Starting phenix.real_space_refine on Wed Nov 15 21:01:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b52_12017/11_2023/7b52_12017.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b52_12017/11_2023/7b52_12017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b52_12017/11_2023/7b52_12017.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b52_12017/11_2023/7b52_12017.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b52_12017/11_2023/7b52_12017.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b52_12017/11_2023/7b52_12017.pdb" } resolution = 3.8 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= 0.065 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: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 8294 2.51 5 N 2229 2.21 5 O 2576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 13": "OE1" <-> "OE2" Residue "A ASP 25": "OD1" <-> "OD2" Residue "A GLU 36": "OE1" <-> "OE2" Residue "A ASP 45": "OD1" <-> "OD2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 65": "OD1" <-> "OD2" Residue "A ASP 76": "OD1" <-> "OD2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A ASP 194": "OD1" <-> "OD2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 286": "OD1" <-> "OD2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 297": "OD1" <-> "OD2" Residue "A GLU 304": "OE1" <-> "OE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 385": "OE1" <-> "OE2" Residue "A TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "A PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 624": "OE1" <-> "OE2" Residue "A ARG 631": "NH1" <-> "NH2" Residue "A TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 654": "OD1" <-> "OD2" Residue "A ASP 698": "OD1" <-> "OD2" Residue "A GLU 706": "OE1" <-> "OE2" Residue "A ARG 708": "NH1" <-> "NH2" Residue "A TYR 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "A PHE 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 798": "OE1" <-> "OE2" Residue "A GLU 806": "OE1" <-> "OE2" Residue "A ARG 834": "NH1" <-> "NH2" Residue "A ASP 836": "OD1" <-> "OD2" Residue "A ARG 841": "NH1" <-> "NH2" Residue "A TYR 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 874": "OE1" <-> "OE2" Residue "A ASP 881": "OD1" <-> "OD2" Residue "A PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 900": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 907": "OD1" <-> "OD2" Residue "A TYR 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 972": "OE1" <-> "OE2" Residue "A TYR 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1041": "OE1" <-> "OE2" Residue "A TYR 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1095": "OE1" <-> "OE2" Residue "A TYR 1100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1122": "NH1" <-> "NH2" Residue "A TYR 1127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1188": "OE1" <-> "OE2" Residue "A GLU 1189": "OE1" <-> "OE2" Residue "A PHE 1191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1220": "OD1" <-> "OD2" Residue "A TYR 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1259": "OD1" <-> "OD2" Residue "A ASP 1326": "OD1" <-> "OD2" Residue "A ASP 1375": "OD1" <-> "OD2" Residue "A GLU 1411": "OE1" <-> "OE2" Residue "A GLU 1456": "OE1" <-> "OE2" Residue "A TYR 1561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1569": "OD1" <-> "OD2" Residue "A TYR 1597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1617": "NH1" <-> "NH2" Residue "A TYR 1623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1635": "OE1" <-> "OE2" Residue "A GLU 1665": "OE1" <-> "OE2" Residue "A ASP 1681": "OD1" <-> "OD2" Residue "A GLU 1722": "OE1" <-> "OE2" Residue "A ASP 1733": "OD1" <-> "OD2" Residue "A PHE 1806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1808": "OE1" <-> "OE2" Residue "A GLU 1815": "OE1" <-> "OE2" Residue "A TYR 1845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1863": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1867": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1868": "NH1" <-> "NH2" Residue "A TYR 1904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1970": "OE1" <-> "OE2" Residue "A ASP 1977": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 13186 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 13186 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1638, 13185 Classifications: {'peptide': 1638} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 65} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 44, 'TRANS': 1589} Chain breaks: 19 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 9, 'ASP:plan': 5, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 132 Conformer: "B" Number of residues, atoms: 1638, 13185 Classifications: {'peptide': 1638} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 65} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 44, 'TRANS': 1589} Chain breaks: 19 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 9, 'ASP:plan': 5, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 132 bond proxies already assigned to first conformer: 13455 Time building chain proxies: 13.29, per 1000 atoms: 1.01 Number of scatterers: 13186 At special positions: 0 Unit cell: (104.58, 134.46, 144.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 2576 8.00 N 2229 7.00 C 8294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 228 " distance=2.02 Simple disulfide: pdb=" SG CYS A 67 " - pdb=" SG CYS A 106 " distance=2.03 Simple disulfide: pdb=" SG CYS A 305 " - pdb=" SG CYS A 322 " distance=2.04 Simple disulfide: pdb=" SG CYS A 645 " - pdb=" SG CYS A 734 " distance=2.03 Simple disulfide: pdb=" SG CYS A 771 " - pdb=" SG CYS A 910 " distance=2.04 Simple disulfide: pdb=" SG CYS A 785 " - pdb=" SG CYS A 803 " distance=2.03 Simple disulfide: pdb=" SG CYS A 799 " - pdb=" SG CYS A 966 " distance=2.03 Simple disulfide: pdb=" SG CYS A 807 " - pdb=" SG CYS A 964 " distance=2.03 Simple disulfide: pdb=" SG CYS A 975 " - pdb=" SG CYS A1099 " distance=2.03 Simple disulfide: pdb=" SG CYS A 987 " - pdb=" SG CYS A1005 " distance=2.03 Simple disulfide: pdb=" SG CYS A1149 " - pdb=" SG CYS A1180 " distance=2.03 Simple disulfide: pdb=" SG ACYS A1219 " - pdb=" SG CYS A1418 " distance=2.03 Simple disulfide: pdb=" SG CYS A1230 " - pdb=" SG CYS A1273 " distance=2.03 Simple disulfide: pdb=" SG CYS A1251 " - pdb=" SG CYS A1264 " distance=2.03 Simple disulfide: pdb=" SG CYS A1344 " - pdb=" SG CYS A1437 " distance=2.02 Simple disulfide: pdb=" SG CYS A1418 " - pdb=" SG BCYS A1219 " distance=2.03 Simple disulfide: pdb=" SG CYS A1462 " - pdb=" SG CYS A1546 " distance=2.02 Simple disulfide: pdb=" SG CYS A1476 " - pdb=" SG CYS A1501 " distance=2.03 Simple disulfide: pdb=" SG CYS A1486 " - pdb=" SG CYS A1576 " distance=2.03 Simple disulfide: pdb=" SG CYS A1505 " - pdb=" SG CYS A1574 " distance=2.03 Simple disulfide: pdb=" SG CYS A1596 " - pdb=" SG CYS A1632 " distance=2.03 Simple disulfide: pdb=" SG CYS A1688 " - pdb=" SG CYS A1782 " distance=2.03 Simple disulfide: pdb=" SG CYS A1689 " - pdb=" SG CYS A1906 " distance=2.03 Simple disulfide: pdb=" SG CYS A1807 " - pdb=" SG CYS A1909 " distance=2.03 Simple disulfide: pdb=" SG CYS A1821 " - pdb=" SG CYS A1838 " distance=2.03 Simple disulfide: pdb=" SG CYS A1842 " - pdb=" SG CYS A1961 " distance=2.03 Simple disulfide: pdb=" SG CYS A1896 " - pdb=" SG CYS A1907 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.41 Conformation dependent library (CDL) restraints added in 2.5 seconds 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3098 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 2 sheets defined 54.2% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 10 through 16 removed outlier: 4.060A pdb=" N TYR A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 29 removed outlier: 3.990A pdb=" N LEU A 27 " --> pdb=" O LYS A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 99 through 104 removed outlier: 3.578A pdb=" N GLU A 103 " --> pdb=" O PRO A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 120 through 141 removed outlier: 4.075A pdb=" N PHE A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 168 Processing helix chain 'A' and resid 176 through 194 removed outlier: 4.010A pdb=" N ASN A 182 " --> pdb=" O ASN A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 206 through 227 removed outlier: 5.447A pdb=" N GLN A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LYS A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 274 through 298 Processing helix chain 'A' and resid 319 through 349 removed outlier: 4.234A pdb=" N LYS A 323 " --> pdb=" O CYS A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.853A pdb=" N ASN A 354 " --> pdb=" O TYR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 removed outlier: 3.892A pdb=" N PHE A 373 " --> pdb=" O TYR A 369 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 378 " --> pdb=" O PHE A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 391 removed outlier: 3.812A pdb=" N LYS A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A 391 " --> pdb=" O TYR A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 575 removed outlier: 3.850A pdb=" N ALA A 575 " --> pdb=" O GLU A 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 572 through 575' Processing helix chain 'A' and resid 609 through 632 Processing helix chain 'A' and resid 642 through 659 removed outlier: 3.661A pdb=" N LYS A 646 " --> pdb=" O GLU A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 684 removed outlier: 3.663A pdb=" N LYS A 683 " --> pdb=" O ASN A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 714 removed outlier: 4.719A pdb=" N TRP A 711 " --> pdb=" O LEU A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 725 Processing helix chain 'A' and resid 757 through 780 removed outlier: 4.626A pdb=" N TRP A 766 " --> pdb=" O PHE A 762 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ASN A 769 " --> pdb=" O GLU A 765 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASP A 780 " --> pdb=" O ALA A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 785 Processing helix chain 'A' and resid 803 through 816 Processing helix chain 'A' and resid 830 through 851 removed outlier: 3.546A pdb=" N ARG A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 890 Processing helix chain 'A' and resid 896 through 905 removed outlier: 3.616A pdb=" N TYR A 900 " --> pdb=" O THR A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 977 removed outlier: 3.665A pdb=" N THR A 974 " --> pdb=" O THR A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1053 removed outlier: 3.992A pdb=" N THR A1030 " --> pdb=" O GLY A1026 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A1032 " --> pdb=" O ASP A1028 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN A1048 " --> pdb=" O TYR A1044 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A1049 " --> pdb=" O GLN A1045 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A1053 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1126 removed outlier: 3.550A pdb=" N LYS A1106 " --> pdb=" O LEU A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1157 removed outlier: 3.550A pdb=" N PHE A1146 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR A1153 " --> pdb=" O CYS A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1180 removed outlier: 3.760A pdb=" N PHE A1175 " --> pdb=" O ASP A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1200 removed outlier: 3.960A pdb=" N SER A1192 " --> pdb=" O GLU A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1271 Processing helix chain 'A' and resid 1274 through 1278 removed outlier: 3.560A pdb=" N LEU A1277 " --> pdb=" O VAL A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1292 through 1317 Processing helix chain 'A' and resid 1342 through 1359 removed outlier: 3.625A pdb=" N LEU A1359 " --> pdb=" O LYS A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1368 through 1381 removed outlier: 3.785A pdb=" N LEU A1372 " --> pdb=" O HIS A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1427 removed outlier: 4.435A pdb=" N ARG A1410 " --> pdb=" O LYS A1406 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU A1411 " --> pdb=" O GLY A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1444 through 1447 Processing helix chain 'A' and resid 1448 through 1476 Processing helix chain 'A' and resid 1499 through 1530 removed outlier: 4.116A pdb=" N GLN A1517 " --> pdb=" O SER A1513 " (cutoff:3.500A) Processing helix chain 'A' and resid 1534 through 1543 Processing helix chain 'A' and resid 1559 through 1564 Processing helix chain 'A' and resid 1567 through 1572 removed outlier: 3.657A pdb=" N SER A1572 " --> pdb=" O ASP A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1625 through 1630 Processing helix chain 'A' and resid 1635 through 1644 removed outlier: 4.407A pdb=" N ILE A1639 " --> pdb=" O GLU A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1674 removed outlier: 4.050A pdb=" N GLU A1653 " --> pdb=" O LYS A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1679 through 1703 Processing helix chain 'A' and resid 1710 through 1725 removed outlier: 3.990A pdb=" N TYR A1715 " --> pdb=" O GLU A1711 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1741 Processing helix chain 'A' and resid 1755 through 1776 removed outlier: 4.987A pdb=" N TRP A1761 " --> pdb=" O ARG A1757 " (cutoff:3.500A) Processing helix chain 'A' and resid 1793 through 1821 removed outlier: 3.635A pdb=" N GLU A1815 " --> pdb=" O THR A1811 " (cutoff:3.500A) Processing helix chain 'A' and resid 1838 through 1867 Proline residue: A1851 - end of helix removed outlier: 3.733A pdb=" N ILE A1854 " --> pdb=" O ASN A1850 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU A1855 " --> pdb=" O PRO A1851 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP A1856 " --> pdb=" O LYS A1852 " (cutoff:3.500A) Processing helix chain 'A' and resid 1887 through 1894 Processing helix chain 'A' and resid 1941 through 1948 removed outlier: 4.283A pdb=" N ASN A1948 " --> pdb=" O ASN A1944 " (cutoff:3.500A) Processing helix chain 'A' and resid 1951 through 1984 removed outlier: 3.629A pdb=" N ALA A1956 " --> pdb=" O LYS A1952 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N HIS A1957 " --> pdb=" O LYS A1953 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET A1959 " --> pdb=" O SER A1955 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LYS A1960 " --> pdb=" O ALA A1956 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 569 through 570 Processing sheet with id=AA2, first strand: chain 'A' and resid 923 through 925 614 hydrogen bonds defined for protein. 1800 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: 4.27 Time building geometry restraints manager: 5.85 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: 4294 1.35 - 1.47: 3298 1.47 - 1.59: 5760 1.59 - 1.72: 0 1.72 - 1.84: 105 Bond restraints: 13457 Sorted by residual: bond pdb=" C LEU A 236 " pdb=" N ILE A 237 " ideal model delta sigma weight residual 1.329 1.301 0.028 1.69e-02 3.50e+03 2.76e+00 bond pdb=" N ASP A 31 " pdb=" CA ASP A 31 " ideal model delta sigma weight residual 1.456 1.434 0.021 1.48e-02 4.57e+03 2.05e+00 bond pdb=" C SER A 951 " pdb=" N PRO A 952 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 1.97e+00 bond pdb=" CB TYR A 655 " pdb=" CG TYR A 655 " ideal model delta sigma weight residual 1.512 1.483 0.029 2.20e-02 2.07e+03 1.75e+00 bond pdb=" N ASP A 891 " pdb=" CA ASP A 891 " ideal model delta sigma weight residual 1.460 1.484 -0.023 1.83e-02 2.99e+03 1.62e+00 ... (remaining 13452 not shown) Histogram of bond angle deviations from ideal: 97.23 - 104.75: 146 104.75 - 112.27: 6409 112.27 - 119.79: 5117 119.79 - 127.32: 6319 127.32 - 134.84: 142 Bond angle restraints: 18133 Sorted by residual: angle pdb=" N GLN A1758 " pdb=" CA GLN A1758 " pdb=" C GLN A1758 " ideal model delta sigma weight residual 113.18 106.45 6.73 1.33e+00 5.65e-01 2.56e+01 angle pdb=" C THR A 146 " pdb=" N ASN A 147 " pdb=" CA ASN A 147 " ideal model delta sigma weight residual 121.70 129.19 -7.49 1.80e+00 3.09e-01 1.73e+01 angle pdb=" N GLU A 504 " pdb=" CA GLU A 504 " pdb=" C GLU A 504 " ideal model delta sigma weight residual 110.53 115.74 -5.21 1.32e+00 5.74e-01 1.55e+01 angle pdb=" N GLY A1621 " pdb=" CA GLY A1621 " pdb=" C GLY A1621 " ideal model delta sigma weight residual 115.08 109.05 6.03 1.54e+00 4.22e-01 1.54e+01 angle pdb=" N TYR A1366 " pdb=" CA TYR A1366 " pdb=" C TYR A1366 " ideal model delta sigma weight residual 110.80 102.48 8.32 2.13e+00 2.20e-01 1.53e+01 ... (remaining 18128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 7367 17.90 - 35.80: 684 35.80 - 53.70: 96 53.70 - 71.60: 26 71.60 - 89.50: 21 Dihedral angle restraints: 8194 sinusoidal: 3384 harmonic: 4810 Sorted by residual: dihedral pdb=" CB CYS A 771 " pdb=" SG CYS A 771 " pdb=" SG CYS A 910 " pdb=" CB CYS A 910 " ideal model delta sinusoidal sigma weight residual 93.00 11.65 81.35 1 1.00e+01 1.00e-02 8.16e+01 dihedral pdb=" CB CYS A1149 " pdb=" SG CYS A1149 " pdb=" SG CYS A1180 " pdb=" CB CYS A1180 " ideal model delta sinusoidal sigma weight residual 93.00 170.90 -77.90 1 1.00e+01 1.00e-02 7.59e+01 dihedral pdb=" CA GLN A 965 " pdb=" C GLN A 965 " pdb=" N CYS A 966 " pdb=" CA CYS A 966 " ideal model delta harmonic sigma weight residual -180.00 -137.00 -43.00 0 5.00e+00 4.00e-02 7.40e+01 ... (remaining 8191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1441 0.050 - 0.101: 393 0.101 - 0.151: 46 0.151 - 0.202: 3 0.202 - 0.252: 1 Chirality restraints: 1884 Sorted by residual: chirality pdb=" CA SER A 951 " pdb=" N SER A 951 " pdb=" C SER A 951 " pdb=" CB SER A 951 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA GLU A1541 " pdb=" N GLU A1541 " pdb=" C GLU A1541 " pdb=" CB GLU A1541 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CB ILE A1165 " pdb=" CA ILE A1165 " pdb=" CG1 ILE A1165 " pdb=" CG2 ILE A1165 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.79e-01 ... (remaining 1881 not shown) Planarity restraints: 2343 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 560 " -0.027 2.00e-02 2.50e+03 2.72e-02 1.86e+01 pdb=" CG TRP A 560 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP A 560 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP A 560 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 560 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 560 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 560 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 560 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 560 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 560 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 766 " 0.020 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C TRP A 766 " -0.067 2.00e-02 2.50e+03 pdb=" O TRP A 766 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL A 767 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 890 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.66e+00 pdb=" C ILE A 890 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE A 890 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP A 891 " -0.016 2.00e-02 2.50e+03 ... (remaining 2340 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 300 2.61 - 3.18: 13719 3.18 - 3.75: 22258 3.75 - 4.33: 29935 4.33 - 4.90: 45762 Nonbonded interactions: 111974 Sorted by model distance: nonbonded pdb=" O TYR A 688 " pdb=" OG SER A 702 " model vdw 2.035 2.440 nonbonded pdb=" O THR A 895 " pdb=" OG SER A 899 " model vdw 2.057 2.440 nonbonded pdb=" OH TYR A 842 " pdb=" O LEU A 894 " model vdw 2.058 2.440 nonbonded pdb=" O GLU A 573 " pdb=" NH2 ARG A 841 " model vdw 2.098 2.520 nonbonded pdb=" O ASN A1027 " pdb=" OG1 THR A1030 " model vdw 2.115 2.440 ... (remaining 111969 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.650 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: 18.180 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 44.570 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13457 Z= 0.255 Angle : 0.845 9.840 18133 Z= 0.496 Chirality : 0.043 0.252 1884 Planarity : 0.005 0.062 2343 Dihedral : 14.200 89.497 5015 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 24.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 16.40 % Favored : 83.42 % Rotamer: Outliers : 0.07 % Allowed : 0.57 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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: -2.23 (0.20), residues: 1598 helix: 0.15 (0.18), residues: 820 sheet: -4.87 (1.00), residues: 10 loop : -3.45 (0.20), residues: 768 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 26 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 27 average time/residue: 0.2811 time to fit residues: 13.2191 Evaluate side-chains 22 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.707 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 9.9990 chunk 123 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 148 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 ASN ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1039 ASN A1498 GLN ** A1601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13457 Z= 0.205 Angle : 0.733 10.773 18133 Z= 0.388 Chirality : 0.043 0.204 1884 Planarity : 0.004 0.056 2343 Dihedral : 6.404 41.161 1761 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.25 % Allowed : 15.89 % Favored : 83.85 % Rotamer: Outliers : 0.07 % Allowed : 4.52 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.21), residues: 1598 helix: 0.50 (0.18), residues: 814 sheet: -4.48 (1.08), residues: 10 loop : -3.27 (0.20), residues: 774 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 1.694 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 26 average time/residue: 0.2625 time to fit residues: 12.4631 Evaluate side-chains 24 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 1.685 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1324 time to fit residues: 2.6106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 40 optimal weight: 0.3980 chunk 148 optimal weight: 4.9990 chunk 160 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 HIS A1672 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13457 Z= 0.171 Angle : 0.687 10.809 18133 Z= 0.361 Chirality : 0.041 0.181 1884 Planarity : 0.004 0.052 2343 Dihedral : 6.084 40.781 1761 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.58 % Favored : 85.23 % Rotamer: Outliers : 0.21 % Allowed : 6.78 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.70 (0.21), residues: 1598 helix: 0.63 (0.18), residues: 814 sheet: -4.28 (1.05), residues: 10 loop : -3.23 (0.20), residues: 774 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 26 time to evaluate : 1.822 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 27 average time/residue: 0.2611 time to fit residues: 12.7809 Evaluate side-chains 24 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 1.740 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 10.0000 chunk 111 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 148 optimal weight: 0.3980 chunk 157 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1542 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13457 Z= 0.174 Angle : 0.669 12.934 18133 Z= 0.350 Chirality : 0.040 0.175 1884 Planarity : 0.004 0.047 2343 Dihedral : 5.895 40.149 1761 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.77 % Favored : 85.11 % Rotamer: Outliers : 0.49 % Allowed : 7.49 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.58 (0.21), residues: 1598 helix: 0.75 (0.18), residues: 819 sheet: -4.12 (1.02), residues: 10 loop : -3.22 (0.20), residues: 769 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 24 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 29 average time/residue: 0.2410 time to fit residues: 12.7285 Evaluate side-chains 26 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 1.509 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1346 time to fit residues: 2.5159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 0.2980 chunk 89 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 134 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 141 optimal weight: 0.5980 chunk 39 optimal weight: 9.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 ASN ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN ** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13457 Z= 0.233 Angle : 0.685 10.836 18133 Z= 0.362 Chirality : 0.041 0.212 1884 Planarity : 0.004 0.047 2343 Dihedral : 5.914 39.997 1761 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 21.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.83 % Favored : 85.04 % Rotamer: Outliers : 0.42 % Allowed : 8.69 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.54 (0.21), residues: 1598 helix: 0.80 (0.18), residues: 822 sheet: -4.14 (1.01), residues: 10 loop : -3.24 (0.20), residues: 766 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 24 time to evaluate : 1.875 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 28 average time/residue: 0.3346 time to fit residues: 16.7629 Evaluate side-chains 25 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 2.036 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1706 time to fit residues: 3.1733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 157 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1847 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13457 Z= 0.163 Angle : 0.664 11.711 18133 Z= 0.346 Chirality : 0.041 0.196 1884 Planarity : 0.004 0.047 2343 Dihedral : 5.785 39.876 1761 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.02 % Favored : 85.79 % Rotamer: Outliers : 0.49 % Allowed : 9.19 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.21), residues: 1598 helix: 0.88 (0.18), residues: 819 sheet: -3.93 (1.03), residues: 10 loop : -3.16 (0.20), residues: 769 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 1.673 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 30 average time/residue: 0.2523 time to fit residues: 13.5726 Evaluate side-chains 23 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 1.579 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1736 time to fit residues: 2.5963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 8.9990 chunk 17 optimal weight: 0.0980 chunk 89 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 157 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13457 Z= 0.187 Angle : 0.663 11.433 18133 Z= 0.346 Chirality : 0.041 0.280 1884 Planarity : 0.004 0.047 2343 Dihedral : 5.696 39.477 1761 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.08 % Favored : 85.73 % Rotamer: Outliers : 0.49 % Allowed : 9.89 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.40 (0.21), residues: 1598 helix: 0.94 (0.18), residues: 820 sheet: -3.97 (1.02), residues: 10 loop : -3.18 (0.20), residues: 768 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 1.552 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 26 average time/residue: 0.2765 time to fit residues: 13.1251 Evaluate side-chains 24 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 1.825 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1468 time to fit residues: 2.9582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 14 optimal weight: 0.5980 chunk 123 optimal weight: 0.8980 chunk 142 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13457 Z= 0.181 Angle : 0.662 11.621 18133 Z= 0.346 Chirality : 0.041 0.261 1884 Planarity : 0.004 0.047 2343 Dihedral : 5.657 41.677 1761 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.89 % Favored : 85.98 % Rotamer: Outliers : 0.21 % Allowed : 10.39 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.21), residues: 1598 helix: 0.94 (0.18), residues: 818 sheet: -3.90 (1.03), residues: 10 loop : -3.17 (0.20), residues: 770 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 1.635 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 24 average time/residue: 0.2589 time to fit residues: 11.5575 Evaluate side-chains 23 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 1.687 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1257 time to fit residues: 2.4848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.0980 chunk 146 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 145 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 678 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13457 Z= 0.157 Angle : 0.657 11.015 18133 Z= 0.342 Chirality : 0.040 0.257 1884 Planarity : 0.004 0.047 2343 Dihedral : 5.545 41.545 1761 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.39 % Favored : 86.48 % Rotamer: Outliers : 0.21 % Allowed : 10.53 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.33 (0.21), residues: 1598 helix: 0.97 (0.18), residues: 818 sheet: -3.81 (1.05), residues: 10 loop : -3.11 (0.21), residues: 770 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 2.045 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.2679 time to fit residues: 11.9232 Evaluate side-chains 22 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.739 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 13 optimal weight: 0.2980 chunk 99 optimal weight: 0.0050 chunk 79 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13457 Z= 0.162 Angle : 0.655 13.307 18133 Z= 0.342 Chirality : 0.041 0.251 1884 Planarity : 0.004 0.047 2343 Dihedral : 5.484 41.478 1761 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.33 % Favored : 86.55 % Rotamer: Outliers : 0.21 % Allowed : 10.46 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.30 (0.21), residues: 1598 helix: 1.02 (0.18), residues: 818 sheet: -3.88 (1.04), residues: 10 loop : -3.13 (0.21), residues: 770 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3196 Ramachandran restraints generated. 1598 Oldfield, 0 Emsley, 1598 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 1.647 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 26 average time/residue: 0.2572 time to fit residues: 12.4583 Evaluate side-chains 25 residues out of total 1485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 1.608 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1193 time to fit residues: 2.4313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 132 optimal weight: 0.3980 chunk 16 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 879 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 = 0.3312 r_free = 0.3312 target = 0.033345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.025952 restraints weight = 167730.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.026709 restraints weight = 106322.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.027234 restraints weight = 77318.112| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13457 Z= 0.186 Angle : 0.667 11.847 18133 Z= 0.348 Chirality : 0.041 0.245 1884 Planarity : 0.004 0.046 2343 Dihedral : 5.483 41.688 1761 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.52 % Favored : 86.36 % Rotamer: Outliers : 0.21 % Allowed : 10.67 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 (0.21), residues: 1598 helix: 1.02 (0.18), residues: 827 sheet: -3.92 (1.03), residues: 10 loop : -3.16 (0.21), residues: 761 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2244.77 seconds wall clock time: 43 minutes 1.61 seconds (2581.61 seconds total)