Starting phenix.real_space_refine on Wed Feb 21 06:12:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ps1_17842/02_2024/8ps1_17842_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ps1_17842/02_2024/8ps1_17842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ps1_17842/02_2024/8ps1_17842.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ps1_17842/02_2024/8ps1_17842.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ps1_17842/02_2024/8ps1_17842_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ps1_17842/02_2024/8ps1_17842_updated.pdb" } resolution = 2.8 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= 0.017 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 P 10 5.49 5 S 108 5.16 5 C 18953 2.51 5 N 4980 2.21 5 O 5736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 38": "OD1" <-> "OD2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 981": "OE1" <-> "OE2" Residue "A ASP 1086": "OD1" <-> "OD2" Residue "A ASP 1203": "OD1" <-> "OD2" Residue "A GLU 1317": "OE1" <-> "OE2" Residue "A TYR 1332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1355": "OE1" <-> "OE2" Residue "A GLU 1473": "OE1" <-> "OE2" Residue "A TYR 1513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B GLU 203": "OE1" <-> "OE2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B ASP 288": "OD1" <-> "OD2" Residue "G ASP 175": "OD1" <-> "OD2" Residue "G GLU 347": "OE1" <-> "OE2" Residue "G PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 668": "OE1" <-> "OE2" Residue "G GLU 696": "OE1" <-> "OE2" Residue "G PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 784": "OE1" <-> "OE2" Residue "G GLU 1256": "OE1" <-> "OE2" Residue "G PHE 1423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1453": "OD1" <-> "OD2" Residue "G GLU 1645": "OE1" <-> "OE2" Residue "G PHE 1804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1846": "OE1" <-> "OE2" Residue "G PHE 1866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1935": "OE1" <-> "OE2" Residue "G PHE 1964": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29787 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 12379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1584, 12379 Classifications: {'peptide': 1584} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1522} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1223 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 8, 'TRANS': 154} Chain: "G" Number of atoms: 16010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2034, 16010 Classifications: {'peptide': 2034} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1924} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'J8W:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 127 Unusual residues: {'COA': 1, 'FMN': 1, 'NAP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 15.93, per 1000 atoms: 0.53 Number of scatterers: 29787 At special positions: 0 Unit cell: (185.68, 182.515, 178.295, 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) S 108 16.00 P 10 15.00 O 5736 8.00 N 4980 7.00 C 18953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.99 Conformation dependent library (CDL) restraints added in 5.6 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7034 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 168 helices and 29 sheets defined 44.3% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.31 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 removed outlier: 3.574A pdb=" N PHE A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ALA A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 37 Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 85 through 88 No H-bonds generated for 'chain 'A' and resid 85 through 88' Processing helix chain 'A' and resid 330 through 350 Processing helix chain 'A' and resid 356 through 381 removed outlier: 3.576A pdb=" N ASP A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 405 through 421 removed outlier: 4.547A pdb=" N LYS A 410 " --> pdb=" O TRP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 442 removed outlier: 3.674A pdb=" N ARG A 442 " --> pdb=" O ASN A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 456 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 464 through 482 Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 609 through 615 removed outlier: 3.602A pdb=" N SER A 615 " --> pdb=" O LYS A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 669 Processing helix chain 'A' and resid 688 through 698 Processing helix chain 'A' and resid 712 through 725 Processing helix chain 'A' and resid 742 through 753 Processing helix chain 'A' and resid 781 through 783 No H-bonds generated for 'chain 'A' and resid 781 through 783' Processing helix chain 'A' and resid 786 through 795 Processing helix chain 'A' and resid 797 through 812 Processing helix chain 'A' and resid 839 through 855 removed outlier: 4.123A pdb=" N GLU A 847 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N PHE A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASN A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N HIS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 891 removed outlier: 4.195A pdb=" N GLU A 886 " --> pdb=" O ILE A 883 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 888 " --> pdb=" O ALA A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 909 removed outlier: 3.784A pdb=" N LEU A 908 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 917 Processing helix chain 'A' and resid 936 through 968 removed outlier: 3.626A pdb=" N LEU A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR A 950 " --> pdb=" O GLU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1001 No H-bonds generated for 'chain 'A' and resid 998 through 1001' Processing helix chain 'A' and resid 1007 through 1009 No H-bonds generated for 'chain 'A' and resid 1007 through 1009' Processing helix chain 'A' and resid 1015 through 1017 No H-bonds generated for 'chain 'A' and resid 1015 through 1017' Processing helix chain 'A' and resid 1033 through 1041 Processing helix chain 'A' and resid 1047 through 1057 Processing helix chain 'A' and resid 1086 through 1099 removed outlier: 4.418A pdb=" N LYS A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N THR A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N SER A1096 " --> pdb=" O LYS A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1110 No H-bonds generated for 'chain 'A' and resid 1108 through 1110' Processing helix chain 'A' and resid 1138 through 1151 removed outlier: 7.101A pdb=" N ASP A1150 " --> pdb=" O HIS A1146 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LYS A1151 " --> pdb=" O GLN A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1198 No H-bonds generated for 'chain 'A' and resid 1195 through 1198' Processing helix chain 'A' and resid 1202 through 1205 No H-bonds generated for 'chain 'A' and resid 1202 through 1205' Processing helix chain 'A' and resid 1210 through 1226 Processing helix chain 'A' and resid 1231 through 1236 Processing helix chain 'A' and resid 1240 through 1242 No H-bonds generated for 'chain 'A' and resid 1240 through 1242' Processing helix chain 'A' and resid 1254 through 1261 Processing helix chain 'A' and resid 1280 through 1290 removed outlier: 3.772A pdb=" N MET A1283 " --> pdb=" O ILE A1280 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A1284 " --> pdb=" O ASN A1281 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A1287 " --> pdb=" O SER A1284 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A1290 " --> pdb=" O VAL A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1320 removed outlier: 5.414A pdb=" N SER A1308 " --> pdb=" O CYS A1305 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A1317 " --> pdb=" O ILE A1314 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A1318 " --> pdb=" O GLY A1315 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A1320 " --> pdb=" O GLU A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1345 Processing helix chain 'A' and resid 1352 through 1357 Processing helix chain 'A' and resid 1362 through 1364 No H-bonds generated for 'chain 'A' and resid 1362 through 1364' Processing helix chain 'A' and resid 1390 through 1396 Processing helix chain 'A' and resid 1424 through 1429 Processing helix chain 'A' and resid 1441 through 1443 No H-bonds generated for 'chain 'A' and resid 1441 through 1443' Processing helix chain 'A' and resid 1445 through 1476 removed outlier: 4.262A pdb=" N GLU A1476 " --> pdb=" O LEU A1472 " (cutoff:3.500A) Processing helix chain 'A' and resid 1482 through 1509 removed outlier: 3.566A pdb=" N GLN A1500 " --> pdb=" O GLU A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1529 removed outlier: 3.617A pdb=" N LEU A1526 " --> pdb=" O LEU A1522 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR A1529 " --> pdb=" O ALA A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1533 through 1535 No H-bonds generated for 'chain 'A' and resid 1533 through 1535' Processing helix chain 'A' and resid 1547 through 1564 removed outlier: 3.813A pdb=" N LYS A1551 " --> pdb=" O LYS A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1581 removed outlier: 3.777A pdb=" N THR A1581 " --> pdb=" O LYS A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1585 through 1602 removed outlier: 4.340A pdb=" N GLY A1589 " --> pdb=" O GLY A1586 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP A1591 " --> pdb=" O ALA A1588 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET A1593 " --> pdb=" O ALA A1590 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN A1601 " --> pdb=" O GLN A1598 " (cutoff:3.500A) Processing helix chain 'A' and resid 1616 through 1620 removed outlier: 3.532A pdb=" N GLN A1620 " --> pdb=" O ILE A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1664 removed outlier: 3.613A pdb=" N TYR A1662 " --> pdb=" O ASP A1659 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY A1663 " --> pdb=" O TYR A1660 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1693 Processing helix chain 'A' and resid 1711 through 1716 Processing helix chain 'A' and resid 1735 through 1737 No H-bonds generated for 'chain 'A' and resid 1735 through 1737' Processing helix chain 'A' and resid 1741 through 1744 No H-bonds generated for 'chain 'A' and resid 1741 through 1744' Processing helix chain 'A' and resid 1747 through 1759 removed outlier: 3.880A pdb=" N MET A1759 " --> pdb=" O MET A1755 " (cutoff:3.500A) Processing helix chain 'A' and resid 1776 through 1778 No H-bonds generated for 'chain 'A' and resid 1776 through 1778' Processing helix chain 'A' and resid 1784 through 1790 Processing helix chain 'A' and resid 1793 through 1799 Processing helix chain 'A' and resid 1805 through 1823 Processing helix chain 'A' and resid 1854 through 1862 Processing helix chain 'B' and resid 147 through 158 removed outlier: 3.629A pdb=" N HIS B 152 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 180 through 193 removed outlier: 3.675A pdb=" N ASN B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 214 removed outlier: 3.611A pdb=" N GLU B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 235 Processing helix chain 'B' and resid 243 through 252 Processing helix chain 'B' and resid 258 through 270 removed outlier: 3.733A pdb=" N GLY B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 298 removed outlier: 3.644A pdb=" N ILE B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 40 removed outlier: 6.071A pdb=" N PHE G 28 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE G 29 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER G 31 " --> pdb=" O PHE G 28 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU G 33 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU G 35 " --> pdb=" O GLN G 32 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE G 37 " --> pdb=" O GLN G 34 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE G 40 " --> pdb=" O PHE G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 71 removed outlier: 3.619A pdb=" N LEU G 71 " --> pdb=" O TYR G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 94 removed outlier: 4.459A pdb=" N ASN G 85 " --> pdb=" O GLN G 82 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU G 88 " --> pdb=" O ASN G 85 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU G 92 " --> pdb=" O THR G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 110 Processing helix chain 'G' and resid 116 through 132 Processing helix chain 'G' and resid 144 through 151 Processing helix chain 'G' and resid 170 through 179 Processing helix chain 'G' and resid 181 through 201 removed outlier: 5.424A pdb=" N ASP G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LEU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 220 Processing helix chain 'G' and resid 228 through 231 No H-bonds generated for 'chain 'G' and resid 228 through 231' Processing helix chain 'G' and resid 234 through 256 Proline residue: G 239 - end of helix Processing helix chain 'G' and resid 260 through 266 Processing helix chain 'G' and resid 274 through 285 removed outlier: 3.648A pdb=" N VAL G 281 " --> pdb=" O VAL G 278 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE G 283 " --> pdb=" O ALA G 280 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA G 284 " --> pdb=" O VAL G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 313 removed outlier: 3.538A pdb=" N TYR G 311 " --> pdb=" O GLY G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 330 Processing helix chain 'G' and resid 346 through 359 removed outlier: 3.503A pdb=" N TYR G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER G 358 " --> pdb=" O ASN G 354 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N HIS G 359 " --> pdb=" O LYS G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 364 No H-bonds generated for 'chain 'G' and resid 362 through 364' Processing helix chain 'G' and resid 383 through 394 Processing helix chain 'G' and resid 409 through 411 No H-bonds generated for 'chain 'G' and resid 409 through 411' Processing helix chain 'G' and resid 430 through 445 Proline residue: G 434 - end of helix removed outlier: 4.059A pdb=" N ASP G 437 " --> pdb=" O PRO G 434 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN G 440 " --> pdb=" O ASP G 437 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU G 443 " --> pdb=" O ASN G 440 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL G 444 " --> pdb=" O LYS G 441 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS G 445 " --> pdb=" O ASP G 442 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 484 Processing helix chain 'G' and resid 490 through 493 No H-bonds generated for 'chain 'G' and resid 490 through 493' Processing helix chain 'G' and resid 508 through 510 No H-bonds generated for 'chain 'G' and resid 508 through 510' Processing helix chain 'G' and resid 512 through 519 Processing helix chain 'G' and resid 544 through 548 Processing helix chain 'G' and resid 561 through 564 No H-bonds generated for 'chain 'G' and resid 561 through 564' Processing helix chain 'G' and resid 582 through 587 removed outlier: 3.575A pdb=" N LEU G 586 " --> pdb=" O LYS G 582 " (cutoff:3.500A) Processing helix chain 'G' and resid 604 through 613 Processing helix chain 'G' and resid 621 through 623 No H-bonds generated for 'chain 'G' and resid 621 through 623' Processing helix chain 'G' and resid 627 through 640 removed outlier: 3.670A pdb=" N GLN G 640 " --> pdb=" O SER G 636 " (cutoff:3.500A) Processing helix chain 'G' and resid 656 through 671 removed outlier: 3.745A pdb=" N TRP G 661 " --> pdb=" O PHE G 657 " (cutoff:3.500A) Proline residue: G 664 - end of helix Processing helix chain 'G' and resid 688 through 697 Processing helix chain 'G' and resid 710 through 722 Processing helix chain 'G' and resid 748 through 758 removed outlier: 5.215A pdb=" N SER G 755 " --> pdb=" O LEU G 751 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LYS G 756 " --> pdb=" O GLN G 752 " (cutoff:3.500A) Processing helix chain 'G' and resid 774 through 781 Proline residue: G 779 - end of helix Processing helix chain 'G' and resid 784 through 786 No H-bonds generated for 'chain 'G' and resid 784 through 786' Processing helix chain 'G' and resid 803 through 805 No H-bonds generated for 'chain 'G' and resid 803 through 805' Processing helix chain 'G' and resid 815 through 823 Processing helix chain 'G' and resid 832 through 836 Processing helix chain 'G' and resid 860 through 871 Processing helix chain 'G' and resid 877 through 898 removed outlier: 4.500A pdb=" N VAL G 881 " --> pdb=" O LYS G 877 " (cutoff:3.500A) Proline residue: G 882 - end of helix removed outlier: 5.769A pdb=" N ASP G 889 " --> pdb=" O GLU G 885 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYR G 890 " --> pdb=" O ALA G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 914 through 916 No H-bonds generated for 'chain 'G' and resid 914 through 916' Processing helix chain 'G' and resid 919 through 930 Processing helix chain 'G' and resid 941 through 958 Processing helix chain 'G' and resid 970 through 974 removed outlier: 3.502A pdb=" N ASP G 974 " --> pdb=" O SER G 971 " (cutoff:3.500A) Processing helix chain 'G' and resid 976 through 986 Processing helix chain 'G' and resid 988 through 991 Processing helix chain 'G' and resid 997 through 1006 Processing helix chain 'G' and resid 1023 through 1030 removed outlier: 4.524A pdb=" N GLU G1026 " --> pdb=" O ARG G1023 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS G1030 " --> pdb=" O ILE G1027 " (cutoff:3.500A) Processing helix chain 'G' and resid 1035 through 1038 Processing helix chain 'G' and resid 1040 through 1042 No H-bonds generated for 'chain 'G' and resid 1040 through 1042' Processing helix chain 'G' and resid 1048 through 1050 No H-bonds generated for 'chain 'G' and resid 1048 through 1050' Processing helix chain 'G' and resid 1059 through 1061 No H-bonds generated for 'chain 'G' and resid 1059 through 1061' Processing helix chain 'G' and resid 1070 through 1089 Processing helix chain 'G' and resid 1094 through 1096 No H-bonds generated for 'chain 'G' and resid 1094 through 1096' Processing helix chain 'G' and resid 1135 through 1143 Processing helix chain 'G' and resid 1149 through 1155 Processing helix chain 'G' and resid 1169 through 1173 Processing helix chain 'G' and resid 1190 through 1192 No H-bonds generated for 'chain 'G' and resid 1190 through 1192' Processing helix chain 'G' and resid 1258 through 1270 Processing helix chain 'G' and resid 1294 through 1304 Processing helix chain 'G' and resid 1309 through 1311 No H-bonds generated for 'chain 'G' and resid 1309 through 1311' Processing helix chain 'G' and resid 1323 through 1338 removed outlier: 4.053A pdb=" N TRP G1331 " --> pdb=" O VAL G1328 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ARG G1332 " --> pdb=" O VAL G1329 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE G1335 " --> pdb=" O ARG G1332 " (cutoff:3.500A) Processing helix chain 'G' and resid 1419 through 1421 No H-bonds generated for 'chain 'G' and resid 1419 through 1421' Processing helix chain 'G' and resid 1438 through 1446 Processing helix chain 'G' and resid 1515 through 1523 Processing helix chain 'G' and resid 1551 through 1557 removed outlier: 3.667A pdb=" N VAL G1556 " --> pdb=" O PRO G1552 " (cutoff:3.500A) Processing helix chain 'G' and resid 1562 through 1564 No H-bonds generated for 'chain 'G' and resid 1562 through 1564' Processing helix chain 'G' and resid 1567 through 1572 Processing helix chain 'G' and resid 1582 through 1596 Processing helix chain 'G' and resid 1602 through 1604 No H-bonds generated for 'chain 'G' and resid 1602 through 1604' Processing helix chain 'G' and resid 1678 through 1683 removed outlier: 3.586A pdb=" N THR G1683 " --> pdb=" O ASP G1679 " (cutoff:3.500A) Processing helix chain 'G' and resid 1685 through 1701 Processing helix chain 'G' and resid 1706 through 1712 Processing helix chain 'G' and resid 1723 through 1734 removed outlier: 3.558A pdb=" N LYS G1727 " --> pdb=" O GLY G1723 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG G1728 " --> pdb=" O GLU G1724 " (cutoff:3.500A) Processing helix chain 'G' and resid 1770 through 1772 No H-bonds generated for 'chain 'G' and resid 1770 through 1772' Processing helix chain 'G' and resid 1774 through 1794 Proline residue: G1779 - end of helix Processing helix chain 'G' and resid 1810 through 1818 Processing helix chain 'G' and resid 1824 through 1839 Processing helix chain 'G' and resid 1859 through 1862 No H-bonds generated for 'chain 'G' and resid 1859 through 1862' Processing helix chain 'G' and resid 1868 through 1881 removed outlier: 3.525A pdb=" N LYS G1880 " --> pdb=" O GLU G1876 " (cutoff:3.500A) Processing helix chain 'G' and resid 1904 through 1920 removed outlier: 3.712A pdb=" N LEU G1919 " --> pdb=" O ASN G1915 " (cutoff:3.500A) Processing helix chain 'G' and resid 1927 through 1930 No H-bonds generated for 'chain 'G' and resid 1927 through 1930' Processing helix chain 'G' and resid 1935 through 1952 removed outlier: 3.787A pdb=" N GLU G1942 " --> pdb=" O GLY G1938 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE G1943 " --> pdb=" O HIS G1939 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS G1950 " --> pdb=" O GLU G1946 " (cutoff:3.500A) Processing helix chain 'G' and resid 1980 through 1982 No H-bonds generated for 'chain 'G' and resid 1980 through 1982' Processing helix chain 'G' and resid 1985 through 1995 removed outlier: 3.583A pdb=" N LYS G1994 " --> pdb=" O SER G1990 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN G1995 " --> pdb=" O PHE G1991 " (cutoff:3.500A) Processing helix chain 'G' and resid 1998 through 2000 No H-bonds generated for 'chain 'G' and resid 1998 through 2000' Processing helix chain 'G' and resid 2003 through 2006 No H-bonds generated for 'chain 'G' and resid 2003 through 2006' Processing helix chain 'G' and resid 2023 through 2030 Processing helix chain 'G' and resid 2036 through 2043 Processing helix chain 'G' and resid 2045 through 2049 Processing sheet with id= A, first strand: chain 'A' and resid 43 through 46 removed outlier: 6.392A pdb=" N GLU A 77 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLU A 46 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU A 79 " --> pdb=" O GLU A 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.588A pdb=" N ALA A 767 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR A 681 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE A 769 " --> pdb=" O THR A 681 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 497 through 503 Processing sheet with id= D, first strand: chain 'A' and resid 649 through 651 removed outlier: 4.605A pdb=" N MET A 923 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA A 820 " --> pdb=" O THR A 863 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N CYS A 865 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL A 822 " --> pdb=" O CYS A 865 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA A 867 " --> pdb=" O VAL A 822 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU A 824 " --> pdb=" O ALA A 867 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE A 869 " --> pdb=" O LEU A 824 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N MET A 826 " --> pdb=" O ILE A 869 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1060 through 1067 removed outlier: 3.781A pdb=" N ARG A1070 " --> pdb=" O LEU A1067 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1103 through 1105 Processing sheet with id= G, first strand: chain 'A' and resid 1119 through 1126 Processing sheet with id= H, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id= I, first strand: chain 'A' and resid 1243 through 1245 removed outlier: 6.681A pdb=" N ILE A1326 " --> pdb=" O GLY A1244 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A1023 " --> pdb=" O ILE A1386 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N MET A1388 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL A1021 " --> pdb=" O MET A1388 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1573 through 1575 removed outlier: 3.597A pdb=" N MET A1406 " --> pdb=" O ILE A1654 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL A1656 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL A1404 " --> pdb=" O VAL A1656 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1768 through 1775 Processing sheet with id= L, first strand: chain 'A' and resid 1838 through 1840 Processing sheet with id= M, first strand: chain 'G' and resid 7 through 13 removed outlier: 3.808A pdb=" N LEU G 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 526 through 529 removed outlier: 7.867A pdb=" N ALA G 158 " --> pdb=" O LYS G 268 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA G 270 " --> pdb=" O ALA G 158 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N PHE G 160 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLY G 272 " --> pdb=" O PHE G 160 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N GLY G 272 " --> pdb=" O PRO G 458 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N TYR G 460 " --> pdb=" O GLY G 272 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 417 through 420 removed outlier: 5.984A pdb=" N SER G 380 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE G 368 " --> pdb=" O SER G 380 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 568 through 571 Processing sheet with id= Q, first strand: chain 'G' and resid 618 through 620 removed outlier: 6.702A pdb=" N GLY G 648 " --> pdb=" O LEU G 619 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE G 649 " --> pdb=" O GLN G 677 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU G 679 " --> pdb=" O ILE G 649 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU G 651 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE G 681 " --> pdb=" O LEU G 651 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TYR G 702 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ILE G 681 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLY G 704 " --> pdb=" O ILE G 681 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N LEU G 705 " --> pdb=" O PRO G 727 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ALA G 729 " --> pdb=" O LEU G 705 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 843 through 847 Processing sheet with id= S, first strand: chain 'G' and resid 1125 through 1128 removed outlier: 6.541A pdb=" N GLU G1199 " --> pdb=" O PRO G1207 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL G1201 " --> pdb=" O LEU G1205 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU G1205 " --> pdb=" O VAL G1201 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N THR G1208 " --> pdb=" O ILE G1224 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE G1218 " --> pdb=" O LEU G1214 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 1158 through 1161 Processing sheet with id= U, first strand: chain 'G' and resid 1285 through 1287 removed outlier: 4.100A pdb=" N THR G1374 " --> pdb=" O GLY G1287 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASP G1391 " --> pdb=" O GLU G1379 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL G1381 " --> pdb=" O ILE G1389 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE G1389 " --> pdb=" O VAL G1381 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASN G1383 " --> pdb=" O GLY G1387 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY G1387 " --> pdb=" O ASN G1383 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER G1354 " --> pdb=" O SER G1409 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE G1411 " --> pdb=" O HIS G1352 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N HIS G1352 " --> pdb=" O PHE G1411 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ARG G1413 " --> pdb=" O LEU G1350 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU G1350 " --> pdb=" O ARG G1413 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU G1353 " --> pdb=" O PHE G1612 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLU G1656 " --> pdb=" O ARG G1606 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR G1608 " --> pdb=" O GLU G1654 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLU G1654 " --> pdb=" O TYR G1608 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N CYS G1610 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR G1652 " --> pdb=" O CYS G1610 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N PHE G1612 " --> pdb=" O VAL G1650 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL G1650 " --> pdb=" O PHE G1612 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR G1642 " --> pdb=" O VAL G1650 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N THR G1652 " --> pdb=" O PHE G1640 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE G1640 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU G1654 " --> pdb=" O ILE G1638 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE G1638 " --> pdb=" O GLU G1654 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU G1656 " --> pdb=" O LYS G1636 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LYS G1636 " --> pdb=" O GLU G1656 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS G1639 " --> pdb=" O HIS G1628 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N HIS G1628 " --> pdb=" O LYS G1639 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N GLU G1641 " --> pdb=" O ILE G1626 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ILE G1626 " --> pdb=" O GLU G1641 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ARG G1643 " --> pdb=" O THR G1624 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR G1624 " --> pdb=" O ARG G1643 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 1357 through 1359 removed outlier: 6.954A pdb=" N LEU G1396 " --> pdb=" O VAL G1403 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 1423 through 1427 removed outlier: 3.936A pdb=" N SER G1482 " --> pdb=" O THR G1473 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL G1483 " --> pdb=" O ALA G1508 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL G1491 " --> pdb=" O GLU G1500 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLU G1500 " --> pdb=" O VAL G1491 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 1431 through 1434 Processing sheet with id= Y, first strand: chain 'G' and resid 1663 through 1666 removed outlier: 6.733A pdb=" N THR G1803 " --> pdb=" O PHE G1664 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N PHE G1666 " --> pdb=" O THR G1803 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ALA G1805 " --> pdb=" O PHE G1666 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'G' and resid 1716 through 1720 Processing sheet with id= AA, first strand: chain 'G' and resid 1737 through 1741 Processing sheet with id= AB, first strand: chain 'G' and resid 1966 through 1968 removed outlier: 6.273A pdb=" N ALA G1901 " --> pdb=" O ILE G1888 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ILE G1888 " --> pdb=" O ALA G1901 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ASP G1903 " --> pdb=" O VAL G1886 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL G1886 " --> pdb=" O ASP G1903 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 1537 through 1545 removed outlier: 7.022A pdb=" N ILE G1626 " --> pdb=" O ILE G1539 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL G1541 " --> pdb=" O THR G1624 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N THR G1624 " --> pdb=" O VAL G1541 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP G1543 " --> pdb=" O LEU G1622 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU G1622 " --> pdb=" O ASP G1543 " (cutoff:3.500A) 1186 hydrogen bonds defined for protein. 3213 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: 14.37 Time building geometry restraints manager: 15.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.73: 30224 1.73 - 2.31: 190 2.31 - 2.89: 0 2.89 - 3.47: 0 3.47 - 4.05: 2 Bond restraints: 30416 Sorted by residual: bond pdb=" AP1 COA G2102 " pdb="AO5* COA G2102 " ideal model delta sigma weight residual 1.610 4.046 -2.436 2.00e-02 2.50e+03 1.48e+04 bond pdb=" AO6 COA G2102 " pdb=" AP2 COA G2102 " ideal model delta sigma weight residual 1.610 3.856 -2.246 2.00e-02 2.50e+03 1.26e+04 bond pdb=" PC9 COA G2102 " pdb=" PO9 COA G2102 " ideal model delta sigma weight residual 1.410 1.232 0.178 2.00e-02 2.50e+03 7.95e+01 bond pdb=" OG J8W G1808 " pdb=" C2 J8W G1808 " ideal model delta sigma weight residual 1.331 1.470 -0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" C ILE A 733 " pdb=" O ILE A 733 " ideal model delta sigma weight residual 1.237 1.158 0.079 1.20e-02 6.94e+03 4.29e+01 ... (remaining 30411 not shown) Histogram of bond angle deviations from ideal: 12.99 - 37.66: 2 37.66 - 62.33: 0 62.33 - 86.99: 1 86.99 - 111.66: 12122 111.66 - 136.33: 29101 Bond angle restraints: 41226 Sorted by residual: angle pdb=" AO3 COA G2102 " pdb=" AP1 COA G2102 " pdb="AO5* COA G2102 " ideal model delta sigma weight residual 102.60 12.99 89.61 3.00e+00 1.11e-01 8.92e+02 angle pdb=" AO3 COA G2102 " pdb=" AP2 COA G2102 " pdb=" AO6 COA G2102 " ideal model delta sigma weight residual 102.60 26.64 75.96 3.00e+00 1.11e-01 6.41e+02 angle pdb=" AP1 COA G2102 " pdb="AO5* COA G2102 " pdb="AC5* COA G2102 " ideal model delta sigma weight residual 120.50 92.01 28.49 3.00e+00 1.11e-01 9.02e+01 angle pdb=" AP2 COA G2102 " pdb=" AO6 COA G2102 " pdb="PC12 COA G2102 " ideal model delta sigma weight residual 120.50 94.91 25.59 3.00e+00 1.11e-01 7.28e+01 angle pdb=" C SER A1417 " pdb=" N VAL A1418 " pdb=" CA VAL A1418 " ideal model delta sigma weight residual 120.24 125.57 -5.33 6.30e-01 2.52e+00 7.15e+01 ... (remaining 41221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.21: 17795 31.21 - 62.42: 548 62.42 - 93.63: 77 93.63 - 124.84: 2 124.84 - 156.05: 1 Dihedral angle restraints: 18423 sinusoidal: 7500 harmonic: 10923 Sorted by residual: dihedral pdb=" AO3 COA G2102 " pdb=" AO6 COA G2102 " pdb=" AP2 COA G2102 " pdb="PC12 COA G2102 " ideal model delta sinusoidal sigma weight residual -81.62 74.43 -156.05 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" C5* FMN G2101 " pdb=" O5* FMN G2101 " pdb=" P FMN G2101 " pdb=" O1P FMN G2101 " ideal model delta sinusoidal sigma weight residual 75.26 -163.46 -121.29 1 2.00e+01 2.50e-03 3.65e+01 dihedral pdb=" AP1 COA G2102 " pdb="AC5* COA G2102 " pdb="AO5* COA G2102 " pdb="AC4* COA G2102 " ideal model delta sinusoidal sigma weight residual 111.68 -137.48 -110.84 1 2.00e+01 2.50e-03 3.25e+01 ... (remaining 18420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2869 0.085 - 0.170: 1499 0.170 - 0.255: 243 0.255 - 0.341: 16 0.341 - 0.426: 1 Chirality restraints: 4628 Sorted by residual: chirality pdb=" CA MET B 237 " pdb=" N MET B 237 " pdb=" C MET B 237 " pdb=" CB MET B 237 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.53e+00 chirality pdb=" CA ILE G1751 " pdb=" N ILE G1751 " pdb=" C ILE G1751 " pdb=" CB ILE G1751 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA ILE G1053 " pdb=" N ILE G1053 " pdb=" C ILE G1053 " pdb=" CB ILE G1053 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 4625 not shown) Planarity restraints: 5301 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1* FMN G2101 " 0.027 2.00e-02 2.50e+03 3.82e-02 6.93e+01 pdb=" C10 FMN G2101 " 0.011 2.00e-02 2.50e+03 pdb=" C2 FMN G2101 " -0.043 2.00e-02 2.50e+03 pdb=" C4 FMN G2101 " -0.006 2.00e-02 2.50e+03 pdb=" C4A FMN G2101 " 0.026 2.00e-02 2.50e+03 pdb=" C5A FMN G2101 " 0.062 2.00e-02 2.50e+03 pdb=" C6 FMN G2101 " 0.021 2.00e-02 2.50e+03 pdb=" C7 FMN G2101 " -0.020 2.00e-02 2.50e+03 pdb=" C7M FMN G2101 " -0.066 2.00e-02 2.50e+03 pdb=" C8 FMN G2101 " -0.015 2.00e-02 2.50e+03 pdb=" C8M FMN G2101 " -0.060 2.00e-02 2.50e+03 pdb=" C9 FMN G2101 " 0.018 2.00e-02 2.50e+03 pdb=" C9A FMN G2101 " 0.057 2.00e-02 2.50e+03 pdb=" N1 FMN G2101 " -0.013 2.00e-02 2.50e+03 pdb=" N10 FMN G2101 " 0.036 2.00e-02 2.50e+03 pdb=" N3 FMN G2101 " -0.050 2.00e-02 2.50e+03 pdb=" N5 FMN G2101 " 0.052 2.00e-02 2.50e+03 pdb=" O2 FMN G2101 " -0.033 2.00e-02 2.50e+03 pdb=" O4 FMN G2101 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 753 " 0.062 2.00e-02 2.50e+03 3.57e-02 2.55e+01 pdb=" CG TYR A 753 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR A 753 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 753 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 753 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 753 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR A 753 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 753 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1286 " 0.062 2.00e-02 2.50e+03 3.08e-02 2.37e+01 pdb=" CG TRP A1286 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP A1286 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A1286 " -0.030 2.00e-02 2.50e+03 pdb=" NE1 TRP A1286 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP A1286 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A1286 " -0.046 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1286 " 0.023 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1286 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A1286 " 0.037 2.00e-02 2.50e+03 ... (remaining 5298 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.27: 2 2.27 - 2.93: 11265 2.93 - 3.59: 41793 3.59 - 4.24: 70863 4.24 - 4.90: 121115 Nonbonded interactions: 245038 Sorted by model distance: nonbonded pdb=" AO6 COA G2102 " pdb=" AP1 COA G2102 " model vdw 1.615 2.720 nonbonded pdb=" AP2 COA G2102 " pdb="AO5* COA G2102 " model vdw 1.616 2.720 nonbonded pdb=" O SER A1293 " pdb=" OG SER A1293 " model vdw 2.279 2.440 nonbonded pdb=" O VAL G1048 " pdb=" OG1 THR G1051 " model vdw 2.281 2.440 nonbonded pdb=" OH TYR G 615 " pdb=" OD1 ASP G1075 " model vdw 2.329 2.440 ... (remaining 245033 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.870 Check model and map are aligned: 0.430 Set scattering table: 0.270 Process input model: 85.450 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.350 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:13.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 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 : 0.024 2.436 30416 Z= 1.547 Angle : 2.025 89.610 41226 Z= 1.404 Chirality : 0.092 0.426 4628 Planarity : 0.007 0.047 5301 Dihedral : 15.628 156.048 11389 Min Nonbonded Distance : 1.615 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.74 % Favored : 94.02 % Rotamer: Outliers : 1.08 % Allowed : 5.42 % Favored : 93.50 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.56 % 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: -3.45 (0.11), residues: 3764 helix: -2.98 (0.09), residues: 1653 sheet: -1.60 (0.20), residues: 508 loop : -1.49 (0.14), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.011 TRP A1286 HIS 0.015 0.004 HIS A1358 PHE 0.067 0.008 PHE G 799 TYR 0.062 0.008 TYR A 753 ARG 0.018 0.002 ARG A1036 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 205 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 170 time to evaluate : 3.493 Fit side-chains REVERT: A 413 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9053 (tm) REVERT: A 431 GLU cc_start: 0.8757 (tp30) cc_final: 0.8491 (tp30) REVERT: A 518 LYS cc_start: 0.8139 (pttt) cc_final: 0.7486 (tptp) REVERT: A 1066 ASN cc_start: 0.7206 (t0) cc_final: 0.6883 (t0) REVERT: A 1160 THR cc_start: 0.7844 (p) cc_final: 0.7218 (t) REVERT: A 1234 MET cc_start: 0.8862 (mtm) cc_final: 0.8583 (mtm) REVERT: A 1332 TYR cc_start: 0.9199 (OUTLIER) cc_final: 0.8176 (p90) REVERT: A 1365 MET cc_start: 0.8805 (mtt) cc_final: 0.8604 (mtt) REVERT: A 1561 MET cc_start: 0.9009 (mmp) cc_final: 0.8729 (mmp) REVERT: A 1838 GLU cc_start: 0.7958 (tt0) cc_final: 0.7271 (tm-30) REVERT: A 1850 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.5954 (tm-30) REVERT: A 1868 LYS cc_start: 0.7425 (tptm) cc_final: 0.6977 (pttt) REVERT: G 91 PHE cc_start: 0.8502 (t80) cc_final: 0.8093 (t80) REVERT: G 138 ASP cc_start: 0.7761 (p0) cc_final: 0.7264 (t0) REVERT: G 442 ASP cc_start: 0.8336 (m-30) cc_final: 0.8084 (m-30) REVERT: G 597 MET cc_start: 0.8998 (mtm) cc_final: 0.8593 (mtm) REVERT: G 630 MET cc_start: 0.8842 (tpp) cc_final: 0.8400 (ttm) REVERT: G 764 MET cc_start: 0.9054 (mtm) cc_final: 0.8831 (mtm) REVERT: G 850 MET cc_start: 0.8078 (mmt) cc_final: 0.7771 (mmm) REVERT: G 877 LYS cc_start: 0.8071 (mmpt) cc_final: 0.7714 (tmmt) REVERT: G 1255 MET cc_start: 0.8869 (mmm) cc_final: 0.8635 (mmm) outliers start: 35 outliers final: 13 residues processed: 205 average time/residue: 1.6242 time to fit residues: 387.1780 Evaluate side-chains 128 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 3.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1332 TYR Chi-restraints excluded: chain A residue 1850 GLU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 599 PRO Chi-restraints excluded: chain G residue 1373 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1650 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 8.9990 chunk 285 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 192 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 295 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 179 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 chunk 342 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN A 344 GLN A 356 ASN A 618 ASN A 743 GLN A1380 GLN A1444 ASN A1790 ASN A1845 ASN B 292 GLN G 36 GLN G 38 ASN G 102 HIS G 155 GLN G 181 HIS G 221 ASN G 245 GLN G 365 GLN G 440 ASN G 500 HIS G 718 ASN G 747 HIS G1217 ASN G1241 ASN G1341 ASN G1355 ASN G1451 GLN G1523 ASN G1697 HIS G1890 ASN G1895 ASN G1912 ASN G1983 ASN G2020 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 30416 Z= 0.300 Angle : 0.595 9.867 41226 Z= 0.311 Chirality : 0.045 0.165 4628 Planarity : 0.004 0.040 5301 Dihedral : 8.200 162.834 4215 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.29 % Allowed : 8.32 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.13), residues: 3764 helix: -0.16 (0.12), residues: 1661 sheet: -0.96 (0.21), residues: 523 loop : -0.43 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 832 HIS 0.007 0.001 HIS A 454 PHE 0.023 0.002 PHE A 35 TYR 0.023 0.002 TYR A 417 ARG 0.006 0.001 ARG G1849 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 157 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 115 time to evaluate : 3.551 Fit side-chains REVERT: A 75 HIS cc_start: 0.8303 (OUTLIER) cc_final: 0.7722 (p90) REVERT: A 518 LYS cc_start: 0.8062 (pttt) cc_final: 0.7535 (tptp) REVERT: A 1066 ASN cc_start: 0.7321 (t0) cc_final: 0.6897 (t0) REVERT: A 1127 VAL cc_start: 0.8214 (t) cc_final: 0.7923 (p) REVERT: A 1160 THR cc_start: 0.7846 (p) cc_final: 0.7259 (t) REVERT: A 1786 PHE cc_start: 0.7555 (t80) cc_final: 0.7313 (t80) REVERT: A 1838 GLU cc_start: 0.7861 (tt0) cc_final: 0.7385 (tm-30) REVERT: A 1850 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.6099 (tm-30) REVERT: B 237 MET cc_start: 0.7061 (mmm) cc_final: 0.6819 (mmt) REVERT: G 38 ASN cc_start: 0.7870 (OUTLIER) cc_final: 0.7654 (m-40) REVERT: G 442 ASP cc_start: 0.8269 (m-30) cc_final: 0.7983 (m-30) REVERT: G 597 MET cc_start: 0.8918 (mtm) cc_final: 0.8495 (mtm) REVERT: G 2036 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8325 (mp0) outliers start: 42 outliers final: 20 residues processed: 151 average time/residue: 1.5593 time to fit residues: 278.7252 Evaluate side-chains 134 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 110 time to evaluate : 3.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1808 SER Chi-restraints excluded: chain A residue 1850 GLU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 777 THR Chi-restraints excluded: chain G residue 784 GLU Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1772 SER Chi-restraints excluded: chain G residue 1925 ILE Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 2033 THR Chi-restraints excluded: chain G residue 2036 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 284 optimal weight: 20.0000 chunk 233 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 342 optimal weight: 7.9990 chunk 370 optimal weight: 0.0970 chunk 305 optimal weight: 5.9990 chunk 340 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 275 optimal weight: 0.0970 overall best weight: 2.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 527 GLN A1794 GLN G 36 GLN G 85 ASN G1529 GLN ** G1890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30416 Z= 0.165 Angle : 0.486 8.837 41226 Z= 0.253 Chirality : 0.041 0.151 4628 Planarity : 0.004 0.059 5301 Dihedral : 7.390 146.899 4202 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.83 % Allowed : 9.76 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.14), residues: 3764 helix: 0.94 (0.13), residues: 1662 sheet: -0.61 (0.22), residues: 532 loop : -0.09 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 832 HIS 0.006 0.001 HIS A1689 PHE 0.025 0.001 PHE A 35 TYR 0.017 0.001 TYR A 417 ARG 0.015 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 138 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 111 time to evaluate : 3.507 Fit side-chains REVERT: A 59 ARG cc_start: 0.7928 (mtm110) cc_final: 0.7635 (mtt180) REVERT: A 75 HIS cc_start: 0.8276 (OUTLIER) cc_final: 0.7711 (p90) REVERT: A 518 LYS cc_start: 0.8103 (pttt) cc_final: 0.7585 (tptp) REVERT: A 632 ARG cc_start: 0.8314 (mmm160) cc_final: 0.8095 (mpt180) REVERT: A 1066 ASN cc_start: 0.7188 (t0) cc_final: 0.6772 (t0) REVERT: A 1127 VAL cc_start: 0.8149 (t) cc_final: 0.7854 (p) REVERT: A 1160 THR cc_start: 0.7845 (p) cc_final: 0.7339 (t) REVERT: B 237 MET cc_start: 0.7028 (mmm) cc_final: 0.6785 (mmt) REVERT: G 442 ASP cc_start: 0.8197 (m-30) cc_final: 0.7868 (m-30) REVERT: G 1223 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8346 (mtp) REVERT: G 2036 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8320 (mp0) REVERT: G 2047 LYS cc_start: 0.8347 (tmmt) cc_final: 0.8100 (mmpt) outliers start: 27 outliers final: 16 residues processed: 133 average time/residue: 1.6735 time to fit residues: 260.7458 Evaluate side-chains 126 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 3.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1305 CYS Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1808 SER Chi-restraints excluded: chain A residue 1836 ASP Chi-restraints excluded: chain A residue 1849 VAL Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 981 GLU Chi-restraints excluded: chain G residue 1223 MET Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1925 ILE Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1959 LYS Chi-restraints excluded: chain G residue 2036 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 338 optimal weight: 9.9990 chunk 257 optimal weight: 6.9990 chunk 177 optimal weight: 40.0000 chunk 37 optimal weight: 9.9990 chunk 163 optimal weight: 0.0040 chunk 230 optimal weight: 10.0000 chunk 344 optimal weight: 0.0370 chunk 364 optimal weight: 7.9990 chunk 179 optimal weight: 6.9990 chunk 326 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 overall best weight: 4.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN A 758 ASN A1794 GLN B 271 ASN G 36 GLN G1055 HIS G1868 GLN ** G1890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1995 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30416 Z= 0.259 Angle : 0.522 10.322 41226 Z= 0.270 Chirality : 0.043 0.154 4628 Planarity : 0.004 0.038 5301 Dihedral : 7.155 142.825 4197 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.32 % Allowed : 10.47 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.14), residues: 3764 helix: 1.13 (0.13), residues: 1663 sheet: -0.54 (0.22), residues: 533 loop : -0.03 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 832 HIS 0.006 0.001 HIS A 454 PHE 0.025 0.002 PHE A 35 TYR 0.017 0.002 TYR A 417 ARG 0.006 0.001 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 152 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 109 time to evaluate : 3.756 Fit side-chains REVERT: A 75 HIS cc_start: 0.8248 (OUTLIER) cc_final: 0.7672 (p90) REVERT: A 518 LYS cc_start: 0.8082 (pttt) cc_final: 0.7578 (tptp) REVERT: A 1127 VAL cc_start: 0.8169 (t) cc_final: 0.7906 (p) REVERT: A 1160 THR cc_start: 0.7800 (p) cc_final: 0.7266 (t) REVERT: A 1180 ARG cc_start: 0.6989 (mpt180) cc_final: 0.6711 (mmt180) REVERT: B 237 MET cc_start: 0.7066 (mmm) cc_final: 0.6851 (mmt) REVERT: B 301 ASP cc_start: 0.6567 (t70) cc_final: 0.6226 (p0) REVERT: G 1064 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7715 (mmmm) REVERT: G 2036 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8339 (mp0) REVERT: G 2047 LYS cc_start: 0.8258 (tmmt) cc_final: 0.8051 (mmpt) outliers start: 43 outliers final: 23 residues processed: 143 average time/residue: 1.5733 time to fit residues: 265.9584 Evaluate side-chains 135 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 109 time to evaluate : 3.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1305 CYS Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1808 SER Chi-restraints excluded: chain A residue 1836 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 777 THR Chi-restraints excluded: chain G residue 981 GLU Chi-restraints excluded: chain G residue 1064 LYS Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1772 SER Chi-restraints excluded: chain G residue 1925 ILE Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1959 LYS Chi-restraints excluded: chain G residue 2036 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 0.3980 chunk 206 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 271 optimal weight: 0.9990 chunk 150 optimal weight: 20.0000 chunk 310 optimal weight: 9.9990 chunk 251 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 186 optimal weight: 10.0000 chunk 327 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1063 HIS A1794 GLN G 752 GLN ** G1890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30416 Z= 0.278 Angle : 0.526 10.432 41226 Z= 0.272 Chirality : 0.044 0.182 4628 Planarity : 0.004 0.065 5301 Dihedral : 7.049 137.361 4196 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.63 % Allowed : 10.72 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.14), residues: 3764 helix: 1.17 (0.13), residues: 1656 sheet: -0.54 (0.21), residues: 542 loop : -0.04 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 865 HIS 0.006 0.001 HIS A 454 PHE 0.023 0.002 PHE A 35 TYR 0.017 0.002 TYR G 624 ARG 0.018 0.001 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 161 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 108 time to evaluate : 3.616 Fit side-chains REVERT: A 74 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8667 (pp) REVERT: A 75 HIS cc_start: 0.8219 (OUTLIER) cc_final: 0.7608 (p90) REVERT: A 518 LYS cc_start: 0.8183 (pttt) cc_final: 0.7599 (tptp) REVERT: A 632 ARG cc_start: 0.8260 (mmm160) cc_final: 0.8054 (mpt180) REVERT: A 1127 VAL cc_start: 0.8229 (t) cc_final: 0.7977 (p) REVERT: A 1160 THR cc_start: 0.7711 (p) cc_final: 0.7296 (t) REVERT: A 1180 ARG cc_start: 0.6892 (mpt180) cc_final: 0.6472 (mmt180) REVERT: B 237 MET cc_start: 0.7007 (mmm) cc_final: 0.6783 (mmt) REVERT: B 301 ASP cc_start: 0.6750 (t70) cc_final: 0.6322 (p0) REVERT: G 11 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7325 (pp) REVERT: G 73 GLU cc_start: 0.6043 (OUTLIER) cc_final: 0.5792 (pp20) REVERT: G 481 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8398 (t70) REVERT: G 1064 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7674 (mmmm) REVERT: G 1223 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8353 (mtp) REVERT: G 1881 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7339 (tpm170) REVERT: G 2036 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8361 (mp0) outliers start: 53 outliers final: 31 residues processed: 154 average time/residue: 1.5216 time to fit residues: 278.2887 Evaluate side-chains 147 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 107 time to evaluate : 3.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1305 CYS Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1808 SER Chi-restraints excluded: chain A residue 1836 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 73 GLU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 481 ASP Chi-restraints excluded: chain G residue 981 GLU Chi-restraints excluded: chain G residue 1064 LYS Chi-restraints excluded: chain G residue 1223 MET Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1736 MET Chi-restraints excluded: chain G residue 1772 SER Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1925 ILE Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1948 SER Chi-restraints excluded: chain G residue 1959 LYS Chi-restraints excluded: chain G residue 2036 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 122 optimal weight: 3.9990 chunk 328 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 213 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 364 optimal weight: 9.9990 chunk 302 optimal weight: 0.7980 chunk 168 optimal weight: 4.9990 chunk 30 optimal weight: 0.3980 chunk 120 optimal weight: 6.9990 chunk 191 optimal weight: 9.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1794 GLN G1851 ASN ** G1890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30416 Z= 0.183 Angle : 0.475 9.435 41226 Z= 0.246 Chirality : 0.042 0.150 4628 Planarity : 0.004 0.044 5301 Dihedral : 6.755 129.977 4196 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.66 % Allowed : 11.06 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.14), residues: 3764 helix: 1.36 (0.13), residues: 1651 sheet: -0.44 (0.21), residues: 546 loop : 0.08 (0.16), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 865 HIS 0.005 0.001 HIS A1689 PHE 0.024 0.001 PHE A 35 TYR 0.016 0.001 TYR A 417 ARG 0.008 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 163 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 109 time to evaluate : 3.623 Fit side-chains REVERT: A 75 HIS cc_start: 0.8216 (OUTLIER) cc_final: 0.7588 (p90) REVERT: A 518 LYS cc_start: 0.8143 (pttt) cc_final: 0.7600 (tptp) REVERT: A 1127 VAL cc_start: 0.8268 (t) cc_final: 0.8004 (p) REVERT: A 1160 THR cc_start: 0.7697 (p) cc_final: 0.7282 (t) REVERT: B 237 MET cc_start: 0.7048 (mmm) cc_final: 0.6809 (mmt) REVERT: B 301 ASP cc_start: 0.6887 (t70) cc_final: 0.6295 (p0) REVERT: G 11 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7242 (pt) REVERT: G 73 GLU cc_start: 0.6077 (OUTLIER) cc_final: 0.5812 (pp20) REVERT: G 168 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7477 (m-30) REVERT: G 481 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8379 (t70) REVERT: G 1223 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8306 (mtp) REVERT: G 1881 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7298 (tpm170) outliers start: 54 outliers final: 28 residues processed: 157 average time/residue: 1.6232 time to fit residues: 305.4414 Evaluate side-chains 145 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 110 time to evaluate : 3.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1130 ASP Chi-restraints excluded: chain A residue 1305 CYS Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1808 SER Chi-restraints excluded: chain A residue 1836 ASP Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 73 GLU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 168 ASP Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 481 ASP Chi-restraints excluded: chain G residue 777 THR Chi-restraints excluded: chain G residue 908 ASN Chi-restraints excluded: chain G residue 981 GLU Chi-restraints excluded: chain G residue 1223 MET Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1479 ILE Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1736 MET Chi-restraints excluded: chain G residue 1772 SER Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1925 ILE Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1959 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 351 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 207 optimal weight: 0.5980 chunk 266 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 307 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 chunk 363 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 chunk 221 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1794 GLN G1421 ASN G1564 HIS G1851 ASN ** G1890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30416 Z= 0.292 Angle : 0.533 10.366 41226 Z= 0.274 Chirality : 0.044 0.156 4628 Planarity : 0.004 0.073 5301 Dihedral : 6.830 124.011 4196 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.91 % Allowed : 11.12 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.14), residues: 3764 helix: 1.25 (0.13), residues: 1651 sheet: -0.47 (0.22), residues: 543 loop : 0.02 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 865 HIS 0.005 0.001 HIS A1100 PHE 0.024 0.002 PHE A1376 TYR 0.017 0.002 TYR G 624 ARG 0.017 0.001 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 172 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 110 time to evaluate : 3.887 Fit side-chains REVERT: A 75 HIS cc_start: 0.8185 (OUTLIER) cc_final: 0.7501 (p90) REVERT: A 518 LYS cc_start: 0.8201 (pttt) cc_final: 0.7598 (tptp) REVERT: A 632 ARG cc_start: 0.8258 (mmm160) cc_final: 0.8012 (mtm-85) REVERT: A 1127 VAL cc_start: 0.8331 (t) cc_final: 0.8090 (p) REVERT: A 1160 THR cc_start: 0.7717 (p) cc_final: 0.7316 (t) REVERT: B 237 MET cc_start: 0.7018 (mmm) cc_final: 0.6761 (mmt) REVERT: B 301 ASP cc_start: 0.6980 (t70) cc_final: 0.6302 (p0) REVERT: G 11 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7327 (pp) REVERT: G 167 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6717 (p0) REVERT: G 168 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7492 (m-30) REVERT: G 481 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8400 (t70) REVERT: G 1064 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7681 (mmmm) REVERT: G 1747 LYS cc_start: 0.3936 (OUTLIER) cc_final: 0.3705 (pttp) REVERT: G 1881 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7321 (tpm170) REVERT: G 1959 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7362 (mmmm) outliers start: 62 outliers final: 41 residues processed: 164 average time/residue: 1.5625 time to fit residues: 308.7549 Evaluate side-chains 157 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 107 time to evaluate : 3.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1121 MET Chi-restraints excluded: chain A residue 1130 ASP Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1380 GLN Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1808 SER Chi-restraints excluded: chain A residue 1836 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 168 ASP Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 481 ASP Chi-restraints excluded: chain G residue 777 THR Chi-restraints excluded: chain G residue 845 THR Chi-restraints excluded: chain G residue 908 ASN Chi-restraints excluded: chain G residue 981 GLU Chi-restraints excluded: chain G residue 1064 LYS Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1479 ILE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1736 MET Chi-restraints excluded: chain G residue 1747 LYS Chi-restraints excluded: chain G residue 1772 SER Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1925 ILE Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1948 SER Chi-restraints excluded: chain G residue 1959 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 224 optimal weight: 0.7980 chunk 145 optimal weight: 7.9990 chunk 217 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 231 optimal weight: 4.9990 chunk 247 optimal weight: 10.0000 chunk 179 optimal weight: 0.0050 chunk 33 optimal weight: 9.9990 chunk 285 optimal weight: 4.9990 overall best weight: 3.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1794 GLN ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30416 Z= 0.209 Angle : 0.496 9.805 41226 Z= 0.254 Chirality : 0.042 0.151 4628 Planarity : 0.004 0.050 5301 Dihedral : 6.643 119.850 4196 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.76 % Allowed : 11.46 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.14), residues: 3764 helix: 1.35 (0.13), residues: 1656 sheet: -0.42 (0.22), residues: 543 loop : 0.09 (0.16), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 865 HIS 0.005 0.001 HIS A1689 PHE 0.023 0.001 PHE A 35 TYR 0.016 0.001 TYR A 417 ARG 0.013 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 166 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 109 time to evaluate : 3.463 Fit side-chains REVERT: A 75 HIS cc_start: 0.8073 (OUTLIER) cc_final: 0.7405 (p90) REVERT: A 518 LYS cc_start: 0.8195 (pttt) cc_final: 0.7582 (tptp) REVERT: A 632 ARG cc_start: 0.8305 (mmm160) cc_final: 0.8084 (mpt180) REVERT: A 1127 VAL cc_start: 0.8279 (t) cc_final: 0.8023 (p) REVERT: A 1160 THR cc_start: 0.7708 (p) cc_final: 0.7303 (t) REVERT: B 237 MET cc_start: 0.7048 (mmm) cc_final: 0.6722 (mmt) REVERT: B 301 ASP cc_start: 0.6853 (t70) cc_final: 0.6177 (p0) REVERT: G 11 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7281 (pp) REVERT: G 481 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8367 (t70) REVERT: G 1223 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8316 (mtp) REVERT: G 1747 LYS cc_start: 0.3938 (OUTLIER) cc_final: 0.3694 (pttp) REVERT: G 1881 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7312 (tpm170) REVERT: G 1959 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7360 (mmmm) REVERT: G 2036 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8322 (mp0) outliers start: 57 outliers final: 41 residues processed: 160 average time/residue: 1.5107 time to fit residues: 290.8942 Evaluate side-chains 157 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 108 time to evaluate : 3.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1121 MET Chi-restraints excluded: chain A residue 1130 ASP Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1380 GLN Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1808 SER Chi-restraints excluded: chain A residue 1836 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 481 ASP Chi-restraints excluded: chain G residue 777 THR Chi-restraints excluded: chain G residue 845 THR Chi-restraints excluded: chain G residue 908 ASN Chi-restraints excluded: chain G residue 981 GLU Chi-restraints excluded: chain G residue 1223 MET Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1479 ILE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1736 MET Chi-restraints excluded: chain G residue 1747 LYS Chi-restraints excluded: chain G residue 1772 SER Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1925 ILE Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1948 SER Chi-restraints excluded: chain G residue 1959 LYS Chi-restraints excluded: chain G residue 2036 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 330 optimal weight: 4.9990 chunk 348 optimal weight: 0.0010 chunk 317 optimal weight: 0.6980 chunk 338 optimal weight: 7.9990 chunk 203 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 chunk 265 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 305 optimal weight: 3.9990 chunk 320 optimal weight: 5.9990 chunk 337 optimal weight: 6.9990 overall best weight: 1.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1482 GLN A1794 GLN G1851 ASN ** G1890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 30416 Z= 0.150 Angle : 0.463 10.566 41226 Z= 0.237 Chirality : 0.041 0.155 4628 Planarity : 0.003 0.045 5301 Dihedral : 6.382 113.504 4196 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.63 % Allowed : 11.67 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.14), residues: 3764 helix: 1.50 (0.13), residues: 1661 sheet: -0.31 (0.22), residues: 544 loop : 0.18 (0.16), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G1138 HIS 0.005 0.001 HIS A1689 PHE 0.024 0.001 PHE A 35 TYR 0.016 0.001 TYR A 417 ARG 0.010 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 166 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 113 time to evaluate : 3.776 Fit side-chains REVERT: A 75 HIS cc_start: 0.8028 (OUTLIER) cc_final: 0.7363 (p90) REVERT: A 518 LYS cc_start: 0.8152 (pttt) cc_final: 0.7598 (tptp) REVERT: A 632 ARG cc_start: 0.8321 (mmm160) cc_final: 0.8111 (mpt180) REVERT: A 1127 VAL cc_start: 0.8203 (t) cc_final: 0.7932 (p) REVERT: A 1160 THR cc_start: 0.7646 (p) cc_final: 0.7254 (t) REVERT: B 237 MET cc_start: 0.6998 (mmm) cc_final: 0.6707 (mmt) REVERT: B 301 ASP cc_start: 0.6892 (t70) cc_final: 0.6183 (p0) REVERT: G 11 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7238 (pt) REVERT: G 167 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.6714 (p0) REVERT: G 168 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7683 (m-30) REVERT: G 481 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8379 (t70) REVERT: G 1223 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8298 (mtp) REVERT: G 1747 LYS cc_start: 0.3382 (OUTLIER) cc_final: 0.3153 (pttp) REVERT: G 1881 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7310 (tpm170) REVERT: G 1959 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7360 (mmmm) REVERT: G 2036 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8307 (mp0) outliers start: 53 outliers final: 35 residues processed: 161 average time/residue: 1.4416 time to fit residues: 278.7029 Evaluate side-chains 153 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 108 time to evaluate : 3.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1380 GLN Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1836 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 168 ASP Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 481 ASP Chi-restraints excluded: chain G residue 777 THR Chi-restraints excluded: chain G residue 908 ASN Chi-restraints excluded: chain G residue 981 GLU Chi-restraints excluded: chain G residue 1223 MET Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1479 ILE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1736 MET Chi-restraints excluded: chain G residue 1747 LYS Chi-restraints excluded: chain G residue 1772 SER Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1925 ILE Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1948 SER Chi-restraints excluded: chain G residue 1959 LYS Chi-restraints excluded: chain G residue 2036 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 222 optimal weight: 10.0000 chunk 358 optimal weight: 10.0000 chunk 218 optimal weight: 9.9990 chunk 169 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 375 optimal weight: 0.0770 chunk 345 optimal weight: 10.0000 chunk 299 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 231 optimal weight: 0.0980 chunk 183 optimal weight: 30.0000 overall best weight: 3.0344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1794 GLN ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30416 Z= 0.193 Angle : 0.484 11.840 41226 Z= 0.247 Chirality : 0.042 0.148 4628 Planarity : 0.004 0.042 5301 Dihedral : 6.375 111.073 4196 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.45 % Allowed : 11.98 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.14), residues: 3764 helix: 1.49 (0.13), residues: 1654 sheet: -0.28 (0.22), residues: 544 loop : 0.18 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 865 HIS 0.005 0.001 HIS A1689 PHE 0.023 0.001 PHE A 35 TYR 0.014 0.001 TYR A 417 ARG 0.010 0.000 ARG A 632 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 156 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 109 time to evaluate : 3.570 Fit side-chains REVERT: A 75 HIS cc_start: 0.8025 (OUTLIER) cc_final: 0.7380 (p90) REVERT: A 518 LYS cc_start: 0.8170 (pttt) cc_final: 0.7600 (tptp) REVERT: A 632 ARG cc_start: 0.8327 (mmm160) cc_final: 0.8124 (mpt180) REVERT: A 1127 VAL cc_start: 0.8263 (t) cc_final: 0.7990 (p) REVERT: A 1160 THR cc_start: 0.7692 (p) cc_final: 0.7311 (t) REVERT: B 237 MET cc_start: 0.7018 (mmm) cc_final: 0.6693 (mmt) REVERT: B 301 ASP cc_start: 0.6976 (t70) cc_final: 0.6262 (p0) REVERT: G 11 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7257 (pt) REVERT: G 481 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8346 (t70) REVERT: G 1064 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7670 (mmmm) REVERT: G 1223 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8293 (mtp) REVERT: G 1881 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7321 (tpm170) REVERT: G 1959 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7360 (mmmm) REVERT: G 2036 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8312 (mp0) outliers start: 47 outliers final: 35 residues processed: 151 average time/residue: 1.6337 time to fit residues: 292.5138 Evaluate side-chains 151 residues out of total 3248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 108 time to evaluate : 3.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 940 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1380 GLN Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1836 ASP Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 481 ASP Chi-restraints excluded: chain G residue 777 THR Chi-restraints excluded: chain G residue 908 ASN Chi-restraints excluded: chain G residue 981 GLU Chi-restraints excluded: chain G residue 1064 LYS Chi-restraints excluded: chain G residue 1223 MET Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1479 ILE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1736 MET Chi-restraints excluded: chain G residue 1772 SER Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1925 ILE Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1948 SER Chi-restraints excluded: chain G residue 1959 LYS Chi-restraints excluded: chain G residue 2036 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 2.9990 chunk 318 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 275 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 299 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 307 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1794 GLN ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1890 ASN ** 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 = 0.3356 r_free = 0.3356 target = 0.065910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.050085 restraints weight = 89504.996| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.84 r_work: 0.2798 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30416 Z= 0.209 Angle : 0.494 11.906 41226 Z= 0.252 Chirality : 0.042 0.148 4628 Planarity : 0.004 0.043 5301 Dihedral : 6.368 108.387 4196 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.48 % Allowed : 12.17 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.14), residues: 3764 helix: 1.49 (0.13), residues: 1649 sheet: -0.27 (0.22), residues: 545 loop : 0.19 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 865 HIS 0.005 0.001 HIS G1581 PHE 0.023 0.001 PHE A 35 TYR 0.015 0.001 TYR A 417 ARG 0.010 0.000 ARG A 632 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7696.01 seconds wall clock time: 140 minutes 28.14 seconds (8428.14 seconds total)