (resid 62 and (name N or name CA or name \ C or name O or name CB )) or resid 63 through 175 or resid 179 through 260 or (r \ esid 261 through 262 and (name N or name CA or name C or name O or name CB )) or \ resid 263 through 320 or resid 330 through 340 or (resid 476 and (name N or nam \ e CA or name C or name O or name CB )) or resid 477 through 482 or resid 495 thr \ ough 499 or (resid 500 through 504 and (name N or name CA or name C or name O or \ name CB )) or resid 505 through 1014 or (resid 1015 through 1031 and (name N or \ name CA or name C or name O or name CB )) or resid 1032 through 1114 or (resid \ 1115 through 1122 and (name N or name CA or name C or name O or name CB )) or re \ sid 1123 through 1152 or (resid 1153 through 1302 and (name N or name CA or name \ C or name O or name CB )) or resid 1303 through 1338 or (resid 1339 and (name N \ or name CA or name C or name O or name CB )) or resid 1340 through 1379 or (res \ id 1380 through 1381 and (name N or name CA or name C or name O or name CB )) or \ resid 1382 through 1393 or (resid 1394 and (name N or name CA or name C or name \ O or name CB )) or resid 1395 through 1404 or (resid 1405 and (name N or name C \ A or name C or name O or name CB or name CG or name CD )) or (resid 1406 through \ 1407 and (name N or name CA or name C or name O or name CB )) or resid 1408 thr \ ough 1419 or (resid 1420 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1421 through 1513 or (resid 1514 and (name N or name CA or name C or \ name O or name CB )) or resid 1515 through 1667 or resid 1691 through 1703 or (r \ esid 1704 and (name N or name CA or name C or name O or name CB )) or resid 1705 \ through 1765 or (resid 1766 through 1767 and (name N or name CA or name C or na \ me O or name CB )) or resid 1768 through 1784 or (resid 1785 through 1787 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1788 through 1789 or \ (resid 1790 through 1791 and (name N or name CA or name C or name O or name CB \ )) or resid 1792 through 1804 or (resid 1805 through 1807 and (name N or name CA \ or name C or name O or name CB )) or resid 1808 through 1836 or resid 1845 thro \ ugh 1858 or resid 1864 through 1873 or (resid 1874 through 1883 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1884 through 1896 or (resid 18 \ 97 through 1921 and (name N or name CA or name C or name O or name CB )) or resi \ d 1922 through 1935 or (resid 1936 and (name N or name CA or name C or name O or \ name CB )) or resid 1937 through 1952 or resid 2297 through 2430)) } ncs_group { reference = chain 'C' selection = chain 'D' } 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 individual isotropic 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: 9.640 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: 0.740 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 45.970 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 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 : 0.009 0.282 15518 Z= 0.375 Angle : 0.633 11.330 21349 Z= 0.354 Chirality : 0.041 0.183 2644 Planarity : 0.005 0.057 2785 Dihedral : 12.492 89.913 4264 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.12 % Allowed : 13.01 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.16), residues: 2313 helix: 0.02 (0.12), residues: 1672 sheet: -2.37 (0.60), residues: 51 loop : -3.14 (0.20), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 33 HIS 0.007 0.001 HIS D 80 PHE 0.020 0.002 PHE A1317 TYR 0.024 0.002 TYR A1501 ARG 0.001 0.000 ARG A1604 Details of bonding type rmsd hydrogen bonds : bond 0.08853 ( 1329) hydrogen bonds : angle 4.80236 ( 3927) metal coordination : bond 0.11575 ( 22) metal coordination : angle 5.10067 ( 12) covalent geometry : bond 0.00739 (15496) covalent geometry : angle 0.62107 (21337) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 2.070 Fit side-chains REVERT: A 243 PHE cc_start: 0.8278 (m-80) cc_final: 0.7939 (m-80) REVERT: A 1352 ASN cc_start: 0.7994 (t0) cc_final: 0.7762 (t0) REVERT: A 1471 ASN cc_start: 0.7960 (m-40) cc_final: 0.7744 (m110) REVERT: A 1545 MET cc_start: 0.8001 (mtp) cc_final: 0.7789 (mtp) REVERT: A 1951 TYR cc_start: 0.7905 (t80) cc_final: 0.7212 (t80) REVERT: B 1558 GLN cc_start: 0.8026 (mt0) cc_final: 0.7790 (mt0) REVERT: B 1644 GLN cc_start: 0.7601 (tp40) cc_final: 0.7359 (tp40) REVERT: B 1658 LEU cc_start: 0.8418 (tp) cc_final: 0.8182 (tt) REVERT: B 1763 GLN cc_start: 0.7146 (tp40) cc_final: 0.6513 (tp40) REVERT: B 1768 ILE cc_start: 0.8448 (mm) cc_final: 0.8206 (mm) outliers start: 1 outliers final: 1 residues processed: 222 average time/residue: 0.2415 time to fit residues: 81.4414 Evaluate side-chains 214 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1608 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 0.9980 chunk 184 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 62 optimal weight: 0.2980 chunk 124 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 115 optimal weight: 9.9990 chunk 141 optimal weight: 0.5980 chunk 220 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1763 GLN C 77 HIS B1598 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.162823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.123352 restraints weight = 26890.427| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.55 r_work: 0.3374 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 2.287 15518 Z= 0.638 Angle : 0.510 8.437 21349 Z= 0.263 Chirality : 0.037 0.149 2644 Planarity : 0.004 0.054 2785 Dihedral : 3.754 31.367 2461 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.67 % Allowed : 15.39 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.18), residues: 2313 helix: 1.75 (0.13), residues: 1683 sheet: -1.80 (0.64), residues: 51 loop : -2.36 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 33 HIS 0.004 0.001 HIS A1155 PHE 0.019 0.002 PHE B1764 TYR 0.018 0.001 TYR A1501 ARG 0.007 0.000 ARG A1486 Details of bonding type rmsd hydrogen bonds : bond 0.05406 ( 1329) hydrogen bonds : angle 4.02652 ( 3927) metal coordination : bond 0.48769 ( 22) metal coordination : angle 3.28759 ( 12) covalent geometry : bond 0.00385 (15496) covalent geometry : angle 0.50431 (21337) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 223 time to evaluate : 1.522 Fit side-chains REVERT: A 243 PHE cc_start: 0.8093 (m-80) cc_final: 0.7694 (m-80) REVERT: A 1352 ASN cc_start: 0.8300 (t0) cc_final: 0.8074 (t0) REVERT: A 1381 GLN cc_start: 0.8689 (tt0) cc_final: 0.8478 (tm-30) REVERT: A 1421 ARG cc_start: 0.8613 (mtt90) cc_final: 0.8372 (mtt90) REVERT: B 261 LYS cc_start: 0.8408 (mtpt) cc_final: 0.8156 (mtpp) REVERT: B 499 TRP cc_start: 0.8415 (t-100) cc_final: 0.8096 (t-100) REVERT: B 1405 ARG cc_start: 0.8176 (tpt-90) cc_final: 0.7924 (tpt-90) REVERT: B 1510 ARG cc_start: 0.8591 (ttp80) cc_final: 0.8350 (ttp80) REVERT: B 1658 LEU cc_start: 0.8613 (tp) cc_final: 0.8407 (tt) REVERT: B 1763 GLN cc_start: 0.7291 (tp40) cc_final: 0.6298 (tp40) outliers start: 14 outliers final: 7 residues processed: 227 average time/residue: 0.2560 time to fit residues: 87.4546 Evaluate side-chains 224 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 217 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1431 HIS Chi-restraints excluded: chain A residue 1554 ASP Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1809 VAL Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 205 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 11 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 234 optimal weight: 9.9990 chunk 224 optimal weight: 9.9990 chunk 191 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 104 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.161321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.121791 restraints weight = 26736.995| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.56 r_work: 0.3350 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 15518 Z= 0.249 Angle : 0.547 9.100 21349 Z= 0.288 Chirality : 0.039 0.150 2644 Planarity : 0.004 0.053 2785 Dihedral : 3.779 17.633 2459 Min Nonbonded Distance : 1.588 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.15 % Allowed : 16.47 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.18), residues: 2313 helix: 2.07 (0.13), residues: 1685 sheet: -1.39 (0.66), residues: 50 loop : -2.08 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 33 HIS 0.036 0.001 HIS C 77 PHE 0.025 0.002 PHE A1650 TYR 0.025 0.002 TYR A1501 ARG 0.007 0.000 ARG A1348 Details of bonding type rmsd hydrogen bonds : bond 0.06230 ( 1329) hydrogen bonds : angle 4.10847 ( 3927) metal coordination : bond 0.01651 ( 22) metal coordination : angle 2.72136 ( 12) covalent geometry : bond 0.00548 (15496) covalent geometry : angle 0.54292 (21337) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 220 time to evaluate : 1.600 Fit side-chains REVERT: A 1352 ASN cc_start: 0.8307 (t0) cc_final: 0.8076 (t0) REVERT: B 261 LYS cc_start: 0.8448 (mtpt) cc_final: 0.8204 (mtpp) REVERT: B 1510 ARG cc_start: 0.8576 (ttp80) cc_final: 0.8324 (ttp80) REVERT: B 1763 GLN cc_start: 0.7346 (tp40) cc_final: 0.6455 (tp40) outliers start: 18 outliers final: 14 residues processed: 229 average time/residue: 0.2464 time to fit residues: 86.0186 Evaluate side-chains 229 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 215 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 1408 SER Chi-restraints excluded: chain A residue 1431 HIS Chi-restraints excluded: chain A residue 1484 VAL Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1570 MET Chi-restraints excluded: chain A residue 1799 LEU Chi-restraints excluded: chain A residue 1809 VAL Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain B residue 1599 HIS Chi-restraints excluded: chain B residue 1849 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 140 optimal weight: 0.0770 chunk 233 optimal weight: 10.0000 chunk 167 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 149 optimal weight: 9.9990 chunk 241 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 230 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1558 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.164001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.125510 restraints weight = 26650.762| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.87 r_work: 0.3375 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15518 Z= 0.158 Angle : 0.482 7.748 21349 Z= 0.247 Chirality : 0.036 0.194 2644 Planarity : 0.004 0.051 2785 Dihedral : 3.487 17.307 2459 Min Nonbonded Distance : 1.598 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.39 % Allowed : 17.90 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.18), residues: 2313 helix: 2.62 (0.13), residues: 1681 sheet: -1.00 (0.69), residues: 50 loop : -1.85 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 33 HIS 0.010 0.001 HIS C 77 PHE 0.019 0.001 PHE B1764 TYR 0.020 0.001 TYR A1501 ARG 0.003 0.000 ARG A1348 Details of bonding type rmsd hydrogen bonds : bond 0.04980 ( 1329) hydrogen bonds : angle 3.77146 ( 3927) metal coordination : bond 0.01417 ( 22) metal coordination : angle 2.46897 ( 12) covalent geometry : bond 0.00339 (15496) covalent geometry : angle 0.47879 (21337) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 213 time to evaluate : 2.215 Fit side-chains revert: symmetry clash REVERT: A 306 VAL cc_start: 0.8768 (t) cc_final: 0.8509 (p) REVERT: A 505 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7687 (m-80) REVERT: A 1352 ASN cc_start: 0.8194 (t0) cc_final: 0.7966 (t0) REVERT: A 1381 GLN cc_start: 0.8455 (tt0) cc_final: 0.8233 (tm-30) REVERT: A 1421 ARG cc_start: 0.8348 (mmt90) cc_final: 0.8063 (mtt90) REVERT: B 261 LYS cc_start: 0.8182 (mtpt) cc_final: 0.7927 (mtpp) REVERT: B 319 TRP cc_start: 0.7295 (m-10) cc_final: 0.7036 (m-10) REVERT: B 499 TRP cc_start: 0.8248 (t-100) cc_final: 0.7919 (t-100) REVERT: B 1510 ARG cc_start: 0.8387 (ttp80) cc_final: 0.8086 (ttp80) REVERT: B 1514 GLU cc_start: 0.8457 (pt0) cc_final: 0.8021 (pt0) REVERT: B 1644 GLN cc_start: 0.7870 (tp40) cc_final: 0.7658 (tp40) REVERT: B 1724 PHE cc_start: 0.8664 (m-10) cc_final: 0.8293 (m-80) REVERT: B 1763 GLN cc_start: 0.7309 (tp40) cc_final: 0.6396 (tp40) outliers start: 20 outliers final: 10 residues processed: 224 average time/residue: 0.2820 time to fit residues: 95.0027 Evaluate side-chains 220 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 209 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 1431 HIS Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1799 LEU Chi-restraints excluded: chain A residue 1809 VAL Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain B residue 1849 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 72 optimal weight: 0.0970 chunk 44 optimal weight: 0.9980 chunk 194 optimal weight: 0.3980 chunk 197 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 192 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 147 optimal weight: 0.0670 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.165705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.126571 restraints weight = 27135.075| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.62 r_work: 0.3420 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15518 Z= 0.121 Angle : 0.463 10.230 21349 Z= 0.232 Chirality : 0.035 0.162 2644 Planarity : 0.004 0.046 2785 Dihedral : 3.282 17.460 2459 Min Nonbonded Distance : 1.622 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.91 % Allowed : 18.62 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.18), residues: 2313 helix: 3.06 (0.13), residues: 1681 sheet: -0.85 (0.71), residues: 50 loop : -1.71 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 33 HIS 0.013 0.001 HIS C 77 PHE 0.023 0.001 PHE B1764 TYR 0.016 0.001 TYR A1501 ARG 0.007 0.000 ARG A1486 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 1329) hydrogen bonds : angle 3.53367 ( 3927) metal coordination : bond 0.01164 ( 22) metal coordination : angle 2.24403 ( 12) covalent geometry : bond 0.00252 (15496) covalent geometry : angle 0.45972 (21337) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 216 time to evaluate : 1.658 Fit side-chains revert: symmetry clash REVERT: A 306 VAL cc_start: 0.8714 (t) cc_final: 0.8461 (p) REVERT: A 505 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7732 (t80) REVERT: A 1352 ASN cc_start: 0.8210 (t0) cc_final: 0.7983 (t0) REVERT: A 1951 TYR cc_start: 0.7894 (t80) cc_final: 0.7287 (t80) REVERT: B 499 TRP cc_start: 0.8201 (t-100) cc_final: 0.7872 (t-100) REVERT: B 1510 ARG cc_start: 0.8343 (ttp80) cc_final: 0.8040 (ttp80) REVERT: B 1514 GLU cc_start: 0.8386 (pt0) cc_final: 0.8002 (pt0) REVERT: B 1724 PHE cc_start: 0.8649 (m-10) cc_final: 0.8278 (m-80) REVERT: B 1763 GLN cc_start: 0.7252 (tp40) cc_final: 0.6338 (tp40) REVERT: D 87 TRP cc_start: 0.8122 (OUTLIER) cc_final: 0.7881 (t60) outliers start: 16 outliers final: 8 residues processed: 223 average time/residue: 0.2495 time to fit residues: 84.1457 Evaluate side-chains 219 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 209 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 1431 HIS Chi-restraints excluded: chain A residue 1554 ASP Chi-restraints excluded: chain A residue 1799 LEU Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1809 VAL Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 1849 ILE Chi-restraints excluded: chain D residue 87 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 233 optimal weight: 50.0000 chunk 30 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 126 optimal weight: 0.0570 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 110 optimal weight: 20.0000 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1323 GLN ** B1644 GLN ** 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 = 0.4068 r_free = 0.4068 target = 0.163713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.124755 restraints weight = 26941.222| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.49 r_work: 0.3408 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15518 Z= 0.157 Angle : 0.475 8.682 21349 Z= 0.242 Chirality : 0.036 0.224 2644 Planarity : 0.004 0.047 2785 Dihedral : 3.304 17.135 2459 Min Nonbonded Distance : 1.628 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.51 % Allowed : 17.66 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.18), residues: 2313 helix: 3.11 (0.13), residues: 1682 sheet: -0.74 (0.72), residues: 50 loop : -1.59 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 33 HIS 0.013 0.001 HIS C 77 PHE 0.021 0.001 PHE B1357 TYR 0.020 0.001 TYR A1501 ARG 0.003 0.000 ARG A1348 Details of bonding type rmsd hydrogen bonds : bond 0.04901 ( 1329) hydrogen bonds : angle 3.57848 ( 3927) metal coordination : bond 0.01179 ( 22) metal coordination : angle 2.09705 ( 12) covalent geometry : bond 0.00341 (15496) covalent geometry : angle 0.47259 (21337) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 1.545 Fit side-chains revert: symmetry clash REVERT: A 306 VAL cc_start: 0.8845 (t) cc_final: 0.8587 (p) REVERT: A 505 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7848 (t80) REVERT: A 1352 ASN cc_start: 0.8366 (t0) cc_final: 0.8135 (t0) REVERT: A 1951 TYR cc_start: 0.8001 (t80) cc_final: 0.7416 (t80) REVERT: C 87 TRP cc_start: 0.7299 (OUTLIER) cc_final: 0.6712 (t60) REVERT: B 499 TRP cc_start: 0.8403 (t-100) cc_final: 0.8094 (t-100) REVERT: B 1357 PHE cc_start: 0.8750 (m-10) cc_final: 0.8509 (m-80) REVERT: B 1514 GLU cc_start: 0.8654 (pt0) cc_final: 0.8297 (pt0) REVERT: B 1724 PHE cc_start: 0.8715 (m-10) cc_final: 0.8353 (m-80) REVERT: B 1763 GLN cc_start: 0.7328 (tp40) cc_final: 0.6391 (tp40) REVERT: D 87 TRP cc_start: 0.8156 (OUTLIER) cc_final: 0.7879 (t60) outliers start: 21 outliers final: 13 residues processed: 225 average time/residue: 0.2507 time to fit residues: 85.6186 Evaluate side-chains 231 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 215 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 1431 HIS Chi-restraints excluded: chain A residue 1554 ASP Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1799 LEU Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1809 VAL Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 87 TRP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain B residue 1658 LEU Chi-restraints excluded: chain B residue 1849 ILE Chi-restraints excluded: chain D residue 87 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 168 optimal weight: 0.9990 chunk 110 optimal weight: 30.0000 chunk 144 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 111 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 176 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1323 GLN ** B1644 GLN ** 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 = 0.4068 r_free = 0.4068 target = 0.163796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.124487 restraints weight = 27028.865| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.61 r_work: 0.3394 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15518 Z= 0.178 Angle : 0.493 10.608 21349 Z= 0.251 Chirality : 0.037 0.206 2644 Planarity : 0.004 0.047 2785 Dihedral : 3.361 17.075 2459 Min Nonbonded Distance : 1.631 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.39 % Allowed : 18.26 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.18), residues: 2313 helix: 3.09 (0.12), residues: 1681 sheet: -0.69 (0.72), residues: 50 loop : -1.54 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 33 HIS 0.013 0.001 HIS C 77 PHE 0.019 0.002 PHE B1148 TYR 0.021 0.001 TYR A1501 ARG 0.006 0.000 ARG B1510 Details of bonding type rmsd hydrogen bonds : bond 0.05160 ( 1329) hydrogen bonds : angle 3.62850 ( 3927) metal coordination : bond 0.01145 ( 22) metal coordination : angle 1.97021 ( 12) covalent geometry : bond 0.00389 (15496) covalent geometry : angle 0.49055 (21337) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 218 time to evaluate : 1.575 Fit side-chains revert: symmetry clash REVERT: A 306 VAL cc_start: 0.8795 (t) cc_final: 0.8519 (p) REVERT: A 505 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7779 (t80) REVERT: A 1352 ASN cc_start: 0.8187 (t0) cc_final: 0.7949 (t0) REVERT: A 1951 TYR cc_start: 0.7888 (t80) cc_final: 0.7332 (t80) REVERT: C 87 TRP cc_start: 0.7308 (OUTLIER) cc_final: 0.6694 (t60) REVERT: B 1514 GLU cc_start: 0.8487 (pt0) cc_final: 0.8130 (pt0) REVERT: B 1724 PHE cc_start: 0.8682 (m-10) cc_final: 0.8321 (m-80) REVERT: B 1763 GLN cc_start: 0.7343 (tp40) cc_final: 0.6429 (tp40) REVERT: D 87 TRP cc_start: 0.8168 (OUTLIER) cc_final: 0.7882 (t60) outliers start: 20 outliers final: 14 residues processed: 230 average time/residue: 0.2507 time to fit residues: 87.3685 Evaluate side-chains 233 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 216 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 1431 HIS Chi-restraints excluded: chain A residue 1554 ASP Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1799 LEU Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1809 VAL Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 87 TRP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain B residue 1849 ILE Chi-restraints excluded: chain D residue 87 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 170 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 234 optimal weight: 10.0000 chunk 229 optimal weight: 7.9990 chunk 223 optimal weight: 10.0000 chunk 84 optimal weight: 0.5980 chunk 158 optimal weight: 0.6980 chunk 232 optimal weight: 7.9990 chunk 236 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1323 GLN ** B1644 GLN ** 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 = 0.4048 r_free = 0.4048 target = 0.162427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.122988 restraints weight = 26852.754| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.57 r_work: 0.3370 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 15518 Z= 0.240 Angle : 0.536 9.492 21349 Z= 0.278 Chirality : 0.039 0.159 2644 Planarity : 0.004 0.050 2785 Dihedral : 3.552 16.755 2459 Min Nonbonded Distance : 1.638 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.51 % Allowed : 18.38 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.18), residues: 2313 helix: 2.89 (0.13), residues: 1688 sheet: -0.83 (0.71), residues: 50 loop : -1.57 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 33 HIS 0.013 0.001 HIS C 77 PHE 0.022 0.002 PHE A1650 TYR 0.025 0.002 TYR A1501 ARG 0.004 0.000 ARG B1510 Details of bonding type rmsd hydrogen bonds : bond 0.05936 ( 1329) hydrogen bonds : angle 3.84089 ( 3927) metal coordination : bond 0.01204 ( 22) metal coordination : angle 1.91457 ( 12) covalent geometry : bond 0.00532 (15496) covalent geometry : angle 0.53440 (21337) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 212 time to evaluate : 1.662 Fit side-chains revert: symmetry clash REVERT: A 306 VAL cc_start: 0.8836 (t) cc_final: 0.8567 (p) REVERT: A 1352 ASN cc_start: 0.8145 (t0) cc_final: 0.7899 (t0) REVERT: A 1951 TYR cc_start: 0.7883 (t80) cc_final: 0.7314 (t80) REVERT: C 87 TRP cc_start: 0.7319 (OUTLIER) cc_final: 0.6686 (t60) REVERT: B 261 LYS cc_start: 0.8185 (mtpt) cc_final: 0.7915 (mtpp) REVERT: B 1514 GLU cc_start: 0.8485 (pt0) cc_final: 0.8135 (pt0) REVERT: B 1724 PHE cc_start: 0.8693 (m-10) cc_final: 0.8464 (m-80) REVERT: B 1763 GLN cc_start: 0.7397 (tp40) cc_final: 0.6491 (tp40) REVERT: D 87 TRP cc_start: 0.8201 (OUTLIER) cc_final: 0.7894 (t60) outliers start: 21 outliers final: 18 residues processed: 223 average time/residue: 0.2605 time to fit residues: 88.4253 Evaluate side-chains 232 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 1431 HIS Chi-restraints excluded: chain A residue 1484 VAL Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1570 MET Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1799 LEU Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1809 VAL Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 87 TRP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain B residue 1599 HIS Chi-restraints excluded: chain B residue 1849 ILE Chi-restraints excluded: chain D residue 87 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 213 optimal weight: 2.9990 chunk 172 optimal weight: 0.2980 chunk 112 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 135 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 205 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1644 GLN ** 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 = 0.4058 r_free = 0.4058 target = 0.163154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.124537 restraints weight = 26743.976| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.86 r_work: 0.3369 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 15518 Z= 0.198 Angle : 0.519 10.069 21349 Z= 0.264 Chirality : 0.037 0.172 2644 Planarity : 0.004 0.052 2785 Dihedral : 3.486 16.769 2459 Min Nonbonded Distance : 1.633 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.39 % Allowed : 18.74 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.18), residues: 2313 helix: 2.99 (0.12), residues: 1682 sheet: -1.00 (0.71), residues: 51 loop : -1.52 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 33 HIS 0.013 0.001 HIS C 77 PHE 0.043 0.002 PHE A1357 TYR 0.022 0.001 TYR A1501 ARG 0.006 0.000 ARG A1486 Details of bonding type rmsd hydrogen bonds : bond 0.05439 ( 1329) hydrogen bonds : angle 3.74460 ( 3927) metal coordination : bond 0.01138 ( 22) metal coordination : angle 1.79824 ( 12) covalent geometry : bond 0.00435 (15496) covalent geometry : angle 0.51708 (21337) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 1.531 Fit side-chains revert: symmetry clash REVERT: A 306 VAL cc_start: 0.8796 (t) cc_final: 0.8549 (p) REVERT: A 505 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7735 (t80) REVERT: A 1352 ASN cc_start: 0.8167 (t0) cc_final: 0.7923 (t0) REVERT: A 1951 TYR cc_start: 0.7873 (t80) cc_final: 0.7302 (t80) REVERT: C 87 TRP cc_start: 0.7280 (OUTLIER) cc_final: 0.6620 (t60) REVERT: B 261 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7938 (mtpp) REVERT: B 499 TRP cc_start: 0.8239 (t-100) cc_final: 0.7926 (t-100) REVERT: B 1514 GLU cc_start: 0.8500 (pt0) cc_final: 0.8154 (pt0) REVERT: B 1724 PHE cc_start: 0.8690 (m-10) cc_final: 0.8425 (m-80) REVERT: B 1763 GLN cc_start: 0.7433 (tp40) cc_final: 0.6525 (tp40) REVERT: D 87 TRP cc_start: 0.8172 (OUTLIER) cc_final: 0.7844 (t60) outliers start: 20 outliers final: 14 residues processed: 223 average time/residue: 0.2634 time to fit residues: 89.7199 Evaluate side-chains 227 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 210 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 1431 HIS Chi-restraints excluded: chain A residue 1484 VAL Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1570 MET Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1799 LEU Chi-restraints excluded: chain A residue 1809 VAL Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 87 TRP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain B residue 1849 ILE Chi-restraints excluded: chain D residue 87 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 25 optimal weight: 0.8980 chunk 179 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 23 optimal weight: 0.0030 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1644 GLN ** 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 = 0.4073 r_free = 0.4073 target = 0.164105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.124882 restraints weight = 26889.190| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.61 r_work: 0.3395 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15518 Z= 0.163 Angle : 0.504 10.669 21349 Z= 0.252 Chirality : 0.037 0.167 2644 Planarity : 0.004 0.050 2785 Dihedral : 3.371 16.670 2459 Min Nonbonded Distance : 1.636 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.03 % Allowed : 19.45 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.18), residues: 2313 helix: 3.15 (0.13), residues: 1681 sheet: -0.91 (0.72), residues: 51 loop : -1.46 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP D 33 HIS 0.012 0.001 HIS C 77 PHE 0.041 0.002 PHE A1357 TYR 0.020 0.001 TYR A1501 ARG 0.005 0.000 ARG B1510 Details of bonding type rmsd hydrogen bonds : bond 0.04984 ( 1329) hydrogen bonds : angle 3.63151 ( 3927) metal coordination : bond 0.01150 ( 22) metal coordination : angle 1.82575 ( 12) covalent geometry : bond 0.00356 (15496) covalent geometry : angle 0.50256 (21337) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 1.638 Fit side-chains revert: symmetry clash REVERT: A 306 VAL cc_start: 0.8759 (t) cc_final: 0.8512 (p) REVERT: A 505 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7752 (t80) REVERT: A 1352 ASN cc_start: 0.8182 (t0) cc_final: 0.7947 (t0) REVERT: A 1951 TYR cc_start: 0.7863 (t80) cc_final: 0.7334 (t80) REVERT: C 87 TRP cc_start: 0.7307 (OUTLIER) cc_final: 0.6586 (t60) REVERT: B 261 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7924 (mtpp) REVERT: B 499 TRP cc_start: 0.8208 (t-100) cc_final: 0.7898 (t-100) REVERT: B 1514 GLU cc_start: 0.8483 (pt0) cc_final: 0.8166 (pt0) REVERT: B 1724 PHE cc_start: 0.8684 (m-10) cc_final: 0.8422 (m-80) REVERT: B 1763 GLN cc_start: 0.7346 (tp40) cc_final: 0.6496 (tp40) REVERT: D 87 TRP cc_start: 0.8187 (OUTLIER) cc_final: 0.7832 (t60) outliers start: 17 outliers final: 14 residues processed: 228 average time/residue: 0.2555 time to fit residues: 87.3043 Evaluate side-chains 232 residues out of total 2163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 215 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 505 PHE Chi-restraints excluded: chain A residue 1431 HIS Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1570 MET Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1799 LEU Chi-restraints excluded: chain A residue 1809 VAL Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain C residue 77 HIS Chi-restraints excluded: chain C residue 87 TRP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain B residue 1849 ILE Chi-restraints excluded: chain D residue 87 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 110 optimal weight: 20.0000 chunk 172 optimal weight: 0.4980 chunk 125 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 194 optimal weight: 0.0670 chunk 144 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 chunk 187 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1644 GLN ** 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 = 0.4086 r_free = 0.4086 target = 0.165241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126065 restraints weight = 26829.249| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.61 r_work: 0.3421 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15518 Z= 0.139 Angle : 0.487 10.214 21349 Z= 0.240 Chirality : 0.036 0.163 2644 Planarity : 0.004 0.048 2785 Dihedral : 3.232 16.611 2459 Min Nonbonded Distance : 1.638 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.79 % Allowed : 19.81 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.18), residues: 2313 helix: 3.34 (0.12), residues: 1681 sheet: -0.74 (0.73), residues: 51 loop : -1.40 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP D 33 HIS 0.012 0.001 HIS C 77 PHE 0.048 0.002 PHE A1357 TYR 0.018 0.001 TYR A1501 ARG 0.005 0.000 ARG B1510 Details of bonding type rmsd hydrogen bonds : bond 0.04502 ( 1329) hydrogen bonds : angle 3.48220 ( 3927) metal coordination : bond 0.01175 ( 22) metal coordination : angle 1.84370 ( 12) covalent geometry : bond 0.00299 (15496) covalent geometry : angle 0.48479 (21337) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10343.29 seconds wall clock time: 178 minutes 38.20 seconds (10718.20 seconds total)