Starting phenix.real_space_refine on Thu Mar 21 10:26:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ps2_17843/03_2024/8ps2_17843_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ps2_17843/03_2024/8ps2_17843.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ps2_17843/03_2024/8ps2_17843_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ps2_17843/03_2024/8ps2_17843_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ps2_17843/03_2024/8ps2_17843_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ps2_17843/03_2024/8ps2_17843.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ps2_17843/03_2024/8ps2_17843.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ps2_17843/03_2024/8ps2_17843_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ps2_17843/03_2024/8ps2_17843_updated.pdb" } resolution = 2.9 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= -0.000 sd= 0.009 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 5 5.49 5 S 109 5.16 5 C 18951 2.51 5 N 4976 2.21 5 O 5720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 6": "OE1" <-> "OE2" Residue "A GLU 16": "OE1" <-> "OE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A ASP 334": "OD1" <-> "OD2" Residue "A ASP 355": "OD1" <-> "OD2" Residue "A TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 754": "OD1" <-> "OD2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A GLU 949": "OE1" <-> "OE2" Residue "A GLU 1010": "OE1" <-> "OE2" Residue "A ASP 1086": "OD1" <-> "OD2" Residue "A GLU 1268": "OE1" <-> "OE2" Residue "A TYR 1332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1391": "OD1" <-> "OD2" Residue "A PHE 1579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1622": "OE1" <-> "OE2" Residue "A GLU 1672": "OE1" <-> "OE2" Residue "A GLU 1757": "OE1" <-> "OE2" Residue "A GLU 1797": "OE1" <-> "OE2" Residue "A ASP 1875": "OD1" <-> "OD2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "G GLU 111": "OE1" <-> "OE2" Residue "G ASP 186": "OD1" <-> "OD2" Residue "G GLU 325": "OE1" <-> "OE2" Residue "G GLU 329": "OE1" <-> "OE2" Residue "G ASP 351": "OD1" <-> "OD2" Residue "G PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 711": "OD1" <-> "OD2" Residue "G PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 889": "OD1" <-> "OD2" Residue "G GLU 992": "OE1" <-> "OE2" Residue "G GLU 1026": "OE1" <-> "OE2" Residue "G GLU 1135": "OE1" <-> "OE2" Residue "G GLU 1253": "OE1" <-> "OE2" Residue "G ASP 1289": "OD1" <-> "OD2" Residue "G TYR 1416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1448": "OE1" <-> "OE2" Residue "G GLU 1500": "OE1" <-> "OE2" Residue "G GLU 1534": "OE1" <-> "OE2" Residue "G TYR 1572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1654": "OE1" <-> "OE2" Residue "G GLU 1731": "OE1" <-> "OE2" Residue "G TYR 1733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1754": "OE1" <-> "OE2" Residue "G GLU 1790": "OE1" <-> "OE2" Residue "G GLU 1811": "OE1" <-> "OE2" Residue "G GLU 1869": "OE1" <-> "OE2" Residue "G GLU 2040": "OE1" <-> "OE2" Residue "G TYR 2048": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29761 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 12409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1589, 12409 Classifications: {'peptide': 1589} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1527} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1222 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 154} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 16018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2036, 16018 Classifications: {'peptide': 2036} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1926} Chain breaks: 1 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'A3Z': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 85 Unusual residues: {'FMN': 1, 'MLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.86, per 1000 atoms: 0.53 Number of scatterers: 29761 At special positions: 0 Unit cell: (184.625, 182.515, 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 109 16.00 P 5 15.00 O 5720 8.00 N 4976 7.00 C 18951 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.38 Conformation dependent library (CDL) restraints added in 5.7 seconds 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7044 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 171 helices and 28 sheets defined 44.9% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.13 Creating SS restraints... Processing helix chain 'A' and resid 3 through 21 Processing helix chain 'A' and resid 28 through 35 Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.791A pdb=" N ASN A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 85 through 89 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: 4.127A pdb=" N LYS A 410 " --> pdb=" O TRP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 442 removed outlier: 3.794A pdb=" N SER A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU A 435 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 439 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN A 441 " --> pdb=" O ASN A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 456 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 464 through 482 Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 609 through 615 removed outlier: 3.577A pdb=" N SER A 615 " --> pdb=" O LYS A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 669 Processing helix chain 'A' and resid 688 through 699 Processing helix chain 'A' and resid 712 through 725 Processing helix chain 'A' and resid 742 through 753 Processing helix chain 'A' and resid 781 through 783 No H-bonds generated for 'chain 'A' and resid 781 through 783' Processing helix chain 'A' and resid 786 through 795 Processing helix chain 'A' and resid 797 through 812 Processing helix chain 'A' and resid 839 through 855 removed outlier: 3.662A pdb=" N LEU A 846 " --> pdb=" O SER A 842 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU A 847 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASN A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N HIS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 891 removed outlier: 4.768A pdb=" N GLU A 886 " --> pdb=" O ILE A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 908 removed outlier: 3.759A pdb=" N LEU A 908 " --> pdb=" O ASN A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 919 Processing helix chain 'A' and resid 936 through 968 Processing helix chain 'A' and resid 971 through 974 Processing helix chain 'A' and resid 998 through 1001 No H-bonds generated for 'chain 'A' and resid 998 through 1001' Processing helix chain 'A' and resid 1007 through 1009 No H-bonds generated for 'chain 'A' and resid 1007 through 1009' Processing helix chain 'A' and resid 1015 through 1017 No H-bonds generated for 'chain 'A' and resid 1015 through 1017' Processing helix chain 'A' and resid 1033 through 1042 Processing helix chain 'A' and resid 1047 through 1056 Processing helix chain 'A' and resid 1086 through 1099 removed outlier: 4.331A pdb=" N LYS A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N THR A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N SER A1096 " --> pdb=" O LYS A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1111 Processing helix chain 'A' and resid 1138 through 1151 removed outlier: 7.159A pdb=" N ASP A1150 " --> pdb=" O HIS A1146 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LYS A1151 " --> pdb=" O GLN A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1198 Processing helix chain 'A' and resid 1202 through 1205 No H-bonds generated for 'chain 'A' and resid 1202 through 1205' Processing helix chain 'A' and resid 1210 through 1226 removed outlier: 3.542A 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 1254 through 1261 Processing helix chain 'A' and resid 1274 through 1278 Processing helix chain 'A' and resid 1282 through 1290 Processing helix chain 'A' and resid 1304 through 1320 removed outlier: 5.422A pdb=" N SER A1308 " --> pdb=" O CYS A1305 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A1309 " --> pdb=" O ALA A1306 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A1316 " --> pdb=" O ASP A1313 " (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 1425 through 1429 Processing helix chain 'A' and resid 1441 through 1443 No H-bonds generated for 'chain 'A' and resid 1441 through 1443' Processing helix chain 'A' and resid 1445 through 1474 removed outlier: 3.598A pdb=" N LEU A1472 " --> pdb=" O GLU A1468 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A1473 " --> pdb=" O ALA A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1479 through 1509 removed outlier: 4.403A pdb=" N ASN A1483 " --> pdb=" O SER A1479 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLU A1484 " --> pdb=" O GLU A1480 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1529 removed outlier: 3.595A pdb=" N LEU A1526 " --> pdb=" O LEU A1522 " (cutoff:3.500A) removed outlier: 4.639A 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: 3.658A pdb=" N LYS A1551 " --> pdb=" O LYS A1547 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A1554 " --> pdb=" O ASP A1550 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1581 removed outlier: 3.958A pdb=" N THR A1581 " --> pdb=" O LYS A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1585 through 1602 removed outlier: 4.375A pdb=" N GLY A1589 " --> pdb=" O GLY A1586 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET A1593 " --> pdb=" O ALA A1590 " (cutoff:3.500A) Processing helix chain 'A' and resid 1616 through 1620 removed outlier: 3.735A pdb=" N GLN A1620 " --> pdb=" O ILE A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1664 removed outlier: 3.933A pdb=" N GLY A1663 " --> pdb=" O TYR A1660 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1693 Processing helix chain 'A' and resid 1711 through 1716 Processing helix chain 'A' and resid 1735 through 1737 No H-bonds generated for 'chain 'A' and resid 1735 through 1737' Processing helix chain 'A' and resid 1741 through 1744 No H-bonds generated for 'chain 'A' and resid 1741 through 1744' Processing helix chain 'A' and resid 1747 through 1759 removed outlier: 3.504A pdb=" N ILE A1756 " --> pdb=" O THR A1752 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET A1759 " --> pdb=" O MET A1755 " (cutoff:3.500A) Processing helix chain 'A' and resid 1776 through 1778 No H-bonds generated for 'chain 'A' and resid 1776 through 1778' Processing helix chain 'A' and resid 1784 through 1790 Processing helix chain 'A' and resid 1793 through 1801 removed outlier: 3.524A pdb=" N ALA A1801 " --> pdb=" O GLU A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1805 through 1823 Processing helix chain 'A' and resid 1854 through 1861 removed outlier: 3.604A pdb=" N GLU A1860 " --> pdb=" O LYS A1856 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 159 Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 180 through 193 Processing helix chain 'B' and resid 206 through 214 Processing helix chain 'B' and resid 224 through 236 Processing helix chain 'B' and resid 243 through 254 removed outlier: 3.648A pdb=" N GLN B 251 " --> pdb=" O ARG B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 271 removed outlier: 3.827A pdb=" N GLY B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 298 Processing helix chain 'G' and resid 27 through 40 Processing helix chain 'G' and resid 57 through 71 removed outlier: 3.645A pdb=" N LEU G 71 " --> pdb=" O TYR G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 95 Processing helix chain 'G' and resid 101 through 111 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: 3.761A pdb=" N ASP G 175 " --> pdb=" O GLU G 172 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU G 176 " --> pdb=" O LEU G 173 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN G 178 " --> pdb=" O ASP G 175 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR G 179 " --> pdb=" O LEU G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 201 removed outlier: 5.910A pdb=" N ASP G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LEU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 220 Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 234 through 256 Proline residue: G 239 - end of helix Processing helix chain 'G' and resid 260 through 265 Processing helix chain 'G' and resid 274 through 285 removed outlier: 3.584A pdb=" N ALA G 280 " --> pdb=" O LEU G 277 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL G 281 " --> pdb=" O VAL G 278 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE G 283 " --> pdb=" O ALA G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 313 removed outlier: 3.675A pdb=" N ARG G 297 " --> pdb=" O PHE G 293 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR G 311 " --> pdb=" O GLY G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 329 Processing helix chain 'G' and resid 346 through 359 removed outlier: 3.854A 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: 3.605A 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 445 Proline residue: G 434 - end of helix removed outlier: 4.047A pdb=" N ASP G 437 " --> pdb=" O PRO G 434 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN G 440 " --> pdb=" O ASP G 437 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LEU G 443 " --> pdb=" O ASN G 440 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS G 445 " --> pdb=" O ASP G 442 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 484 Processing helix chain 'G' and resid 490 through 493 No H-bonds generated for 'chain 'G' and resid 490 through 493' Processing helix chain 'G' and resid 508 through 510 No H-bonds generated for 'chain 'G' and resid 508 through 510' Processing helix chain 'G' and resid 512 through 519 Processing helix chain 'G' and resid 544 through 548 Processing helix chain 'G' and resid 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: 3.782A 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: 3.755A pdb=" N GLN G 660 " --> pdb=" O PRO G 656 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TRP G 661 " --> pdb=" O PHE G 657 " (cutoff:3.500A) Proline residue: G 664 - end of helix Processing helix chain 'G' and resid 688 through 697 Processing helix chain 'G' and resid 710 through 722 Processing helix chain 'G' and resid 748 through 758 removed outlier: 4.982A pdb=" N SER G 755 " --> pdb=" O LEU G 751 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LYS G 756 " --> pdb=" O GLN G 752 " (cutoff:3.500A) Processing helix chain 'G' and resid 774 through 782 Proline residue: G 779 - end of helix Processing helix chain 'G' and resid 784 through 786 No H-bonds generated for 'chain 'G' and resid 784 through 786' Processing helix chain 'G' and resid 803 through 805 No H-bonds generated for 'chain 'G' and resid 803 through 805' Processing helix chain 'G' and resid 815 through 823 Processing helix chain 'G' and resid 829 through 831 No H-bonds generated for 'chain 'G' and resid 829 through 831' Processing helix chain 'G' and resid 833 through 836 Processing helix chain 'G' and resid 860 through 871 Processing helix chain 'G' and resid 880 through 898 removed outlier: 5.565A pdb=" N ASP G 889 " --> pdb=" O GLU G 885 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR G 890 " --> pdb=" O ALA G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 914 through 916 No H-bonds generated for 'chain 'G' and resid 914 through 916' Processing helix chain 'G' and resid 919 through 930 Processing helix chain 'G' and resid 941 through 958 Processing helix chain 'G' and resid 970 through 974 Processing helix chain 'G' and resid 976 through 986 removed outlier: 3.579A pdb=" N ALA G 986 " --> pdb=" O LYS G 982 " (cutoff:3.500A) 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: 4.269A pdb=" N GLU G1026 " --> pdb=" O ARG G1023 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE G1029 " --> pdb=" O GLU G1026 " (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 1174 Processing helix chain 'G' and resid 1258 through 1270 Processing helix chain 'G' and resid 1294 through 1304 Processing helix chain 'G' and resid 1309 through 1311 No H-bonds generated for 'chain 'G' and resid 1309 through 1311' Processing helix chain 'G' and resid 1323 through 1338 removed outlier: 4.034A pdb=" N TRP G1331 " --> pdb=" O VAL G1328 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ARG G1332 " --> pdb=" O VAL G1329 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE G1335 " --> pdb=" O ARG G1332 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS G1336 " --> pdb=" O ALA G1333 " (cutoff:3.500A) 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 1419 through 1421 No H-bonds generated for 'chain 'G' and resid 1419 through 1421' Processing helix chain 'G' and resid 1438 through 1446 Processing helix chain 'G' and resid 1515 through 1523 Processing helix chain 'G' and resid 1551 through 1557 removed outlier: 3.666A pdb=" N VAL G1556 " --> pdb=" O PRO G1552 " (cutoff:3.500A) Processing helix chain 'G' and resid 1562 through 1564 No H-bonds generated for 'chain 'G' and resid 1562 through 1564' Processing helix chain 'G' and resid 1567 through 1572 Processing helix chain 'G' and resid 1582 through 1596 Processing helix chain 'G' and resid 1602 through 1604 No H-bonds generated for 'chain 'G' and resid 1602 through 1604' Processing helix chain 'G' and resid 1678 through 1683 removed outlier: 3.713A pdb=" N THR G1683 " --> pdb=" O ASP G1679 " (cutoff:3.500A) Processing helix chain 'G' and resid 1685 through 1701 removed outlier: 3.508A pdb=" N VAL G1690 " --> pdb=" O ALA G1686 " (cutoff:3.500A) Processing helix chain 'G' and resid 1706 through 1712 Processing helix chain 'G' and resid 1725 through 1734 Processing helix chain 'G' and resid 1770 through 1772 No H-bonds generated for 'chain 'G' and resid 1770 through 1772' Processing helix chain 'G' and resid 1774 through 1795 Proline residue: G1779 - end of helix Processing helix chain 'G' and resid 1808 through 1818 removed outlier: 3.631A pdb=" N GLU G1811 " --> pdb=" O SER G1808 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA G1814 " --> pdb=" O GLU G1811 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU G1815 " --> pdb=" O TYR G1812 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU G1818 " --> pdb=" O LEU G1815 " (cutoff:3.500A) Processing helix chain 'G' and resid 1824 through 1841 removed outlier: 3.588A pdb=" N ALA G1841 " --> pdb=" O THR G1837 " (cutoff:3.500A) 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 removed outlier: 3.610A pdb=" N GLN G1872 " --> pdb=" O GLN G1868 " (cutoff:3.500A) Processing helix chain 'G' and resid 1904 through 1920 Processing helix chain 'G' and resid 1924 through 1929 removed outlier: 4.049A pdb=" N LYS G1929 " --> pdb=" O ILE G1925 " (cutoff:3.500A) Processing helix chain 'G' and resid 1936 through 1953 removed outlier: 3.953A pdb=" N GLU G1942 " --> pdb=" O GLY G1938 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE G1943 " --> pdb=" O HIS G1939 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA G1947 " --> pdb=" O ILE G1943 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS G1950 " --> pdb=" O GLU G1946 " (cutoff:3.500A) Processing helix chain 'G' and resid 1979 through 1995 removed outlier: 4.517A pdb=" N ASN G1983 " --> pdb=" O TYR G1980 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS G1986 " --> pdb=" O ASN G1983 " (cutoff:3.500A) Proline residue: G1987 - end of helix removed outlier: 4.021A pdb=" N SER G1990 " --> pdb=" O PRO G1987 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE G1991 " --> pdb=" O PHE G1988 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS G1993 " --> pdb=" O SER G1990 " (cutoff:3.500A) Processing helix chain 'G' and resid 1998 through 2000 No H-bonds generated for 'chain 'G' and resid 1998 through 2000' Processing helix chain 'G' and resid 2003 through 2005 No H-bonds generated for 'chain 'G' and resid 2003 through 2005' 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: 7.107A pdb=" N GLU A 77 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N GLU A 46 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 6.958A 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: 6.488A pdb=" N ALA A 767 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N THR A 681 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 6.676A 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: 4.468A pdb=" N MET A 923 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA A 820 " --> pdb=" O THR A 863 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N CYS A 865 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 5.855A 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: 6.035A pdb=" N LEU A 824 " --> pdb=" O ALA A 867 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE A 869 " --> pdb=" O LEU A 824 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N MET A 826 " --> pdb=" O ILE A 869 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1060 through 1066 Processing sheet with id= F, first strand: chain 'A' and resid 1103 through 1105 Processing sheet with id= G, first strand: chain 'A' and resid 1119 through 1126 Processing sheet with id= H, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id= I, first strand: chain 'A' and resid 1243 through 1245 removed outlier: 6.649A pdb=" N ILE A1326 " --> pdb=" O GLY A1244 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A1023 " --> pdb=" O ILE A1386 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N MET A1388 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL A1021 " --> pdb=" O MET A1388 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1573 through 1575 removed outlier: 7.532A pdb=" N ALA A1638 " --> pdb=" O GLY A1537 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ALA A1539 " --> pdb=" O ALA A1638 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER A1640 " --> pdb=" O ALA A1539 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET A1406 " --> pdb=" O ILE A1654 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL A1656 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL A1404 " --> pdb=" O VAL A1656 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1769 through 1775 Processing sheet with id= L, first strand: chain 'A' and resid 1837 through 1839 Processing sheet with id= M, first strand: chain 'G' and resid 6 through 13 removed outlier: 3.711A pdb=" N VAL G 22 " --> pdb=" O ARG G 7 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU G 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 526 through 529 removed outlier: 7.946A pdb=" N ALA G 158 " --> pdb=" O LYS G 268 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA G 270 " --> pdb=" O ALA G 158 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N PHE G 160 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLY G 272 " --> pdb=" O PHE G 160 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N GLY G 272 " --> pdb=" O PRO G 458 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N TYR G 460 " --> pdb=" O GLY G 272 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 338 through 342 removed outlier: 5.993A pdb=" N SER G 380 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ILE G 368 " --> pdb=" O SER G 380 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 568 through 571 Processing sheet with id= Q, first strand: chain 'G' and resid 618 through 620 removed outlier: 6.721A pdb=" N GLY G 648 " --> pdb=" O LEU G 619 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE G 649 " --> pdb=" O GLN G 677 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU G 679 " --> pdb=" O ILE G 649 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU G 651 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE G 681 " --> pdb=" O LEU G 651 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TYR G 702 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ILE G 681 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLY G 704 " --> pdb=" O ILE G 681 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N LEU G 705 " --> pdb=" O PRO G 727 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ALA G 729 " --> pdb=" O LEU G 705 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY G 798 " --> pdb=" O PHE G 767 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 843 through 847 Processing sheet with id= S, first strand: chain 'G' and resid 1126 through 1128 removed outlier: 5.895A pdb=" N GLU G1199 " --> pdb=" O PRO G1207 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N THR G1208 " --> pdb=" O ILE G1224 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU G1238 " --> pdb=" O MET G1221 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 1158 through 1161 Processing sheet with id= U, first strand: chain 'G' and resid 1376 through 1383 removed outlier: 7.035A pdb=" N ASP G1391 " --> pdb=" O GLU G1379 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL G1381 " --> pdb=" O ILE G1389 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE G1389 " --> pdb=" O VAL G1381 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASN G1383 " --> pdb=" O GLY G1387 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY G1387 " --> pdb=" O ASN G1383 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ARG G1398 " --> pdb=" O PRO G1402 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER G1354 " --> pdb=" O SER G1409 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N PHE G1411 " --> pdb=" O HIS G1352 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N HIS G1352 " --> pdb=" O PHE G1411 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ARG G1413 " --> pdb=" O LEU G1350 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU G1350 " --> pdb=" O ARG G1413 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU G1353 " --> pdb=" O PHE G1612 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ARG G1606 " --> pdb=" O MET G1359 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU G1656 " --> pdb=" O ARG G1606 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR G1608 " --> pdb=" O GLU G1654 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU G1654 " --> pdb=" O TYR G1608 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N CYS G1610 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR G1652 " --> pdb=" O CYS G1610 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N PHE G1612 " --> pdb=" O VAL G1650 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL G1650 " --> pdb=" O PHE G1612 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR G1642 " --> pdb=" O VAL G1650 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N THR G1652 " --> pdb=" O PHE G1640 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N PHE G1640 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU G1654 " --> pdb=" O ILE G1638 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE G1638 " --> pdb=" O GLU G1654 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU G1656 " --> pdb=" O LYS G1636 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LYS G1636 " --> pdb=" O GLU G1656 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS G1639 " --> pdb=" O HIS G1628 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N HIS G1628 " --> pdb=" O LYS G1639 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 1423 through 1427 removed outlier: 3.617A pdb=" N SER G1482 " --> pdb=" O THR G1473 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL G1491 " --> pdb=" O GLU G1500 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLU G1500 " --> pdb=" O VAL G1491 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 1431 through 1435 removed outlier: 3.530A pdb=" N LYS G1462 " --> pdb=" O ILE G1435 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 1663 through 1666 removed outlier: 7.025A pdb=" N THR G1803 " --> pdb=" O PHE G1664 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N PHE G1666 " --> pdb=" O THR G1803 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ALA G1805 " --> pdb=" O PHE G1666 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'G' and resid 1717 through 1720 Processing sheet with id= Z, first strand: chain 'G' and resid 1737 through 1741 Processing sheet with id= AA, first strand: chain 'G' and resid 1966 through 1968 removed outlier: 6.377A pdb=" N ALA G1901 " --> pdb=" O ILE G1888 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ILE G1888 " --> pdb=" O ALA G1901 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ASP G1903 " --> pdb=" O VAL G1886 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL G1886 " --> pdb=" O ASP G1903 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 1537 through 1545 removed outlier: 7.093A pdb=" N ILE G1626 " --> pdb=" O ILE G1539 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL G1541 " --> pdb=" O THR G1624 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR G1624 " --> pdb=" O VAL G1541 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP G1543 " --> pdb=" O LEU G1622 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU G1622 " --> pdb=" O ASP G1543 " (cutoff:3.500A) 1189 hydrogen bonds defined for protein. 3222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.51 Time building geometry restraints manager: 11.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5105 1.31 - 1.45: 7667 1.45 - 1.58: 17408 1.58 - 1.72: 9 1.72 - 1.85: 192 Bond restraints: 30381 Sorted by residual: bond pdb=" C1' MLC G2102 " pdb=" C2' MLC G2102 " ideal model delta sigma weight residual 1.323 1.514 -0.191 2.00e-02 2.50e+03 9.11e+01 bond pdb=" C3' MLC G2102 " pdb=" C4' MLC G2102 " ideal model delta sigma weight residual 1.365 1.533 -0.168 2.00e-02 2.50e+03 7.06e+01 bond pdb=" C1' MLC G2102 " pdb=" O4' MLC G2102 " ideal model delta sigma weight residual 1.603 1.436 0.167 2.00e-02 2.50e+03 6.99e+01 bond pdb=" C4 MLC G2102 " pdb=" C5 MLC G2102 " ideal model delta sigma weight residual 1.335 1.472 -0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" O23 A3Z B1901 " pdb=" P24 A3Z B1901 " ideal model delta sigma weight residual 1.510 1.645 -0.135 2.00e-02 2.50e+03 4.59e+01 ... (remaining 30376 not shown) Histogram of bond angle deviations from ideal: 96.99 - 104.93: 683 104.93 - 112.87: 14983 112.87 - 120.81: 15421 120.81 - 128.75: 9912 128.75 - 136.69: 159 Bond angle restraints: 41158 Sorted by residual: angle pdb=" CA GLY B 222 " pdb=" C GLY B 222 " pdb=" O GLY B 222 " ideal model delta sigma weight residual 122.45 117.76 4.69 7.20e-01 1.93e+00 4.25e+01 angle pdb=" CA ASP A1612 " pdb=" CB ASP A1612 " pdb=" CG ASP A1612 " ideal model delta sigma weight residual 112.60 118.63 -6.03 1.00e+00 1.00e+00 3.63e+01 angle pdb=" C THR G1422 " pdb=" CA THR G1422 " pdb=" CB THR G1422 " ideal model delta sigma weight residual 109.46 120.48 -11.02 1.84e+00 2.95e-01 3.59e+01 angle pdb=" C TRP G 661 " pdb=" N GLY G 662 " pdb=" CA GLY G 662 " ideal model delta sigma weight residual 120.00 126.56 -6.56 1.10e+00 8.26e-01 3.56e+01 angle pdb=" C MET A1592 " pdb=" N MET A1593 " pdb=" CA MET A1593 " ideal model delta sigma weight residual 120.44 127.42 -6.98 1.30e+00 5.92e-01 2.88e+01 ... (remaining 41153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.88: 17703 30.88 - 61.76: 546 61.76 - 92.64: 69 92.64 - 123.52: 2 123.52 - 154.40: 1 Dihedral angle restraints: 18321 sinusoidal: 7381 harmonic: 10940 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 -177.51 -107.23 1 2.00e+01 2.50e-03 3.11e+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 180.00 154.07 25.93 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA THR G2015 " pdb=" C THR G2015 " pdb=" N ALA G2016 " pdb=" CA ALA G2016 " ideal model delta harmonic sigma weight residual -180.00 -154.76 -25.24 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 18318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2213 0.063 - 0.126: 1655 0.126 - 0.189: 630 0.189 - 0.252: 107 0.252 - 0.314: 14 Chirality restraints: 4619 Sorted by residual: chirality pdb=" CA VAL A1027 " pdb=" N VAL A1027 " pdb=" C VAL A1027 " pdb=" CB VAL A1027 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA ILE A1403 " pdb=" N ILE A1403 " pdb=" C ILE A1403 " pdb=" CB ILE A1403 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA ILE G1626 " pdb=" N ILE G1626 " pdb=" C ILE G1626 " pdb=" CB ILE G1626 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 4616 not shown) Planarity restraints: 5308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CP5 MLC G2102 " -0.089 2.00e-02 2.50e+03 7.43e-02 6.89e+01 pdb=" CP6 MLC G2102 " 0.043 2.00e-02 2.50e+03 pdb=" CP7 MLC G2102 " -0.073 2.00e-02 2.50e+03 pdb=" NP2 MLC G2102 " 0.112 2.00e-02 2.50e+03 pdb=" OP2 MLC G2102 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN G2101 " 0.022 2.00e-02 2.50e+03 3.55e-02 5.99e+01 pdb=" C10 FMN G2101 " 0.013 2.00e-02 2.50e+03 pdb=" C2 FMN G2101 " -0.041 2.00e-02 2.50e+03 pdb=" C4 FMN G2101 " -0.002 2.00e-02 2.50e+03 pdb=" C4A FMN G2101 " 0.039 2.00e-02 2.50e+03 pdb=" C5A FMN G2101 " 0.059 2.00e-02 2.50e+03 pdb=" C6 FMN G2101 " 0.025 2.00e-02 2.50e+03 pdb=" C7 FMN G2101 " -0.022 2.00e-02 2.50e+03 pdb=" C7M FMN G2101 " -0.072 2.00e-02 2.50e+03 pdb=" C8 FMN G2101 " -0.030 2.00e-02 2.50e+03 pdb=" C8M FMN G2101 " -0.022 2.00e-02 2.50e+03 pdb=" C9 FMN G2101 " 0.000 2.00e-02 2.50e+03 pdb=" C9A FMN G2101 " 0.046 2.00e-02 2.50e+03 pdb=" N1 FMN G2101 " -0.025 2.00e-02 2.50e+03 pdb=" N10 FMN G2101 " 0.035 2.00e-02 2.50e+03 pdb=" N3 FMN G2101 " -0.027 2.00e-02 2.50e+03 pdb=" N5 FMN G2101 " 0.052 2.00e-02 2.50e+03 pdb=" O2 FMN G2101 " -0.036 2.00e-02 2.50e+03 pdb=" O4 FMN G2101 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1529 " 0.063 2.00e-02 2.50e+03 3.21e-02 2.06e+01 pdb=" CG TYR A1529 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A1529 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A1529 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR A1529 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A1529 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A1529 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A1529 " 0.034 2.00e-02 2.50e+03 ... (remaining 5305 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4692 2.81 - 3.33: 30941 3.33 - 3.86: 48452 3.86 - 4.38: 63763 4.38 - 4.90: 101659 Nonbonded interactions: 249507 Sorted by model distance: nonbonded pdb=" O TYR G 67 " pdb=" OG SER G 70 " model vdw 2.288 2.440 nonbonded pdb=" OH TYR A1694 " pdb=" OD2 ASP G1001 " model vdw 2.296 2.440 nonbonded pdb=" O VAL G 602 " pdb=" OH TYR G 624 " model vdw 2.319 2.440 nonbonded pdb=" OH TYR A 89 " pdb=" OD2 ASP G1791 " model vdw 2.320 2.440 nonbonded pdb=" OD2 ASP A 353 " pdb=" NH2 ARG A 359 " model vdw 2.336 2.520 ... (remaining 249502 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: 0.720 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: 0.030 Extract box with map and model: 4.820 Check model and map are aligned: 0.430 Set scattering table: 0.230 Process input model: 82.500 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 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 0.191 30381 Z= 0.876 Angle : 1.838 11.020 41158 Z= 1.346 Chirality : 0.089 0.314 4619 Planarity : 0.006 0.074 5308 Dihedral : 14.945 154.399 11277 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.77 % Favored : 94.97 % Rotamer: Outliers : 0.37 % Allowed : 3.51 % Favored : 96.12 % Cbeta Deviations : 0.03 % 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: -2.78 (0.12), residues: 3774 helix: -2.39 (0.10), residues: 1661 sheet: -1.67 (0.21), residues: 495 loop : -1.02 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.008 TRP G1270 HIS 0.012 0.003 HIS G 740 PHE 0.051 0.006 PHE A1376 TYR 0.063 0.007 TYR A1529 ARG 0.019 0.001 ARG A1036 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 374 time to evaluate : 2.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASN cc_start: 0.8533 (m-40) cc_final: 0.7860 (t0) REVERT: A 419 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8704 (mt-10) REVERT: A 431 GLU cc_start: 0.8884 (mp0) cc_final: 0.8628 (mp0) REVERT: A 518 LYS cc_start: 0.8328 (mmpt) cc_final: 0.7946 (tppt) REVERT: A 618 ASN cc_start: 0.8452 (m110) cc_final: 0.7801 (p0) REVERT: A 654 GLN cc_start: 0.8710 (mm110) cc_final: 0.8387 (tp40) REVERT: A 785 ASP cc_start: 0.8666 (t0) cc_final: 0.8336 (t70) REVERT: A 816 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8406 (mm-30) REVERT: A 1000 GLN cc_start: 0.8586 (mt0) cc_final: 0.8276 (mt0) REVERT: A 1003 GLN cc_start: 0.8691 (mt0) cc_final: 0.8447 (mm-40) REVERT: A 1044 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8532 (pm20) REVERT: A 1267 ASP cc_start: 0.8704 (t0) cc_final: 0.8495 (t70) REVERT: A 1317 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8588 (tm-30) REVERT: A 1354 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8324 (mt-10) REVERT: A 1365 MET cc_start: 0.9157 (mtt) cc_final: 0.8899 (mtt) REVERT: A 1370 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.9005 (p) REVERT: A 1468 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8260 (mt-10) REVERT: A 1492 GLU cc_start: 0.8215 (tt0) cc_final: 0.7790 (tt0) REVERT: A 1813 TRP cc_start: 0.8919 (t60) cc_final: 0.8536 (t60) REVERT: B 145 VAL cc_start: 0.5204 (m) cc_final: 0.4982 (t) REVERT: B 151 LEU cc_start: 0.7875 (tt) cc_final: 0.7660 (tt) REVERT: B 168 MET cc_start: 0.7740 (mmm) cc_final: 0.7490 (mmm) REVERT: B 200 LYS cc_start: 0.7913 (mtpt) cc_final: 0.7393 (ttmm) REVERT: B 202 GLU cc_start: 0.7558 (pm20) cc_final: 0.7192 (pm20) REVERT: B 207 GLU cc_start: 0.7900 (mp0) cc_final: 0.7481 (mp0) REVERT: B 208 GLU cc_start: 0.7600 (mp0) cc_final: 0.7193 (mp0) REVERT: B 231 ARG cc_start: 0.7445 (mtm110) cc_final: 0.7179 (mtm110) REVERT: G 59 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7463 (mp0) REVERT: G 126 TYR cc_start: 0.9033 (t80) cc_final: 0.8829 (t80) REVERT: G 287 ASP cc_start: 0.8276 (t0) cc_final: 0.8016 (t0) REVERT: G 497 LYS cc_start: 0.8587 (mmtm) cc_final: 0.8180 (pptt) REVERT: G 642 GLU cc_start: 0.8463 (mp0) cc_final: 0.8236 (mp0) REVERT: G 863 MET cc_start: 0.9183 (mmm) cc_final: 0.8911 (mmm) REVERT: G 1265 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8730 (ttp) REVERT: G 1486 PHE cc_start: 0.8748 (p90) cc_final: 0.8331 (p90) REVERT: G 1615 MET cc_start: 0.8726 (mtm) cc_final: 0.8463 (mtp) REVERT: G 1851 ASN cc_start: 0.7872 (p0) cc_final: 0.7640 (t0) REVERT: G 1872 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8290 (tp-100) outliers start: 12 outliers final: 4 residues processed: 384 average time/residue: 1.7352 time to fit residues: 763.4039 Evaluate side-chains 266 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 258 time to evaluate : 3.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1317 GLU Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1643 SER Chi-restraints excluded: chain G residue 599 PRO Chi-restraints excluded: chain G residue 1265 MET Chi-restraints excluded: chain G residue 1422 THR Chi-restraints excluded: chain G residue 1586 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 4.9990 chunk 285 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 192 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 295 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 342 optimal weight: 1.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 379 ASN A 527 GLN A 618 ASN A 829 ASN A 882 ASN A 904 ASN A 987 ASN A 989 GLN A1239 HIS A1380 GLN A1432 HIS A1549 ASN A1610 ASN A1695 ASN A1854 ASN B 214 GLN B 271 ASN B 292 GLN G 38 ASN G 102 HIS G 181 HIS G 224 ASN G 245 GLN G 440 ASN G 553 ASN G 572 ASN G 715 GLN G 718 ASN G 747 HIS G 993 GLN G1046 GLN G1241 ASN G1341 ASN G1355 ASN G1619 ASN G1659 GLN G1669 GLN G1912 ASN G2020 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 30381 Z= 0.305 Angle : 0.584 9.468 41158 Z= 0.305 Chirality : 0.044 0.192 4619 Planarity : 0.004 0.040 5308 Dihedral : 6.912 142.201 4088 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.85 % Favored : 98.09 % Rotamer: Outliers : 1.60 % Allowed : 8.80 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.13), residues: 3774 helix: 0.20 (0.12), residues: 1686 sheet: -1.02 (0.22), residues: 503 loop : -0.22 (0.16), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 661 HIS 0.006 0.001 HIS G1581 PHE 0.023 0.002 PHE A1786 TYR 0.018 0.002 TYR A 453 ARG 0.006 0.001 ARG A1637 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 256 time to evaluate : 3.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ASN cc_start: 0.8537 (m-40) cc_final: 0.8127 (t0) REVERT: A 366 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7962 (p0) REVERT: A 419 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8788 (mt-10) REVERT: A 431 GLU cc_start: 0.8882 (mp0) cc_final: 0.8634 (mp0) REVERT: A 654 GLN cc_start: 0.8701 (mm110) cc_final: 0.8365 (tp-100) REVERT: A 709 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.5566 (mtm-85) REVERT: A 785 ASP cc_start: 0.8540 (t0) cc_final: 0.8169 (t0) REVERT: A 1044 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8507 (pm20) REVERT: A 1267 ASP cc_start: 0.8712 (t0) cc_final: 0.8495 (t70) REVERT: A 1354 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8265 (mt-10) REVERT: A 1492 GLU cc_start: 0.8313 (tt0) cc_final: 0.7937 (tt0) REVERT: A 1813 TRP cc_start: 0.8823 (t60) cc_final: 0.8522 (t60) REVERT: B 143 GLU cc_start: 0.4613 (tm-30) cc_final: 0.4348 (tm-30) REVERT: B 168 MET cc_start: 0.7700 (mmm) cc_final: 0.7428 (mmm) REVERT: B 200 LYS cc_start: 0.7689 (mtpt) cc_final: 0.7155 (ttmm) REVERT: B 202 GLU cc_start: 0.7348 (pm20) cc_final: 0.6814 (pm20) REVERT: G 59 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7350 (mt-10) REVERT: G 325 GLU cc_start: 0.8200 (tp30) cc_final: 0.7850 (tp30) REVERT: G 329 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8270 (mm-30) REVERT: G 1486 PHE cc_start: 0.8677 (p90) cc_final: 0.8356 (p90) REVERT: G 1765 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7480 (mmm160) outliers start: 52 outliers final: 21 residues processed: 296 average time/residue: 1.6174 time to fit residues: 560.2171 Evaluate side-chains 259 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 234 time to evaluate : 3.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 709 ARG Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1499 SER Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1643 SER Chi-restraints excluded: chain A residue 1779 ILE Chi-restraints excluded: chain A residue 1781 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 972 LEU Chi-restraints excluded: chain G residue 1422 THR Chi-restraints excluded: chain G residue 1731 GLU Chi-restraints excluded: chain G residue 1765 ARG Chi-restraints excluded: chain G residue 1862 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 284 optimal weight: 10.0000 chunk 233 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 342 optimal weight: 2.9990 chunk 370 optimal weight: 2.9990 chunk 305 optimal weight: 5.9990 chunk 340 optimal weight: 0.6980 chunk 116 optimal weight: 8.9990 chunk 275 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN A 904 ASN A 969 ASN A1380 GLN B 157 HIS B 214 GLN B 271 ASN G 38 ASN G 110 GLN G 155 GLN G 500 HIS G 517 HIS G1186 ASN G1217 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30381 Z= 0.198 Angle : 0.508 8.862 41158 Z= 0.261 Chirality : 0.042 0.172 4619 Planarity : 0.003 0.040 5308 Dihedral : 6.493 136.721 4077 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.04 % Favored : 97.93 % Rotamer: Outliers : 1.72 % Allowed : 9.84 % Favored : 88.43 % 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: 0.48 (0.14), residues: 3774 helix: 1.00 (0.13), residues: 1684 sheet: -0.75 (0.22), residues: 512 loop : 0.13 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G1138 HIS 0.009 0.001 HIS B 157 PHE 0.022 0.001 PHE A1786 TYR 0.014 0.001 TYR A 722 ARG 0.010 0.000 ARG A1789 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 250 time to evaluate : 3.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ASN cc_start: 0.8397 (m-40) cc_final: 0.8136 (t0) REVERT: A 366 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7972 (p0) REVERT: A 431 GLU cc_start: 0.8861 (mp0) cc_final: 0.8602 (mp0) REVERT: A 946 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8521 (mp0) REVERT: A 1044 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8551 (pm20) REVERT: A 1129 GLU cc_start: 0.7434 (tp30) cc_final: 0.7169 (tp30) REVERT: A 1267 ASP cc_start: 0.8735 (t0) cc_final: 0.8535 (t70) REVERT: A 1492 GLU cc_start: 0.8323 (tt0) cc_final: 0.7936 (tt0) REVERT: A 1515 ARG cc_start: 0.5302 (mtm180) cc_final: 0.4887 (mtm180) REVERT: A 1813 TRP cc_start: 0.8849 (t60) cc_final: 0.8567 (t60) REVERT: A 1817 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8392 (mp0) REVERT: B 143 GLU cc_start: 0.4750 (tm-30) cc_final: 0.4253 (tm-30) REVERT: B 200 LYS cc_start: 0.7773 (mtpt) cc_final: 0.7254 (ttmm) REVERT: B 202 GLU cc_start: 0.7354 (pm20) cc_final: 0.6765 (pm20) REVERT: B 207 GLU cc_start: 0.7795 (mp0) cc_final: 0.7497 (mp0) REVERT: G 59 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7433 (mt-10) REVERT: G 325 GLU cc_start: 0.8220 (tp30) cc_final: 0.7820 (tp30) REVERT: G 329 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8280 (mm-30) REVERT: G 1222 GLU cc_start: 0.8515 (tt0) cc_final: 0.8303 (tt0) REVERT: G 1379 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8408 (tt0) REVERT: G 1486 PHE cc_start: 0.8740 (p90) cc_final: 0.8398 (p90) REVERT: G 1765 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7436 (mmm160) REVERT: G 1784 MET cc_start: 0.8838 (ppp) cc_final: 0.8602 (tmt) outliers start: 56 outliers final: 18 residues processed: 291 average time/residue: 1.5690 time to fit residues: 533.5838 Evaluate side-chains 254 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 231 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1817 GLU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 324 LEU Chi-restraints excluded: chain G residue 693 GLU Chi-restraints excluded: chain G residue 1015 VAL Chi-restraints excluded: chain G residue 1422 THR Chi-restraints excluded: chain G residue 1667 THR Chi-restraints excluded: chain G residue 1731 GLU Chi-restraints excluded: chain G residue 1751 ILE Chi-restraints excluded: chain G residue 1765 ARG Chi-restraints excluded: chain G residue 1862 VAL Chi-restraints excluded: chain G residue 2015 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 338 optimal weight: 7.9990 chunk 257 optimal weight: 9.9990 chunk 177 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 230 optimal weight: 9.9990 chunk 344 optimal weight: 9.9990 chunk 364 optimal weight: 6.9990 chunk 179 optimal weight: 0.9990 chunk 326 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 861 GLN A 904 ASN A1380 GLN B 157 HIS B 214 GLN B 271 ASN G 36 GLN G 38 ASN G 572 ASN G1217 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 30381 Z= 0.337 Angle : 0.558 9.721 41158 Z= 0.286 Chirality : 0.044 0.203 4619 Planarity : 0.004 0.043 5308 Dihedral : 6.543 137.803 4076 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.37 % Allowed : 10.80 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.14), residues: 3774 helix: 1.00 (0.13), residues: 1690 sheet: -0.63 (0.22), residues: 504 loop : 0.14 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G1138 HIS 0.009 0.001 HIS B 157 PHE 0.021 0.002 PHE A1786 TYR 0.017 0.002 TYR A 377 ARG 0.010 0.001 ARG A1789 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 238 time to evaluate : 3.127 Fit side-chains revert: symmetry clash REVERT: A 63 ASN cc_start: 0.8480 (m-40) cc_final: 0.8110 (t0) REVERT: A 366 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7995 (p0) REVERT: A 431 GLU cc_start: 0.8862 (mp0) cc_final: 0.8581 (mp0) REVERT: A 611 LYS cc_start: 0.8961 (ttpp) cc_final: 0.8308 (tptp) REVERT: A 633 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8001 (pp20) REVERT: A 946 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8523 (mp0) REVERT: A 1044 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8574 (pm20) REVERT: A 1129 GLU cc_start: 0.7420 (tp30) cc_final: 0.7090 (tp30) REVERT: A 1142 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8582 (tm-30) REVERT: A 1492 GLU cc_start: 0.8312 (tt0) cc_final: 0.7669 (tm-30) REVERT: A 1813 TRP cc_start: 0.8844 (t60) cc_final: 0.8605 (t60) REVERT: A 1817 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8288 (mp0) REVERT: B 143 GLU cc_start: 0.4498 (OUTLIER) cc_final: 0.4031 (tm-30) REVERT: B 202 GLU cc_start: 0.7246 (pm20) cc_final: 0.6926 (pm20) REVERT: B 237 MET cc_start: 0.6473 (mmm) cc_final: 0.6261 (mmm) REVERT: G 59 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7567 (mt-10) REVERT: G 325 GLU cc_start: 0.8221 (tp30) cc_final: 0.7838 (tp30) REVERT: G 329 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8317 (mm-30) REVERT: G 1379 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8438 (tt0) REVERT: G 1486 PHE cc_start: 0.8722 (p90) cc_final: 0.8371 (p90) REVERT: G 1765 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7473 (mmm160) REVERT: G 1784 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8607 (tmt) outliers start: 77 outliers final: 38 residues processed: 290 average time/residue: 1.6600 time to fit residues: 569.4696 Evaluate side-chains 271 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 224 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 713 GLN Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1050 CYS Chi-restraints excluded: chain A residue 1142 GLU Chi-restraints excluded: chain A residue 1262 LYS Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1643 SER Chi-restraints excluded: chain A residue 1781 VAL Chi-restraints excluded: chain A residue 1817 GLU Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 693 GLU Chi-restraints excluded: chain G residue 844 VAL Chi-restraints excluded: chain G residue 850 MET Chi-restraints excluded: chain G residue 972 LEU Chi-restraints excluded: chain G residue 1005 SER Chi-restraints excluded: chain G residue 1015 VAL Chi-restraints excluded: chain G residue 1106 GLU Chi-restraints excluded: chain G residue 1422 THR Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1667 THR Chi-restraints excluded: chain G residue 1731 GLU Chi-restraints excluded: chain G residue 1751 ILE Chi-restraints excluded: chain G residue 1765 ARG Chi-restraints excluded: chain G residue 1784 MET Chi-restraints excluded: chain G residue 1801 ASP Chi-restraints excluded: chain G residue 1862 VAL Chi-restraints excluded: chain G residue 1941 PHE Chi-restraints excluded: chain G residue 2015 THR Chi-restraints excluded: chain G residue 2032 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 8.9990 chunk 206 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 271 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 310 optimal weight: 9.9990 chunk 251 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 186 optimal weight: 6.9990 chunk 327 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 904 ASN B 157 HIS B 214 GLN B 271 ASN G 38 ASN G1217 ASN G1302 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30381 Z= 0.184 Angle : 0.490 7.650 41158 Z= 0.251 Chirality : 0.041 0.174 4619 Planarity : 0.003 0.047 5308 Dihedral : 6.293 134.528 4076 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.12 % Allowed : 11.63 % Favored : 86.25 % 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: 0.82 (0.14), residues: 3774 helix: 1.23 (0.13), residues: 1684 sheet: -0.45 (0.22), residues: 511 loop : 0.31 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 865 HIS 0.010 0.001 HIS B 157 PHE 0.021 0.001 PHE A1786 TYR 0.014 0.001 TYR A 417 ARG 0.010 0.000 ARG A1789 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 238 time to evaluate : 3.537 Fit side-chains revert: symmetry clash REVERT: A 63 ASN cc_start: 0.8474 (m-40) cc_final: 0.8169 (t0) REVERT: A 366 ASP cc_start: 0.8190 (p0) cc_final: 0.7962 (p0) REVERT: A 431 GLU cc_start: 0.8862 (mp0) cc_final: 0.8607 (mp0) REVERT: A 611 LYS cc_start: 0.8961 (ttpp) cc_final: 0.8333 (tptp) REVERT: A 633 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7978 (pp20) REVERT: A 669 ASN cc_start: 0.9130 (OUTLIER) cc_final: 0.8580 (m-40) REVERT: A 946 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8455 (mp0) REVERT: A 1044 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8554 (pm20) REVERT: A 1129 GLU cc_start: 0.7299 (tp30) cc_final: 0.7041 (tp30) REVERT: A 1365 MET cc_start: 0.9040 (mtt) cc_final: 0.8840 (mtt) REVERT: A 1492 GLU cc_start: 0.8332 (tt0) cc_final: 0.7683 (tm-30) REVERT: A 1813 TRP cc_start: 0.8765 (t60) cc_final: 0.8523 (t60) REVERT: A 1817 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: B 143 GLU cc_start: 0.4299 (OUTLIER) cc_final: 0.3853 (tm-30) REVERT: B 200 LYS cc_start: 0.7917 (mtpt) cc_final: 0.7612 (mtpp) REVERT: B 202 GLU cc_start: 0.7354 (pm20) cc_final: 0.6985 (pm20) REVERT: B 203 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7377 (mp0) REVERT: B 237 MET cc_start: 0.6553 (mmm) cc_final: 0.6335 (mmm) REVERT: G 59 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7514 (mt-10) REVERT: G 325 GLU cc_start: 0.8278 (tp30) cc_final: 0.7910 (tp30) REVERT: G 1295 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8450 (ttmm) REVERT: G 1379 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8399 (tt0) REVERT: G 1486 PHE cc_start: 0.8719 (p90) cc_final: 0.8278 (p90) REVERT: G 1880 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8626 (mtpm) outliers start: 69 outliers final: 29 residues processed: 289 average time/residue: 1.5958 time to fit residues: 537.1091 Evaluate side-chains 263 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 225 time to evaluate : 3.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 669 ASN Chi-restraints excluded: chain A residue 713 GLN Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1499 SER Chi-restraints excluded: chain A residue 1528 THR Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1643 SER Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1817 GLU Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 324 LEU Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 1295 LYS Chi-restraints excluded: chain G residue 1422 THR Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1667 THR Chi-restraints excluded: chain G residue 1699 LYS Chi-restraints excluded: chain G residue 1731 GLU Chi-restraints excluded: chain G residue 1751 ILE Chi-restraints excluded: chain G residue 1801 ASP Chi-restraints excluded: chain G residue 1862 VAL Chi-restraints excluded: chain G residue 1880 LYS Chi-restraints excluded: chain G residue 1941 PHE Chi-restraints excluded: chain G residue 2015 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 122 optimal weight: 4.9990 chunk 328 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 364 optimal weight: 5.9990 chunk 302 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 120 optimal weight: 8.9990 chunk 191 optimal weight: 9.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 904 ASN B 157 HIS B 214 GLN B 271 ASN G 38 ASN G1217 ASN G1983 ASN G2013 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 30381 Z= 0.297 Angle : 0.536 11.612 41158 Z= 0.273 Chirality : 0.043 0.196 4619 Planarity : 0.004 0.046 5308 Dihedral : 6.359 135.505 4076 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.43 % Allowed : 12.18 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.14), residues: 3774 helix: 1.14 (0.13), residues: 1691 sheet: -0.35 (0.23), residues: 501 loop : 0.28 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 865 HIS 0.010 0.001 HIS B 157 PHE 0.021 0.002 PHE A 35 TYR 0.017 0.002 TYR A 417 ARG 0.012 0.000 ARG A1789 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 234 time to evaluate : 3.433 Fit side-chains revert: symmetry clash REVERT: A 63 ASN cc_start: 0.8510 (m-40) cc_final: 0.8220 (t0) REVERT: A 366 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7977 (p0) REVERT: A 431 GLU cc_start: 0.8846 (mp0) cc_final: 0.8574 (mp0) REVERT: A 611 LYS cc_start: 0.8936 (ttpp) cc_final: 0.8291 (tptp) REVERT: A 633 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8101 (pp20) REVERT: A 669 ASN cc_start: 0.9161 (OUTLIER) cc_final: 0.8585 (m-40) REVERT: A 709 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.4855 (mtm180) REVERT: A 946 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8507 (mp0) REVERT: A 1044 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8591 (pm20) REVERT: A 1129 GLU cc_start: 0.7522 (tp30) cc_final: 0.7292 (tp30) REVERT: A 1365 MET cc_start: 0.9109 (mtt) cc_final: 0.8909 (mtt) REVERT: A 1492 GLU cc_start: 0.8306 (tt0) cc_final: 0.7595 (tm-30) REVERT: A 1813 TRP cc_start: 0.8785 (t60) cc_final: 0.8541 (t60) REVERT: B 202 GLU cc_start: 0.7221 (pm20) cc_final: 0.6916 (pm20) REVERT: B 203 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: B 237 MET cc_start: 0.6604 (mmm) cc_final: 0.6398 (mmm) REVERT: G 59 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7543 (mt-10) REVERT: G 325 GLU cc_start: 0.8317 (tp30) cc_final: 0.7961 (tp30) REVERT: G 1295 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8474 (ttmm) REVERT: G 1379 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8486 (tt0) REVERT: G 1486 PHE cc_start: 0.8721 (p90) cc_final: 0.8308 (p90) REVERT: G 1765 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7459 (mmm160) REVERT: G 1790 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8193 (mp0) REVERT: G 1880 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8502 (tmmm) outliers start: 79 outliers final: 39 residues processed: 291 average time/residue: 1.7129 time to fit residues: 582.8500 Evaluate side-chains 273 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 223 time to evaluate : 3.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 669 ASN Chi-restraints excluded: chain A residue 709 ARG Chi-restraints excluded: chain A residue 713 GLN Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1050 CYS Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1528 THR Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1643 SER Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1781 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 324 LEU Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 844 VAL Chi-restraints excluded: chain G residue 972 LEU Chi-restraints excluded: chain G residue 1005 SER Chi-restraints excluded: chain G residue 1015 VAL Chi-restraints excluded: chain G residue 1295 LYS Chi-restraints excluded: chain G residue 1422 THR Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1667 THR Chi-restraints excluded: chain G residue 1699 LYS Chi-restraints excluded: chain G residue 1731 GLU Chi-restraints excluded: chain G residue 1751 ILE Chi-restraints excluded: chain G residue 1765 ARG Chi-restraints excluded: chain G residue 1790 GLU Chi-restraints excluded: chain G residue 1801 ASP Chi-restraints excluded: chain G residue 1862 VAL Chi-restraints excluded: chain G residue 1880 LYS Chi-restraints excluded: chain G residue 1941 PHE Chi-restraints excluded: chain G residue 2015 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 351 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 207 optimal weight: 9.9990 chunk 266 optimal weight: 0.0040 chunk 206 optimal weight: 5.9990 chunk 307 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 363 optimal weight: 6.9990 chunk 227 optimal weight: 6.9990 chunk 221 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 904 ASN B 157 HIS B 214 GLN B 271 ASN G 38 ASN G1217 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30381 Z= 0.186 Angle : 0.489 8.769 41158 Z= 0.250 Chirality : 0.041 0.173 4619 Planarity : 0.003 0.048 5308 Dihedral : 6.196 133.293 4076 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.03 % Allowed : 13.01 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.14), residues: 3774 helix: 1.30 (0.13), residues: 1684 sheet: -0.22 (0.23), residues: 511 loop : 0.39 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 865 HIS 0.009 0.001 HIS B 157 PHE 0.022 0.001 PHE G1916 TYR 0.014 0.001 TYR A 417 ARG 0.013 0.000 ARG A1789 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 245 time to evaluate : 3.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ASN cc_start: 0.8474 (m-40) cc_final: 0.8181 (t0) REVERT: A 366 ASP cc_start: 0.8190 (p0) cc_final: 0.7963 (p0) REVERT: A 431 GLU cc_start: 0.8845 (mp0) cc_final: 0.8596 (mp0) REVERT: A 611 LYS cc_start: 0.8921 (ttpp) cc_final: 0.8296 (tptp) REVERT: A 633 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8015 (pp20) REVERT: A 669 ASN cc_start: 0.9116 (OUTLIER) cc_final: 0.8594 (m-40) REVERT: A 709 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.4880 (mtm180) REVERT: A 1044 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8602 (pm20) REVERT: A 1492 GLU cc_start: 0.8313 (tt0) cc_final: 0.7610 (tm-30) REVERT: A 1813 TRP cc_start: 0.8749 (t60) cc_final: 0.8471 (t60) REVERT: B 200 LYS cc_start: 0.7888 (mtpt) cc_final: 0.7608 (mtpp) REVERT: B 202 GLU cc_start: 0.7192 (pm20) cc_final: 0.6890 (pm20) REVERT: B 203 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: B 237 MET cc_start: 0.6684 (mmm) cc_final: 0.6465 (mmm) REVERT: B 254 TRP cc_start: 0.6068 (m100) cc_final: 0.5742 (m100) REVERT: G 59 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7520 (mt-10) REVERT: G 325 GLU cc_start: 0.8320 (tp30) cc_final: 0.7950 (tp30) REVERT: G 471 LEU cc_start: 0.8844 (mt) cc_final: 0.8600 (mp) REVERT: G 1295 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8497 (tttm) REVERT: G 1379 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8482 (tt0) REVERT: G 1486 PHE cc_start: 0.8717 (p90) cc_final: 0.8175 (p90) REVERT: G 1765 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7448 (mmm160) REVERT: G 1790 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8187 (mp0) REVERT: G 1880 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8626 (mtpm) outliers start: 66 outliers final: 32 residues processed: 291 average time/residue: 1.5796 time to fit residues: 539.4197 Evaluate side-chains 270 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 229 time to evaluate : 3.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 669 ASN Chi-restraints excluded: chain A residue 709 ARG Chi-restraints excluded: chain A residue 713 GLN Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1528 THR Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1643 SER Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1781 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 444 VAL Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 693 GLU Chi-restraints excluded: chain G residue 1015 VAL Chi-restraints excluded: chain G residue 1295 LYS Chi-restraints excluded: chain G residue 1422 THR Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1667 THR Chi-restraints excluded: chain G residue 1699 LYS Chi-restraints excluded: chain G residue 1731 GLU Chi-restraints excluded: chain G residue 1751 ILE Chi-restraints excluded: chain G residue 1765 ARG Chi-restraints excluded: chain G residue 1790 GLU Chi-restraints excluded: chain G residue 1801 ASP Chi-restraints excluded: chain G residue 1862 VAL Chi-restraints excluded: chain G residue 1880 LYS Chi-restraints excluded: chain G residue 1941 PHE Chi-restraints excluded: chain G residue 2015 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 224 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 217 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 231 optimal weight: 7.9990 chunk 247 optimal weight: 20.0000 chunk 179 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 285 optimal weight: 5.9990 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 904 ASN A1790 ASN B 157 HIS B 214 GLN B 271 ASN G 38 ASN G 572 ASN G1217 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30381 Z= 0.209 Angle : 0.499 11.326 41158 Z= 0.253 Chirality : 0.041 0.174 4619 Planarity : 0.003 0.047 5308 Dihedral : 6.175 132.916 4076 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.09 % Allowed : 13.29 % Favored : 84.62 % 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: 1.01 (0.14), residues: 3774 helix: 1.33 (0.13), residues: 1684 sheet: -0.17 (0.23), residues: 509 loop : 0.41 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 865 HIS 0.010 0.001 HIS B 157 PHE 0.021 0.001 PHE A 35 TYR 0.014 0.001 TYR A 417 ARG 0.006 0.000 ARG A1789 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 233 time to evaluate : 3.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8675 (tt0) cc_final: 0.8416 (mm-30) REVERT: A 63 ASN cc_start: 0.8516 (m-40) cc_final: 0.8210 (t0) REVERT: A 366 ASP cc_start: 0.8197 (p0) cc_final: 0.7970 (p0) REVERT: A 431 GLU cc_start: 0.8843 (mp0) cc_final: 0.8596 (mp0) REVERT: A 611 LYS cc_start: 0.8957 (ttpp) cc_final: 0.8285 (tptp) REVERT: A 633 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8063 (pp20) REVERT: A 669 ASN cc_start: 0.9115 (OUTLIER) cc_final: 0.8579 (m-40) REVERT: A 709 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.4982 (mtm180) REVERT: A 1044 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8627 (pm20) REVERT: A 1492 GLU cc_start: 0.8312 (tt0) cc_final: 0.7606 (tm-30) REVERT: A 1790 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.7946 (m110) REVERT: A 1813 TRP cc_start: 0.8755 (t60) cc_final: 0.8482 (t60) REVERT: B 200 LYS cc_start: 0.7878 (mtpt) cc_final: 0.7609 (mtpp) REVERT: B 202 GLU cc_start: 0.7149 (pm20) cc_final: 0.6843 (pm20) REVERT: B 203 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: B 207 GLU cc_start: 0.7976 (mp0) cc_final: 0.7726 (mp0) REVERT: B 237 MET cc_start: 0.6635 (mmm) cc_final: 0.6420 (mmm) REVERT: B 254 TRP cc_start: 0.6070 (m100) cc_final: 0.5539 (m100) REVERT: B 280 GLU cc_start: 0.5967 (mm-30) cc_final: 0.5671 (mm-30) REVERT: G 59 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7541 (mt-10) REVERT: G 119 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8789 (p) REVERT: G 325 GLU cc_start: 0.8318 (tp30) cc_final: 0.7954 (tp30) REVERT: G 471 LEU cc_start: 0.8842 (mt) cc_final: 0.8617 (mp) REVERT: G 1295 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8495 (tttm) REVERT: G 1379 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8487 (tt0) REVERT: G 1765 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7455 (mmm160) REVERT: G 1790 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8185 (mp0) REVERT: G 1880 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8513 (tmmm) REVERT: G 1927 LEU cc_start: 0.7892 (mt) cc_final: 0.7107 (tt) outliers start: 68 outliers final: 38 residues processed: 285 average time/residue: 1.5608 time to fit residues: 527.3031 Evaluate side-chains 275 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 226 time to evaluate : 3.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 669 ASN Chi-restraints excluded: chain A residue 709 ARG Chi-restraints excluded: chain A residue 713 GLN Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1528 THR Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1643 SER Chi-restraints excluded: chain A residue 1692 MET Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain A residue 1781 VAL Chi-restraints excluded: chain A residue 1790 ASN Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 444 VAL Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 646 THR Chi-restraints excluded: chain G residue 693 GLU Chi-restraints excluded: chain G residue 1005 SER Chi-restraints excluded: chain G residue 1015 VAL Chi-restraints excluded: chain G residue 1295 LYS Chi-restraints excluded: chain G residue 1422 THR Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1667 THR Chi-restraints excluded: chain G residue 1699 LYS Chi-restraints excluded: chain G residue 1731 GLU Chi-restraints excluded: chain G residue 1751 ILE Chi-restraints excluded: chain G residue 1765 ARG Chi-restraints excluded: chain G residue 1790 GLU Chi-restraints excluded: chain G residue 1801 ASP Chi-restraints excluded: chain G residue 1862 VAL Chi-restraints excluded: chain G residue 1880 LYS Chi-restraints excluded: chain G residue 1941 PHE Chi-restraints excluded: chain G residue 2015 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 330 optimal weight: 6.9990 chunk 348 optimal weight: 5.9990 chunk 317 optimal weight: 0.3980 chunk 338 optimal weight: 10.0000 chunk 203 optimal weight: 3.9990 chunk 147 optimal weight: 20.0000 chunk 265 optimal weight: 0.4980 chunk 103 optimal weight: 4.9990 chunk 305 optimal weight: 0.9980 chunk 320 optimal weight: 6.9990 chunk 337 optimal weight: 0.7980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 904 ASN B 157 HIS B 214 GLN B 271 ASN G 38 ASN G1217 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30381 Z= 0.152 Angle : 0.478 10.535 41158 Z= 0.243 Chirality : 0.041 0.176 4619 Planarity : 0.003 0.073 5308 Dihedral : 6.053 131.132 4076 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.63 % Allowed : 13.93 % Favored : 84.44 % 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: 1.10 (0.14), residues: 3774 helix: 1.41 (0.13), residues: 1683 sheet: -0.14 (0.23), residues: 514 loop : 0.47 (0.16), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G1138 HIS 0.009 0.001 HIS B 157 PHE 0.024 0.001 PHE G1916 TYR 0.013 0.001 TYR A 417 ARG 0.016 0.000 ARG A1789 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 245 time to evaluate : 3.729 Fit side-chains REVERT: A 42 GLU cc_start: 0.8661 (tt0) cc_final: 0.8407 (mm-30) REVERT: A 63 ASN cc_start: 0.8407 (m-40) cc_final: 0.8202 (t0) REVERT: A 366 ASP cc_start: 0.8175 (p0) cc_final: 0.7966 (p0) REVERT: A 431 GLU cc_start: 0.8848 (mp0) cc_final: 0.8618 (mp0) REVERT: A 611 LYS cc_start: 0.8947 (ttpp) cc_final: 0.8276 (tptp) REVERT: A 633 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8029 (pp20) REVERT: A 709 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.5056 (mtm180) REVERT: A 1044 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8652 (pm20) REVERT: A 1492 GLU cc_start: 0.8326 (tt0) cc_final: 0.7809 (tt0) REVERT: A 1813 TRP cc_start: 0.8722 (t60) cc_final: 0.8461 (t60) REVERT: A 1817 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8311 (mp0) REVERT: B 143 GLU cc_start: 0.4634 (tm-30) cc_final: 0.4375 (tm-30) REVERT: B 200 LYS cc_start: 0.7894 (mtpt) cc_final: 0.7621 (mtpp) REVERT: B 202 GLU cc_start: 0.7156 (pm20) cc_final: 0.6852 (pm20) REVERT: B 203 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: B 237 MET cc_start: 0.6605 (mmm) cc_final: 0.6149 (mpm) REVERT: B 254 TRP cc_start: 0.5813 (m100) cc_final: 0.5525 (m100) REVERT: B 272 GLU cc_start: 0.6483 (tt0) cc_final: 0.6249 (tp30) REVERT: B 280 GLU cc_start: 0.5989 (mm-30) cc_final: 0.5633 (mm-30) REVERT: G 59 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7530 (mt-10) REVERT: G 119 THR cc_start: 0.9026 (OUTLIER) cc_final: 0.8783 (p) REVERT: G 325 GLU cc_start: 0.8322 (tp30) cc_final: 0.7970 (tp30) REVERT: G 471 LEU cc_start: 0.8827 (mt) cc_final: 0.8620 (mp) REVERT: G 1295 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8429 (tttm) REVERT: G 1379 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8477 (tt0) REVERT: G 1486 PHE cc_start: 0.8372 (p90) cc_final: 0.8163 (p90) REVERT: G 1731 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8318 (mp0) REVERT: G 1765 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7438 (mmm160) REVERT: G 1790 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8166 (mp0) REVERT: G 1880 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8634 (mtpp) REVERT: G 1927 LEU cc_start: 0.7886 (mt) cc_final: 0.6992 (tt) outliers start: 53 outliers final: 25 residues processed: 284 average time/residue: 1.5895 time to fit residues: 526.5691 Evaluate side-chains 266 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 230 time to evaluate : 3.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 709 ARG Chi-restraints excluded: chain A residue 713 GLN Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1817 GLU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 444 VAL Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 646 THR Chi-restraints excluded: chain G residue 693 GLU Chi-restraints excluded: chain G residue 850 MET Chi-restraints excluded: chain G residue 1005 SER Chi-restraints excluded: chain G residue 1015 VAL Chi-restraints excluded: chain G residue 1295 LYS Chi-restraints excluded: chain G residue 1422 THR Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1667 THR Chi-restraints excluded: chain G residue 1731 GLU Chi-restraints excluded: chain G residue 1751 ILE Chi-restraints excluded: chain G residue 1765 ARG Chi-restraints excluded: chain G residue 1790 GLU Chi-restraints excluded: chain G residue 1801 ASP Chi-restraints excluded: chain G residue 1862 VAL Chi-restraints excluded: chain G residue 1880 LYS Chi-restraints excluded: chain G residue 1941 PHE Chi-restraints excluded: chain G residue 2015 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 222 optimal weight: 6.9990 chunk 358 optimal weight: 6.9990 chunk 218 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 375 optimal weight: 10.0000 chunk 345 optimal weight: 6.9990 chunk 299 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 231 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 904 ASN A1790 ASN B 157 HIS B 214 GLN B 271 ASN G 38 ASN G 896 ASN G1217 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 30381 Z= 0.368 Angle : 0.571 12.386 41158 Z= 0.291 Chirality : 0.044 0.203 4619 Planarity : 0.004 0.051 5308 Dihedral : 6.365 134.034 4076 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.66 % Allowed : 14.18 % Favored : 84.16 % 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: 0.83 (0.14), residues: 3774 helix: 1.16 (0.13), residues: 1692 sheet: -0.25 (0.23), residues: 502 loop : 0.33 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G1596 HIS 0.011 0.001 HIS B 157 PHE 0.021 0.002 PHE A 35 TYR 0.019 0.002 TYR A 417 ARG 0.006 0.001 ARG B 253 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 235 time to evaluate : 3.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8735 (tt0) cc_final: 0.8473 (tp30) REVERT: A 366 ASP cc_start: 0.8235 (p0) cc_final: 0.7996 (p0) REVERT: A 431 GLU cc_start: 0.8845 (mp0) cc_final: 0.8596 (mp0) REVERT: A 611 LYS cc_start: 0.8992 (ttpp) cc_final: 0.8288 (tptp) REVERT: A 633 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8019 (pp20) REVERT: A 669 ASN cc_start: 0.9129 (OUTLIER) cc_final: 0.8518 (m-40) REVERT: A 709 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.4845 (mtm180) REVERT: A 1044 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8585 (pm20) REVERT: A 1813 TRP cc_start: 0.8789 (t60) cc_final: 0.8504 (t60) REVERT: A 1817 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8291 (mp0) REVERT: B 143 GLU cc_start: 0.4579 (tm-30) cc_final: 0.4276 (tm-30) REVERT: B 200 LYS cc_start: 0.7752 (mtpt) cc_final: 0.7536 (mtpp) REVERT: B 202 GLU cc_start: 0.7146 (pm20) cc_final: 0.6824 (pm20) REVERT: B 203 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: B 254 TRP cc_start: 0.5710 (m100) cc_final: 0.5366 (m100) REVERT: B 280 GLU cc_start: 0.6169 (mm-30) cc_final: 0.5829 (mm-30) REVERT: G 59 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7548 (mt-10) REVERT: G 119 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8776 (p) REVERT: G 325 GLU cc_start: 0.8314 (tp30) cc_final: 0.7950 (tp30) REVERT: G 471 LEU cc_start: 0.8829 (mt) cc_final: 0.8619 (mp) REVERT: G 1379 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8481 (tt0) REVERT: G 1765 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7447 (mmm160) REVERT: G 1790 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8236 (mp0) REVERT: G 1880 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8558 (tmmm) REVERT: G 1927 LEU cc_start: 0.7871 (mt) cc_final: 0.7127 (tt) outliers start: 54 outliers final: 33 residues processed: 274 average time/residue: 1.5884 time to fit residues: 509.1546 Evaluate side-chains 269 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 226 time to evaluate : 3.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 669 ASN Chi-restraints excluded: chain A residue 709 ARG Chi-restraints excluded: chain A residue 713 GLN Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1437 LYS Chi-restraints excluded: chain A residue 1528 THR Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1692 MET Chi-restraints excluded: chain A residue 1727 LYS Chi-restraints excluded: chain A residue 1817 GLU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 444 VAL Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 646 THR Chi-restraints excluded: chain G residue 693 GLU Chi-restraints excluded: chain G residue 972 LEU Chi-restraints excluded: chain G residue 1005 SER Chi-restraints excluded: chain G residue 1015 VAL Chi-restraints excluded: chain G residue 1422 THR Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1667 THR Chi-restraints excluded: chain G residue 1731 GLU Chi-restraints excluded: chain G residue 1751 ILE Chi-restraints excluded: chain G residue 1765 ARG Chi-restraints excluded: chain G residue 1790 GLU Chi-restraints excluded: chain G residue 1801 ASP Chi-restraints excluded: chain G residue 1862 VAL Chi-restraints excluded: chain G residue 1880 LYS Chi-restraints excluded: chain G residue 1941 PHE Chi-restraints excluded: chain G residue 2015 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 4.9990 chunk 318 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 275 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 299 optimal weight: 7.9990 chunk 125 optimal weight: 0.9990 chunk 307 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 904 ASN B 157 HIS B 214 GLN B 271 ASN G 38 ASN G1217 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.086093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.064143 restraints weight = 61211.493| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 1.94 r_work: 0.2676 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30381 Z= 0.164 Angle : 0.486 11.364 41158 Z= 0.248 Chirality : 0.041 0.161 4619 Planarity : 0.003 0.054 5308 Dihedral : 6.092 131.048 4076 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.45 % Allowed : 14.64 % Favored : 83.91 % 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: 1.06 (0.14), residues: 3774 helix: 1.39 (0.13), residues: 1682 sheet: -0.14 (0.23), residues: 505 loop : 0.41 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G1138 HIS 0.011 0.001 HIS B 157 PHE 0.022 0.001 PHE G1916 TYR 0.013 0.001 TYR A 417 ARG 0.013 0.000 ARG A1789 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10112.73 seconds wall clock time: 180 minutes 55.00 seconds (10855.00 seconds total)