Starting phenix.real_space_refine on Wed Feb 21 00:54:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psf_17851/02_2024/8psf_17851_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psf_17851/02_2024/8psf_17851.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psf_17851/02_2024/8psf_17851_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psf_17851/02_2024/8psf_17851_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psf_17851/02_2024/8psf_17851_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psf_17851/02_2024/8psf_17851.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psf_17851/02_2024/8psf_17851.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psf_17851/02_2024/8psf_17851_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psf_17851/02_2024/8psf_17851_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= -0.002 sd= 0.008 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 2 5.49 5 S 104 5.16 5 C 18578 2.51 5 N 4914 2.21 5 O 5606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 42": "OE1" <-> "OE2" Residue "A ASP 355": "OD1" <-> "OD2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A ASP 492": "OD1" <-> "OD2" Residue "A GLU 664": "OE1" <-> "OE2" Residue "A ASP 675": "OD1" <-> "OD2" Residue "A PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 754": "OD1" <-> "OD2" Residue "A GLU 915": "OE1" <-> "OE2" Residue "A ASP 1085": "OD1" <-> "OD2" Residue "A GLU 1099": "OE1" <-> "OE2" Residue "A GLU 1120": "OE1" <-> "OE2" Residue "A GLU 1124": "OE1" <-> "OE2" Residue "A GLU 1132": "OE1" <-> "OE2" Residue "A ASP 1203": "OD1" <-> "OD2" Residue "A GLU 1221": "OE1" <-> "OE2" Residue "A TYR 1237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1378": "OE1" <-> "OE2" Residue "A TYR 1401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1456": "OE1" <-> "OE2" Residue "A GLU 1468": "OE1" <-> "OE2" Residue "A GLU 1473": "OE1" <-> "OE2" Residue "A GLU 1476": "OE1" <-> "OE2" Residue "A GLU 1568": "OE1" <-> "OE2" Residue "A ASP 1612": "OD1" <-> "OD2" Residue "A PHE 1646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1681": "OE1" <-> "OE2" Residue "A PHE 1786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 111": "OE1" <-> "OE2" Residue "G GLU 347": "OE1" <-> "OE2" Residue "G GLU 411": "OE1" <-> "OE2" Residue "G ASP 538": "OD1" <-> "OD2" Residue "G GLU 668": "OE1" <-> "OE2" Residue "G GLU 744": "OE1" <-> "OE2" Residue "G ASP 830": "OD1" <-> "OD2" Residue "G ASP 889": "OD1" <-> "OD2" Residue "G GLU 978": "OE1" <-> "OE2" Residue "G PHE 1423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1448": "OE1" <-> "OE2" Residue "G ASP 1456": "OD1" <-> "OD2" Residue "G GLU 1469": "OE1" <-> "OE2" Residue "G GLU 1500": "OE1" <-> "OE2" Residue "G ASP 1647": "OD1" <-> "OD2" Residue "G GLU 1658": "OE1" <-> "OE2" Residue "G GLU 1790": "OE1" <-> "OE2" Residue "G TYR 1833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1876": "OE1" <-> "OE2" Residue "G GLU 1926": "OE1" <-> "OE2" Residue "G TYR 1980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 2019": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 2024": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29204 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 12346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1579, 12346 Classifications: {'peptide': 1579} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1517} Chain breaks: 4 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: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 802 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PTRANS': 8, 'TRANS': 154} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 440 Unresolved non-hydrogen angles: 556 Unresolved non-hydrogen dihedrals: 359 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 11, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 189 Chain: "G" Number of atoms: 16004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2034, 16004 Classifications: {'peptide': 2034} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1924} Chain breaks: 1 Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.58, per 1000 atoms: 0.53 Number of scatterers: 29204 At special positions: 0 Unit cell: (181.46, 183.57, 175.13, 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 104 16.00 P 2 15.00 O 5606 8.00 N 4914 7.00 C 18578 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1246 " - pdb=" SG CYS A1327 " distance=2.18 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.60 Conformation dependent library (CDL) restraints added in 5.1 seconds 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7026 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 172 helices and 27 sheets defined 44.7% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.71 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 removed outlier: 3.748A pdb=" N PHE A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 4.780A 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 53 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 382 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: 4.116A pdb=" N LYS A 410 " --> pdb=" O TRP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 442 removed outlier: 3.535A 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 530 Processing helix chain 'A' and resid 609 through 614 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 813 Processing helix chain 'A' and resid 839 through 855 removed outlier: 3.997A pdb=" N GLU A 847 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N THR A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LEU A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N PHE A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N HIS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 891 removed outlier: 4.037A pdb=" N MET A 891 " --> pdb=" O GLY A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 909 removed outlier: 3.667A pdb=" N LEU A 908 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 4.071A 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 930 through 932 No H-bonds generated for 'chain 'A' and resid 930 through 932' Processing helix chain 'A' and resid 936 through 969 removed outlier: 4.094A pdb=" N THR A 950 " --> pdb=" O GLU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1003 removed outlier: 3.721A pdb=" N GLN A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) 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 1056 Processing helix chain 'A' and resid 1086 through 1100 removed outlier: 4.254A pdb=" N LYS A1090 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A1091 " --> pdb=" O ASP A1088 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A1093 " --> pdb=" O LYS A1090 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLU A1094 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N THR A1095 " --> 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: 7.578A pdb=" N ASP A1150 " --> pdb=" O HIS A1146 " (cutoff:3.500A) removed outlier: 7.501A 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 1207 Processing helix chain 'A' and resid 1210 through 1226 removed outlier: 3.555A pdb=" N PHE A1214 " --> pdb=" O PRO A1210 " (cutoff:3.500A) 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 1272 through 1274 No H-bonds generated for 'chain 'A' and resid 1272 through 1274' Processing helix chain 'A' and resid 1280 through 1290 removed outlier: 3.881A pdb=" N MET A1283 " --> pdb=" O ILE A1280 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A1284 " --> pdb=" O ASN A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1320 removed outlier: 5.205A pdb=" N SER A1308 " --> pdb=" O CYS A1305 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A1310 " --> pdb=" O THR A1307 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A1312 " --> pdb=" O VAL A1309 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A1314 " --> pdb=" O SER A1311 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A1316 " --> pdb=" O ASP A1313 " (cutoff:3.500A) removed outlier: 3.557A 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 1445 through 1476 removed outlier: 3.729A pdb=" N ALA A1469 " --> pdb=" O ASN A1465 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A1471 " --> pdb=" O LEU A1467 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A1472 " --> pdb=" O GLU A1468 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU A1476 " --> pdb=" O LEU A1472 " (cutoff:3.500A) Processing helix chain 'A' and resid 1482 through 1508 Processing helix chain 'A' and resid 1521 through 1529 removed outlier: 3.680A pdb=" N LEU A1526 " --> pdb=" O LEU A1522 " (cutoff:3.500A) removed outlier: 4.643A 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 1563 removed outlier: 3.896A pdb=" N LYS A1551 " --> pdb=" O LYS A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1581 removed outlier: 3.867A pdb=" N THR A1581 " --> pdb=" O LYS A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1585 through 1600 removed outlier: 4.492A pdb=" N GLY A1589 " --> pdb=" O GLY A1586 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A1600 " --> pdb=" O LEU A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1616 through 1620 Processing helix chain 'A' and resid 1658 through 1664 removed outlier: 3.698A pdb=" N TYR A1662 " --> pdb=" O ASP A1659 " (cutoff:3.500A) removed outlier: 4.045A 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 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 1801 Processing helix chain 'A' and resid 1805 through 1823 Processing helix chain 'A' and resid 1854 through 1861 Processing helix chain 'B' and resid 147 through 159 Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 181 through 193 removed outlier: 4.174A pdb=" N GLU B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU B 193 " --> pdb=" O ASP B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 206 through 213 Processing helix chain 'B' and resid 224 through 233 removed outlier: 3.795A pdb=" N LEU B 228 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU B 229 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER B 230 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 233 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 252 Processing helix chain 'B' and resid 258 through 270 removed outlier: 3.926A pdb=" N GLY B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 298 Processing helix chain 'G' and resid 24 through 40 removed outlier: 5.784A pdb=" N PHE G 28 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE G 29 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER G 31 " --> pdb=" O PHE G 28 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU G 33 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE G 37 " --> pdb=" O GLN G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 69 Processing helix chain 'G' and resid 81 through 94 removed outlier: 3.622A pdb=" N LEU G 86 " --> pdb=" O GLN G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 110 removed outlier: 3.668A pdb=" N GLN G 110 " --> pdb=" O ALA G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 132 Processing helix chain 'G' and resid 144 through 151 Processing helix chain 'G' and resid 169 through 179 removed outlier: 3.521A pdb=" N LEU G 173 " --> pdb=" O TYR G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 201 removed outlier: 5.197A pdb=" N ASP G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 208 No H-bonds generated for 'chain 'G' and resid 205 through 208' Processing helix chain 'G' and resid 215 through 220 Processing helix chain 'G' and resid 222 through 224 No H-bonds generated for 'chain 'G' and resid 222 through 224' Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 234 through 255 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: 3.668A pdb=" N ALA G 280 " --> pdb=" O LEU G 277 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL G 281 " --> pdb=" O VAL G 278 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE G 283 " --> pdb=" O ALA G 280 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU G 285 " --> pdb=" O ALA G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 313 Processing helix chain 'G' and resid 321 through 329 Processing helix chain 'G' and resid 346 through 359 removed outlier: 4.019A 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 396 removed outlier: 3.536A pdb=" N ALA G 396 " --> pdb=" O THR G 392 " (cutoff:3.500A) 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 443 Proline residue: G 434 - end of helix removed outlier: 4.139A pdb=" N ASP G 437 " --> pdb=" O PRO G 434 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU G 443 " --> pdb=" O ASN G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 454 No H-bonds generated for 'chain 'G' and resid 452 through 454' 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 520 Processing helix chain 'G' and resid 544 through 548 Processing helix chain 'G' and resid 552 through 554 No H-bonds generated for 'chain 'G' and resid 552 through 554' 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: 3.695A pdb=" N LEU G 586 " --> pdb=" O LYS G 582 " (cutoff:3.500A) Processing helix chain 'G' and resid 604 through 612 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 638 Processing helix chain 'G' and resid 656 through 671 removed outlier: 3.710A 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 759 removed outlier: 5.238A pdb=" N SER G 755 " --> pdb=" O LEU G 751 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LYS G 756 " --> pdb=" O GLN G 752 " (cutoff:3.500A) Processing helix chain 'G' and resid 775 through 781 Proline residue: G 779 - end of helix No H-bonds generated for 'chain 'G' and resid 775 through 781' 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 807 removed outlier: 4.327A pdb=" N ILE G 807 " --> pdb=" O ARG G 804 " (cutoff:3.500A) Processing helix chain 'G' and resid 815 through 822 Processing helix chain 'G' and resid 832 through 836 removed outlier: 3.523A pdb=" N TYR G 836 " --> pdb=" O GLU G 833 " (cutoff:3.500A) Processing helix chain 'G' and resid 860 through 871 Processing helix chain 'G' and resid 877 through 886 removed outlier: 4.263A pdb=" N VAL G 881 " --> pdb=" O LYS G 877 " (cutoff:3.500A) Proline residue: G 882 - end of helix Processing helix chain 'G' and resid 888 through 897 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 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: 4.585A pdb=" N GLU G1026 " --> pdb=" O ARG G1023 " (cutoff:3.500A) removed outlier: 3.857A 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 1324 through 1338 removed outlier: 3.810A pdb=" N TRP G1331 " --> pdb=" O VAL G1328 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ARG G1332 " --> pdb=" O VAL G1329 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE G1335 " --> pdb=" O ARG G1332 " (cutoff:3.500A) Processing helix chain 'G' and resid 1341 through 1343 No H-bonds generated for 'chain 'G' and resid 1341 through 1343' Processing helix chain 'G' and resid 1347 through 1349 No H-bonds generated for 'chain 'G' and resid 1347 through 1349' Processing helix chain 'G' and resid 1439 through 1446 Processing helix chain 'G' and resid 1515 through 1523 Processing helix chain 'G' and resid 1551 through 1557 removed outlier: 3.540A 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 1678 through 1683 removed outlier: 3.801A pdb=" N THR G1683 " --> pdb=" O ASP G1679 " (cutoff:3.500A) Processing helix chain 'G' and resid 1685 through 1702 Processing helix chain 'G' and resid 1706 through 1712 Processing helix chain 'G' and resid 1723 through 1734 Processing helix chain 'G' and resid 1774 through 1795 Proline residue: G1779 - end of helix Processing helix chain 'G' and resid 1808 through 1818 removed outlier: 3.877A pdb=" N LEU G1818 " --> pdb=" O LEU G1815 " (cutoff:3.500A) Processing helix chain 'G' and resid 1824 through 1840 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 1882 Processing helix chain 'G' and resid 1904 through 1920 removed outlier: 3.505A pdb=" N ASP G1908 " --> pdb=" O LEU G1904 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS G1918 " --> pdb=" O LEU G1914 " (cutoff:3.500A) Processing helix chain 'G' and resid 1924 through 1930 removed outlier: 3.538A pdb=" N LYS G1929 " --> pdb=" O ILE G1925 " (cutoff:3.500A) Processing helix chain 'G' and resid 1936 through 1952 removed outlier: 3.587A pdb=" N GLU G1942 " --> pdb=" O GLY G1938 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE G1943 " --> pdb=" O HIS G1939 " (cutoff:3.500A) Processing helix chain 'G' and resid 1980 through 1995 removed outlier: 4.025A pdb=" N ASN G1983 " --> pdb=" O TYR G1980 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS G1986 " --> pdb=" O ASN G1983 " (cutoff:3.500A) Proline residue: G1987 - end of helix removed outlier: 3.903A pdb=" N SER G1990 " --> pdb=" O PRO G1987 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU G1992 " --> pdb=" O LYS G1989 " (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 2023 through 2032 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: 6.943A pdb=" N GLU A 77 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLU A 46 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 6.770A 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: 6.508A pdb=" N ALA A 767 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N THR A 681 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 6.639A 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: 4.449A pdb=" N MET A 923 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA A 820 " --> pdb=" O THR A 863 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N CYS A 865 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL A 822 " --> pdb=" O CYS A 865 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA A 867 " --> pdb=" O VAL A 822 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU A 824 " --> pdb=" O ALA A 867 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE A 869 " --> pdb=" O LEU A 824 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET A 826 " --> pdb=" O ILE A 869 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1243 through 1245 removed outlier: 6.740A pdb=" N ILE A1326 " --> pdb=" O GLY A1244 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N MET A1388 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL A1021 " --> pdb=" O MET A1388 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE A1019 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A1402 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE A1654 " --> pdb=" O ALA A1405 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA A1407 " --> pdb=" O GLN A1652 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN A1652 " --> pdb=" O ALA A1407 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR A1409 " --> pdb=" O GLY A1650 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY A1650 " --> pdb=" O THR A1409 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N SER A1640 " --> pdb=" O GLY A1537 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ALA A1539 " --> pdb=" O SER A1640 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR A1642 " --> pdb=" O ALA A1539 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE A1573 " --> pdb=" O ALA A1539 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1060 through 1066 Processing sheet with id= G, first strand: chain 'A' and resid 1103 through 1105 Processing sheet with id= H, first strand: chain 'A' and resid 1119 through 1126 Processing sheet with id= I, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id= J, first strand: chain 'A' and resid 1768 through 1775 Processing sheet with id= K, first strand: chain 'A' and resid 1837 through 1840 Processing sheet with id= L, first strand: chain 'G' and resid 6 through 13 removed outlier: 3.673A pdb=" N LEU G 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 526 through 529 removed outlier: 7.848A pdb=" N ALA G 158 " --> pdb=" O LYS G 268 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA G 270 " --> pdb=" O ALA G 158 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N PHE G 160 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY G 272 " --> pdb=" O PHE G 160 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 417 through 420 removed outlier: 3.757A pdb=" N SER G 417 " --> pdb=" O SER G 342 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N SER G 380 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE G 368 " --> pdb=" O SER G 380 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 568 through 571 Processing sheet with id= P, first strand: chain 'G' and resid 618 through 620 removed outlier: 6.518A pdb=" N GLY G 648 " --> pdb=" O LEU G 619 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE G 649 " --> pdb=" O GLN G 677 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU G 679 " --> pdb=" O ILE G 649 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU G 651 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE G 681 " --> pdb=" O LEU G 651 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N TYR G 702 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ILE G 681 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY G 704 " --> pdb=" O ILE G 681 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N LEU G 705 " --> pdb=" O PRO G 727 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ALA G 729 " --> pdb=" O LEU G 705 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLY G 798 " --> pdb=" O PHE G 767 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 843 through 847 Processing sheet with id= R, first strand: chain 'G' and resid 1125 through 1128 removed outlier: 3.548A pdb=" N VAL G1209 " --> pdb=" O LEU G1197 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU G1199 " --> pdb=" O PRO G1207 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N THR G1208 " --> pdb=" O ILE G1224 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE G1218 " --> pdb=" O LEU G1214 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU G1238 " --> pdb=" O MET G1221 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 1158 through 1161 Processing sheet with id= T, first strand: chain 'G' and resid 1372 through 1383 removed outlier: 6.823A pdb=" N ASP G1391 " --> pdb=" O GLU G1379 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL G1381 " --> pdb=" O ILE G1389 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE G1389 " --> pdb=" O VAL G1381 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASN G1383 " --> pdb=" O GLY G1387 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLY G1387 " --> pdb=" O ASN G1383 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ARG G1398 " --> pdb=" O PRO G1402 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER G1354 " --> pdb=" O SER G1409 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N PHE G1411 " --> pdb=" O HIS G1352 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N HIS G1352 " --> pdb=" O PHE G1411 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG G1413 " --> pdb=" O LEU G1350 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU G1350 " --> pdb=" O ARG G1413 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU G1353 " --> pdb=" O PHE G1612 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ARG G1606 " --> pdb=" O MET G1359 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU G1656 " --> pdb=" O ARG G1606 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR G1608 " --> pdb=" O GLU G1654 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLU G1654 " --> pdb=" O TYR G1608 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N CYS G1610 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR G1652 " --> pdb=" O CYS G1610 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N PHE G1612 " --> pdb=" O VAL G1650 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL G1650 " --> pdb=" O PHE G1612 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR G1642 " --> pdb=" O VAL G1650 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N THR G1652 " --> pdb=" O PHE G1640 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE G1640 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLU G1654 " --> pdb=" O ILE G1638 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE G1638 " --> pdb=" O GLU G1654 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU G1656 " --> pdb=" O LYS G1636 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LYS G1636 " --> pdb=" O GLU G1656 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS G1639 " --> pdb=" O HIS G1628 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N HIS G1628 " --> pdb=" O LYS G1639 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N GLU G1641 " --> pdb=" O ILE G1626 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ILE G1626 " --> pdb=" O GLU G1641 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ARG G1643 " --> pdb=" O THR G1624 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N THR G1624 " --> pdb=" O ARG G1643 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 1423 through 1427 removed outlier: 3.725A pdb=" N GLY G1487 " --> pdb=" O VAL G1504 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY G1502 " --> pdb=" O ILE G1489 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL G1491 " --> pdb=" O GLU G1500 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLU G1500 " --> pdb=" O VAL G1491 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 1525 through 1527 removed outlier: 4.606A pdb=" N VAL G1430 " --> pdb=" O LEU G1527 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 1663 through 1666 removed outlier: 6.859A pdb=" N THR G1803 " --> pdb=" O PHE G1664 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N PHE G1666 " --> pdb=" O THR G1803 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA G1805 " --> pdb=" O PHE G1666 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'G' and resid 1716 through 1720 Processing sheet with id= Y, first strand: chain 'G' and resid 1739 through 1741 removed outlier: 3.832A pdb=" N THR G1740 " --> pdb=" O LYS G1747 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 1852 through 1857 removed outlier: 6.326A pdb=" N ALA G1901 " --> pdb=" O ILE G1888 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ILE G1888 " --> pdb=" O ALA G1901 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASP G1903 " --> pdb=" O VAL G1886 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL G1886 " --> pdb=" O ASP G1903 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 1537 through 1545 removed outlier: 6.908A pdb=" N ILE G1626 " --> pdb=" O ILE G1539 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL G1541 " --> pdb=" O THR G1624 " (cutoff:3.500A) removed outlier: 6.016A 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: 6.644A pdb=" N LEU G1622 " --> pdb=" O ASP G1543 " (cutoff:3.500A) 1185 hydrogen bonds defined for protein. 3195 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: 13.65 Time building geometry restraints manager: 12.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 5048 1.31 - 1.45: 7516 1.45 - 1.59: 17054 1.59 - 1.72: 2 1.72 - 1.86: 182 Bond restraints: 29802 Sorted by residual: bond pdb=" C34 PNS B1901 " pdb=" N36 PNS B1901 " ideal model delta sigma weight residual 1.452 1.335 0.117 2.00e-02 2.50e+03 3.43e+01 bond pdb=" C MET A1388 " pdb=" O MET A1388 " ideal model delta sigma weight residual 1.233 1.172 0.061 1.17e-02 7.31e+03 2.72e+01 bond pdb=" C PHE A1688 " pdb=" O PHE A1688 " ideal model delta sigma weight residual 1.236 1.177 0.060 1.15e-02 7.56e+03 2.71e+01 bond pdb=" C39 PNS B1901 " pdb=" N41 PNS B1901 " ideal model delta sigma weight residual 1.452 1.351 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" N ILE A1157 " pdb=" CA ILE A1157 " ideal model delta sigma weight residual 1.460 1.495 -0.034 7.30e-03 1.88e+04 2.21e+01 ... (remaining 29797 not shown) Histogram of bond angle deviations from ideal: 96.56 - 104.18: 512 104.18 - 111.80: 12001 111.80 - 119.42: 15433 119.42 - 127.04: 12215 127.04 - 134.65: 237 Bond angle restraints: 40398 Sorted by residual: angle pdb=" CA GLY A 383 " pdb=" C GLY A 383 " pdb=" O GLY A 383 " ideal model delta sigma weight residual 122.23 117.91 4.32 6.90e-01 2.10e+00 3.92e+01 angle pdb=" CA THR A1282 " pdb=" CB THR A1282 " pdb=" OG1 THR A1282 " ideal model delta sigma weight residual 109.60 100.56 9.04 1.50e+00 4.44e-01 3.63e+01 angle pdb=" CA ASP G1316 " pdb=" CB ASP G1316 " pdb=" CG ASP G1316 " ideal model delta sigma weight residual 112.60 118.32 -5.72 1.00e+00 1.00e+00 3.27e+01 angle pdb=" N PRO G 599 " pdb=" CA PRO G 599 " pdb=" CB PRO G 599 " ideal model delta sigma weight residual 102.60 96.61 5.99 1.10e+00 8.26e-01 2.97e+01 angle pdb=" CA GLY A1375 " pdb=" C GLY A1375 " pdb=" O GLY A1375 " ideal model delta sigma weight residual 122.22 118.69 3.53 6.50e-01 2.37e+00 2.95e+01 ... (remaining 40393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.76: 16956 23.76 - 47.52: 843 47.52 - 71.27: 117 71.27 - 95.03: 33 95.03 - 118.79: 1 Dihedral angle restraints: 17950 sinusoidal: 7043 harmonic: 10907 Sorted by residual: 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 -165.95 -118.79 1 2.00e+01 2.50e-03 3.56e+01 dihedral pdb=" CA ASP G 974 " pdb=" C ASP G 974 " pdb=" N LYS G 975 " pdb=" CA LYS G 975 " ideal model delta harmonic sigma weight residual 180.00 153.64 26.36 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA ILE G1503 " pdb=" C ILE G1503 " pdb=" N VAL G1504 " pdb=" CA VAL G1504 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 17947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2141 0.062 - 0.124: 1670 0.124 - 0.187: 596 0.187 - 0.249: 129 0.249 - 0.311: 17 Chirality restraints: 4553 Sorted by residual: chirality pdb=" CA VAL A 893 " pdb=" N VAL A 893 " pdb=" C VAL A 893 " pdb=" CB VAL A 893 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA GLN A1389 " pdb=" N GLN A1389 " pdb=" C GLN A1389 " pdb=" CB GLN A1389 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA ILE A1326 " pdb=" N ILE A1326 " pdb=" C ILE A1326 " pdb=" CB ILE A1326 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 4550 not shown) Planarity restraints: 5235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN G2101 " 0.014 2.00e-02 2.50e+03 3.52e-02 5.90e+01 pdb=" C10 FMN G2101 " 0.027 2.00e-02 2.50e+03 pdb=" C2 FMN G2101 " -0.051 2.00e-02 2.50e+03 pdb=" C4 FMN G2101 " 0.001 2.00e-02 2.50e+03 pdb=" C4A FMN G2101 " 0.042 2.00e-02 2.50e+03 pdb=" C5A FMN G2101 " 0.049 2.00e-02 2.50e+03 pdb=" C6 FMN G2101 " 0.024 2.00e-02 2.50e+03 pdb=" C7 FMN G2101 " -0.013 2.00e-02 2.50e+03 pdb=" C7M FMN G2101 " -0.064 2.00e-02 2.50e+03 pdb=" C8 FMN G2101 " -0.025 2.00e-02 2.50e+03 pdb=" C8M FMN G2101 " -0.039 2.00e-02 2.50e+03 pdb=" C9 FMN G2101 " 0.004 2.00e-02 2.50e+03 pdb=" C9A FMN G2101 " 0.044 2.00e-02 2.50e+03 pdb=" N1 FMN G2101 " -0.010 2.00e-02 2.50e+03 pdb=" N10 FMN G2101 " 0.038 2.00e-02 2.50e+03 pdb=" N3 FMN G2101 " -0.044 2.00e-02 2.50e+03 pdb=" N5 FMN G2101 " 0.047 2.00e-02 2.50e+03 pdb=" O2 FMN G2101 " -0.030 2.00e-02 2.50e+03 pdb=" O4 FMN G2101 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C32 PNS B1901 " -0.061 2.00e-02 2.50e+03 6.08e-02 4.62e+01 pdb=" C34 PNS B1901 " 0.039 2.00e-02 2.50e+03 pdb=" C37 PNS B1901 " -0.073 2.00e-02 2.50e+03 pdb=" N36 PNS B1901 " 0.089 2.00e-02 2.50e+03 pdb=" O35 PNS B1901 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 722 " 0.073 2.00e-02 2.50e+03 3.93e-02 3.09e+01 pdb=" CG TYR A 722 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR A 722 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR A 722 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A 722 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 722 " -0.032 2.00e-02 2.50e+03 pdb=" CZ TYR A 722 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 722 " 0.051 2.00e-02 2.50e+03 ... (remaining 5232 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1546 2.74 - 3.28: 30219 3.28 - 3.82: 46030 3.82 - 4.36: 64328 4.36 - 4.90: 102169 Nonbonded interactions: 244292 Sorted by model distance: nonbonded pdb=" O LYS G 355 " pdb=" OG SER G 358 " model vdw 2.200 2.440 nonbonded pdb=" OH TYR A 81 " pdb=" OH TYR A 89 " model vdw 2.261 2.440 nonbonded pdb=" NH1 ARG G 894 " pdb=" OD2 ASP G 898 " model vdw 2.286 2.520 nonbonded pdb=" O VAL G1048 " pdb=" OG1 THR G1051 " model vdw 2.286 2.440 nonbonded pdb=" OH TYR A1694 " pdb=" OD2 ASP G1001 " model vdw 2.292 2.440 ... (remaining 244287 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: 0.610 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: 4.840 Check model and map are aligned: 0.490 Set scattering table: 0.290 Process input model: 79.270 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 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 : 0.013 0.117 29802 Z= 0.888 Angle : 1.849 9.584 40398 Z= 1.356 Chirality : 0.090 0.311 4553 Planarity : 0.007 0.061 5235 Dihedral : 14.523 118.791 10921 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.68 % Favored : 95.03 % Rotamer: Outliers : 0.71 % Allowed : 3.76 % Favored : 95.53 % 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: -3.14 (0.11), residues: 3760 helix: -2.59 (0.09), residues: 1666 sheet: -1.75 (0.20), residues: 512 loop : -1.35 (0.14), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.009 TRP G1449 HIS 0.018 0.004 HIS A1689 PHE 0.061 0.007 PHE A1376 TYR 0.073 0.007 TYR A 722 ARG 0.013 0.002 ARG A1036 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 253 time to evaluate : 3.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 MET cc_start: 0.8644 (mmp) cc_final: 0.8359 (mmp) REVERT: A 1121 MET cc_start: 0.8804 (mtp) cc_final: 0.8551 (tpt) REVERT: A 1150 ASP cc_start: 0.8928 (p0) cc_final: 0.8705 (p0) REVERT: A 1515 ARG cc_start: 0.8996 (mtp85) cc_final: 0.8309 (ptt180) REVERT: A 1755 MET cc_start: 0.8833 (mtp) cc_final: 0.8626 (mtp) REVERT: A 1841 ARG cc_start: 0.8075 (ttm170) cc_final: 0.7753 (mtp180) REVERT: G 599 PRO cc_start: 0.9089 (OUTLIER) cc_final: 0.8797 (Cg_endo) REVERT: G 908 ASN cc_start: 0.9088 (m-40) cc_final: 0.8886 (p0) REVERT: G 1872 GLN cc_start: 0.9329 (tp40) cc_final: 0.8890 (tp-100) outliers start: 22 outliers final: 5 residues processed: 271 average time/residue: 1.7950 time to fit residues: 554.6112 Evaluate side-chains 189 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 183 time to evaluate : 3.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1305 CYS Chi-restraints excluded: chain A residue 1332 TYR Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 599 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 10.0000 chunk 284 optimal weight: 0.7980 chunk 158 optimal weight: 30.0000 chunk 97 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 294 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 chunk 219 optimal weight: 1.9990 chunk 341 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 63 ASN A 356 ASN A 379 ASN A 475 GLN A 618 ASN A 971 ASN A1380 GLN A1549 ASN A1620 GLN A1695 ASN A1703 HIS G 36 GLN G 102 HIS G 245 GLN G 273 HIS G 354 ASN G 440 ASN G 456 GLN G 718 ASN G 723 HIS G 747 HIS G 752 GLN G 993 GLN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1217 ASN G1241 ASN G1352 HIS G1355 ASN G1432 GLN G1529 GLN G1535 ASN G1595 ASN G1619 ASN G1839 GLN G1890 ASN G1912 ASN G1977 HIS G2013 ASN G2020 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29802 Z= 0.211 Angle : 0.546 10.645 40398 Z= 0.287 Chirality : 0.042 0.178 4553 Planarity : 0.004 0.036 5235 Dihedral : 5.366 108.518 4040 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.86 % Favored : 98.11 % Rotamer: Outliers : 1.13 % Allowed : 7.59 % Favored : 91.29 % 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: -0.30 (0.13), residues: 3760 helix: 0.32 (0.12), residues: 1683 sheet: -1.06 (0.21), residues: 509 loop : -0.28 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G1449 HIS 0.005 0.001 HIS A1689 PHE 0.024 0.001 PHE A 35 TYR 0.016 0.001 TYR G1553 ARG 0.006 0.000 ARG G1765 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 201 time to evaluate : 3.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 GLU cc_start: 0.7258 (pp20) cc_final: 0.7030 (pp20) REVERT: A 522 LEU cc_start: 0.8825 (mt) cc_final: 0.8620 (tp) REVERT: A 529 MET cc_start: 0.8687 (mmp) cc_final: 0.8424 (mmp) REVERT: A 1121 MET cc_start: 0.8871 (mtp) cc_final: 0.8640 (tpt) REVERT: A 1593 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.7957 (tpp) REVERT: A 1834 LEU cc_start: 0.9048 (mt) cc_final: 0.8618 (pp) REVERT: G 1164 MET cc_start: 0.8989 (mmp) cc_final: 0.8690 (mmm) REVERT: G 1872 GLN cc_start: 0.9247 (tp40) cc_final: 0.8836 (tp-100) outliers start: 35 outliers final: 13 residues processed: 220 average time/residue: 1.7199 time to fit residues: 436.3918 Evaluate side-chains 188 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 174 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1593 MET Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1861 GLU Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 493 THR Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 711 ASP Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1679 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 284 optimal weight: 0.0030 chunk 232 optimal weight: 0.0980 chunk 94 optimal weight: 4.9990 chunk 342 optimal weight: 0.0770 chunk 369 optimal weight: 10.0000 chunk 304 optimal weight: 0.5980 chunk 339 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 274 optimal weight: 2.9990 overall best weight: 0.7550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN A 374 GLN A 506 ASN A 971 ASN A1380 GLN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 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 : 0.002 0.048 29802 Z= 0.135 Angle : 0.477 8.659 40398 Z= 0.249 Chirality : 0.041 0.156 4553 Planarity : 0.003 0.042 5235 Dihedral : 4.701 97.900 4030 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.42 % Favored : 97.55 % Rotamer: Outliers : 1.06 % Allowed : 8.52 % Favored : 90.42 % 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: 0.56 (0.14), residues: 3760 helix: 1.17 (0.13), residues: 1684 sheet: -0.80 (0.21), residues: 539 loop : 0.09 (0.16), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1813 HIS 0.004 0.001 HIS A1689 PHE 0.027 0.001 PHE A 35 TYR 0.014 0.001 TYR A 417 ARG 0.008 0.000 ARG G1962 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 201 time to evaluate : 3.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 LYS cc_start: 0.9137 (ptpp) cc_final: 0.8920 (ptpp) REVERT: A 342 GLN cc_start: 0.8890 (mt0) cc_final: 0.8682 (mt0) REVERT: A 522 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8534 (tp) REVERT: A 529 MET cc_start: 0.8740 (mmp) cc_final: 0.8238 (mmp) REVERT: A 1057 MET cc_start: 0.8754 (mtp) cc_final: 0.8483 (mtp) REVERT: A 1121 MET cc_start: 0.8845 (mtp) cc_final: 0.8614 (tpt) REVERT: A 1593 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.7862 (tpp) REVERT: A 1834 LEU cc_start: 0.8910 (mt) cc_final: 0.8690 (pp) REVERT: G 1164 MET cc_start: 0.9040 (mmp) cc_final: 0.8744 (mmm) REVERT: G 1323 MET cc_start: 0.8844 (ptp) cc_final: 0.8619 (ttm) REVERT: G 1872 GLN cc_start: 0.9207 (tp40) cc_final: 0.8790 (tp-100) outliers start: 33 outliers final: 10 residues processed: 220 average time/residue: 1.7459 time to fit residues: 442.7275 Evaluate side-chains 188 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 176 time to evaluate : 3.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1593 MET Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1861 GLU Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1946 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 0.4980 chunk 257 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 163 optimal weight: 7.9990 chunk 229 optimal weight: 6.9990 chunk 343 optimal weight: 5.9990 chunk 363 optimal weight: 3.9990 chunk 179 optimal weight: 20.0000 chunk 325 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 971 ASN A1380 GLN G 365 GLN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1302 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29802 Z= 0.201 Angle : 0.476 8.838 40398 Z= 0.246 Chirality : 0.041 0.159 4553 Planarity : 0.003 0.060 5235 Dihedral : 4.582 91.885 4029 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.09 % Allowed : 9.71 % Favored : 89.20 % 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: 0.89 (0.14), residues: 3760 helix: 1.41 (0.13), residues: 1692 sheet: -0.58 (0.21), residues: 538 loop : 0.27 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1813 HIS 0.005 0.001 HIS A1689 PHE 0.023 0.001 PHE A 35 TYR 0.012 0.001 TYR A 722 ARG 0.013 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 183 time to evaluate : 3.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLN cc_start: 0.8922 (mt0) cc_final: 0.8715 (mt0) REVERT: A 529 MET cc_start: 0.8755 (mmp) cc_final: 0.8226 (mmp) REVERT: A 1094 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8018 (tp30) REVERT: A 1121 MET cc_start: 0.8840 (mtp) cc_final: 0.8594 (tpt) REVERT: A 1593 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.7888 (tpp) REVERT: A 1834 LEU cc_start: 0.8955 (mt) cc_final: 0.8711 (pp) REVERT: G 1164 MET cc_start: 0.9043 (mmp) cc_final: 0.8753 (mmm) REVERT: G 1323 MET cc_start: 0.8902 (ptp) cc_final: 0.8688 (ttm) REVERT: G 1872 GLN cc_start: 0.9217 (tp40) cc_final: 0.8797 (tp-100) outliers start: 34 outliers final: 20 residues processed: 204 average time/residue: 1.7194 time to fit residues: 406.6359 Evaluate side-chains 192 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 170 time to evaluate : 3.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1593 MET Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1861 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 711 ASP Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1470 THR Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 1946 GLU Chi-restraints excluded: chain G residue 2032 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 5.9990 chunk 206 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 270 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 310 optimal weight: 9.9990 chunk 251 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 185 optimal weight: 0.1980 chunk 326 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 971 ASN A1380 GLN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1977 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29802 Z= 0.187 Angle : 0.467 9.234 40398 Z= 0.241 Chirality : 0.041 0.156 4553 Planarity : 0.003 0.044 5235 Dihedral : 4.492 87.382 4029 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.32 % Allowed : 10.32 % Favored : 88.36 % 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: 1.08 (0.14), residues: 3760 helix: 1.56 (0.13), residues: 1683 sheet: -0.44 (0.22), residues: 539 loop : 0.37 (0.16), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1813 HIS 0.005 0.001 HIS A1689 PHE 0.023 0.001 PHE A 35 TYR 0.012 0.001 TYR G1553 ARG 0.008 0.000 ARG A 709 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 179 time to evaluate : 3.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 MET cc_start: 0.8764 (mmp) cc_final: 0.8220 (mmp) REVERT: A 1094 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8004 (tp30) REVERT: A 1121 MET cc_start: 0.8829 (mtp) cc_final: 0.8587 (tpt) REVERT: A 1515 ARG cc_start: 0.9061 (mtp85) cc_final: 0.8243 (ptt180) REVERT: A 1593 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.7876 (tpp) REVERT: G 1164 MET cc_start: 0.9047 (mmp) cc_final: 0.8758 (mmm) REVERT: G 1872 GLN cc_start: 0.9212 (tp40) cc_final: 0.8796 (tp-100) outliers start: 41 outliers final: 22 residues processed: 204 average time/residue: 1.7859 time to fit residues: 422.6628 Evaluate side-chains 191 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 167 time to evaluate : 3.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1593 MET Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1861 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 493 THR Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 794 MET Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 1946 GLU Chi-restraints excluded: chain G residue 2032 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 3.9990 chunk 327 optimal weight: 0.0060 chunk 71 optimal weight: 1.9990 chunk 213 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 363 optimal weight: 9.9990 chunk 301 optimal weight: 1.9990 chunk 168 optimal weight: 0.0000 chunk 30 optimal weight: 0.5980 chunk 120 optimal weight: 10.0000 chunk 190 optimal weight: 2.9990 overall best weight: 0.9204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1380 GLN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1977 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 29802 Z= 0.133 Angle : 0.458 9.356 40398 Z= 0.235 Chirality : 0.041 0.166 4553 Planarity : 0.003 0.065 5235 Dihedral : 4.344 81.041 4029 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.09 % Allowed : 11.19 % Favored : 87.72 % 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: 1.22 (0.14), residues: 3760 helix: 1.63 (0.13), residues: 1693 sheet: -0.24 (0.22), residues: 540 loop : 0.43 (0.17), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1813 HIS 0.004 0.001 HIS A1689 PHE 0.025 0.001 PHE A 35 TYR 0.013 0.001 TYR G 754 ARG 0.017 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 182 time to evaluate : 3.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 MET cc_start: 0.8741 (mmp) cc_final: 0.8178 (mmp) REVERT: A 1094 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7880 (tp30) REVERT: A 1121 MET cc_start: 0.8809 (mtp) cc_final: 0.8579 (tpt) REVERT: A 1515 ARG cc_start: 0.9017 (mtp85) cc_final: 0.8228 (ptt180) REVERT: A 1593 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.7776 (tpp) REVERT: G 1164 MET cc_start: 0.9038 (mmp) cc_final: 0.8778 (mmm) REVERT: G 1872 GLN cc_start: 0.9195 (tp40) cc_final: 0.8790 (tp-100) outliers start: 34 outliers final: 20 residues processed: 204 average time/residue: 1.7252 time to fit residues: 406.3984 Evaluate side-chains 190 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 168 time to evaluate : 3.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1593 MET Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1861 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 711 ASP Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 2032 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 207 optimal weight: 0.7980 chunk 265 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 306 optimal weight: 9.9990 chunk 203 optimal weight: 10.0000 chunk 362 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 167 optimal weight: 40.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN ** A1380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 430 HIS G1915 ASN G1977 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29802 Z= 0.274 Angle : 0.507 9.731 40398 Z= 0.260 Chirality : 0.042 0.171 4553 Planarity : 0.003 0.045 5235 Dihedral : 4.450 80.475 4029 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.29 % Allowed : 11.54 % Favored : 87.17 % 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: 1.28 (0.14), residues: 3760 helix: 1.67 (0.13), residues: 1686 sheet: -0.20 (0.22), residues: 542 loop : 0.47 (0.17), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1813 HIS 0.007 0.001 HIS A1689 PHE 0.021 0.001 PHE A1376 TYR 0.014 0.001 TYR G1553 ARG 0.012 0.000 ARG G1962 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 173 time to evaluate : 3.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLN cc_start: 0.8987 (mt0) cc_final: 0.8729 (mt0) REVERT: A 492 ASP cc_start: 0.8487 (t0) cc_final: 0.8254 (t0) REVERT: A 529 MET cc_start: 0.8789 (mmp) cc_final: 0.8245 (mmp) REVERT: A 1094 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8040 (tp30) REVERT: A 1121 MET cc_start: 0.8820 (mtp) cc_final: 0.8534 (tpt) REVERT: A 1515 ARG cc_start: 0.9069 (mtp85) cc_final: 0.8244 (ptt180) REVERT: G 1164 MET cc_start: 0.9035 (mmp) cc_final: 0.8739 (mmm) REVERT: G 1872 GLN cc_start: 0.9219 (tp40) cc_final: 0.8804 (tp-100) outliers start: 40 outliers final: 25 residues processed: 199 average time/residue: 1.7117 time to fit residues: 394.3646 Evaluate side-chains 196 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 3.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1070 ARG Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1861 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 493 THR Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 711 ASP Chi-restraints excluded: chain G residue 794 MET Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1386 THR Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 2032 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 9.9990 chunk 144 optimal weight: 7.9990 chunk 216 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 71 optimal weight: 0.0370 chunk 70 optimal weight: 2.9990 chunk 230 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 chunk 179 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 284 optimal weight: 10.0000 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1977 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29802 Z= 0.198 Angle : 0.483 11.191 40398 Z= 0.247 Chirality : 0.041 0.158 4553 Planarity : 0.004 0.084 5235 Dihedral : 4.390 76.661 4029 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.06 % Allowed : 11.77 % Favored : 87.17 % 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: 1.31 (0.14), residues: 3760 helix: 1.67 (0.13), residues: 1696 sheet: -0.15 (0.22), residues: 540 loop : 0.50 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1813 HIS 0.005 0.001 HIS A1689 PHE 0.023 0.001 PHE A 35 TYR 0.011 0.001 TYR A 722 ARG 0.017 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 168 time to evaluate : 3.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLN cc_start: 0.8967 (mt0) cc_final: 0.8700 (mt0) REVERT: A 529 MET cc_start: 0.8779 (mmp) cc_final: 0.8242 (mmp) REVERT: A 1057 MET cc_start: 0.8733 (mtp) cc_final: 0.8403 (mtp) REVERT: A 1094 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7987 (tp30) REVERT: A 1121 MET cc_start: 0.8810 (mtp) cc_final: 0.8539 (tpt) REVERT: A 1515 ARG cc_start: 0.9060 (mtp85) cc_final: 0.8237 (ptt180) REVERT: A 1789 ARG cc_start: 0.8406 (tmt170) cc_final: 0.8106 (tmt-80) REVERT: G 1164 MET cc_start: 0.9026 (mmp) cc_final: 0.8735 (mmm) REVERT: G 1583 MET cc_start: 0.9024 (mmm) cc_final: 0.8805 (mmp) REVERT: G 1872 GLN cc_start: 0.9208 (tp40) cc_final: 0.8803 (tp-100) outliers start: 33 outliers final: 24 residues processed: 192 average time/residue: 1.7515 time to fit residues: 390.6588 Evaluate side-chains 188 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 163 time to evaluate : 3.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1070 ARG Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain A residue 1861 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 493 THR Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 711 ASP Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1386 THR Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 2032 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 3.9990 chunk 347 optimal weight: 9.9990 chunk 316 optimal weight: 3.9990 chunk 337 optimal weight: 0.8980 chunk 203 optimal weight: 5.9990 chunk 147 optimal weight: 30.0000 chunk 265 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 305 optimal weight: 0.0870 chunk 319 optimal weight: 9.9990 chunk 336 optimal weight: 8.9990 overall best weight: 2.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1977 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 29802 Z= 0.235 Angle : 0.505 11.829 40398 Z= 0.256 Chirality : 0.042 0.164 4553 Planarity : 0.003 0.055 5235 Dihedral : 4.381 73.322 4029 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.93 % Allowed : 12.09 % Favored : 86.98 % 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: 1.34 (0.14), residues: 3760 helix: 1.70 (0.13), residues: 1689 sheet: -0.12 (0.22), residues: 536 loop : 0.51 (0.17), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1813 HIS 0.006 0.001 HIS A1689 PHE 0.022 0.001 PHE A 35 TYR 0.012 0.001 TYR A 722 ARG 0.013 0.000 ARG A 709 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 3.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLN cc_start: 0.8978 (mt0) cc_final: 0.8732 (mt0) REVERT: A 529 MET cc_start: 0.8713 (mmp) cc_final: 0.8182 (mmp) REVERT: A 1094 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8016 (tp30) REVERT: A 1121 MET cc_start: 0.8802 (mtp) cc_final: 0.8530 (tpt) REVERT: A 1515 ARG cc_start: 0.9061 (mtp85) cc_final: 0.8239 (ptt180) REVERT: G 1164 MET cc_start: 0.9031 (mmp) cc_final: 0.8740 (mmm) REVERT: G 1872 GLN cc_start: 0.9221 (tp40) cc_final: 0.8815 (tp-100) REVERT: G 1881 ARG cc_start: 0.9213 (tpm170) cc_final: 0.8894 (ttt90) outliers start: 29 outliers final: 25 residues processed: 187 average time/residue: 1.7525 time to fit residues: 381.3366 Evaluate side-chains 192 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 3.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1070 ARG Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1861 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 493 THR Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 711 ASP Chi-restraints excluded: chain G residue 995 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1386 THR Chi-restraints excluded: chain G residue 1679 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 5.9990 chunk 357 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 169 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 374 optimal weight: 3.9990 chunk 344 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 182 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1915 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29802 Z= 0.222 Angle : 0.496 12.392 40398 Z= 0.252 Chirality : 0.041 0.159 4553 Planarity : 0.004 0.095 5235 Dihedral : 4.350 68.950 4029 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.90 % Allowed : 12.25 % Favored : 86.85 % 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: 1.34 (0.14), residues: 3760 helix: 1.69 (0.13), residues: 1693 sheet: -0.10 (0.22), residues: 536 loop : 0.52 (0.17), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1813 HIS 0.005 0.001 HIS A1689 PHE 0.022 0.001 PHE A 35 TYR 0.011 0.001 TYR A 722 ARG 0.022 0.000 ARG A 632 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 3.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLN cc_start: 0.8974 (mt0) cc_final: 0.8734 (mt0) REVERT: A 529 MET cc_start: 0.8712 (mmp) cc_final: 0.8189 (mmp) REVERT: A 1094 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8014 (tp30) REVERT: A 1121 MET cc_start: 0.8796 (mtp) cc_final: 0.8518 (tpt) REVERT: A 1515 ARG cc_start: 0.9053 (mtp85) cc_final: 0.8229 (ptt180) REVERT: G 1164 MET cc_start: 0.9029 (mmp) cc_final: 0.8741 (mmm) REVERT: G 1872 GLN cc_start: 0.9215 (tp40) cc_final: 0.8803 (tp-100) REVERT: G 1881 ARG cc_start: 0.9213 (tpm170) cc_final: 0.8776 (ttt90) outliers start: 28 outliers final: 26 residues processed: 187 average time/residue: 1.7368 time to fit residues: 376.6499 Evaluate side-chains 193 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 166 time to evaluate : 3.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1070 ARG Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1140 THR Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1742 ASP Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1861 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 493 THR Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 711 ASP Chi-restraints excluded: chain G residue 995 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1386 THR Chi-restraints excluded: chain G residue 1679 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 7.9990 chunk 317 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 275 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 298 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 chunk 306 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.067440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.048871 restraints weight = 88270.708| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.80 r_work: 0.2614 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2494 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29802 Z= 0.220 Angle : 0.501 12.450 40398 Z= 0.254 Chirality : 0.041 0.159 4553 Planarity : 0.003 0.059 5235 Dihedral : 4.322 66.289 4029 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.93 % Allowed : 12.28 % Favored : 86.78 % 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: 1.37 (0.14), residues: 3760 helix: 1.71 (0.13), residues: 1693 sheet: -0.08 (0.22), residues: 536 loop : 0.53 (0.17), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1813 HIS 0.005 0.001 HIS A1689 PHE 0.022 0.001 PHE A 35 TYR 0.012 0.001 TYR G 754 ARG 0.013 0.000 ARG G1962 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9069.07 seconds wall clock time: 163 minutes 35.08 seconds (9815.08 seconds total)