Starting phenix.real_space_refine on Mon Mar 18 19:22:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gl6_40191/03_2024/8gl6_40191_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gl6_40191/03_2024/8gl6_40191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gl6_40191/03_2024/8gl6_40191.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gl6_40191/03_2024/8gl6_40191.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gl6_40191/03_2024/8gl6_40191_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gl6_40191/03_2024/8gl6_40191_updated.pdb" } resolution = 3.2 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 13840 2.51 5 N 3671 2.21 5 O 4339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1599": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2045": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21896 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 17380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2191, 17380 Classifications: {'peptide': 2191} Link IDs: {'PCIS': 3, 'PTRANS': 99, 'TRANS': 2088} Chain breaks: 3 Chain: "B" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 990 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain breaks: 1 Chain: "F" Number of atoms: 2861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2861 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Chain: "D" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 596 Classifications: {'peptide': 76} Link IDs: {'TRANS': 75} Chain: "F" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.47, per 1000 atoms: 0.52 Number of scatterers: 21896 At special positions: 0 Unit cell: (118.368, 127.41, 134.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 4339 8.00 N 3671 7.00 C 13840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.77 Conformation dependent library (CDL) restraints added in 4.2 seconds 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5122 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 29 sheets defined 10.8% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.46 Creating SS restraints... Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 306 removed outlier: 4.526A pdb=" N ASP A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL A 304 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'A' and resid 402 through 405 Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 436 through 438 No H-bonds generated for 'chain 'A' and resid 436 through 438' Processing helix chain 'A' and resid 518 through 521 No H-bonds generated for 'chain 'A' and resid 518 through 521' Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 579 through 582 No H-bonds generated for 'chain 'A' and resid 579 through 582' Processing helix chain 'A' and resid 627 through 632 Processing helix chain 'A' and resid 644 through 646 No H-bonds generated for 'chain 'A' and resid 644 through 646' Processing helix chain 'A' and resid 651 through 654 No H-bonds generated for 'chain 'A' and resid 651 through 654' Processing helix chain 'A' and resid 664 through 669 removed outlier: 4.203A pdb=" N GLN A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 673 No H-bonds generated for 'chain 'A' and resid 671 through 673' Processing helix chain 'A' and resid 731 through 736 removed outlier: 4.015A pdb=" N ALA A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER A 736 " --> pdb=" O SER A 732 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 731 through 736' Processing helix chain 'A' and resid 811 through 819 Processing helix chain 'A' and resid 899 through 902 Processing helix chain 'A' and resid 915 through 917 No H-bonds generated for 'chain 'A' and resid 915 through 917' Processing helix chain 'A' and resid 940 through 943 No H-bonds generated for 'chain 'A' and resid 940 through 943' Processing helix chain 'A' and resid 983 through 985 No H-bonds generated for 'chain 'A' and resid 983 through 985' Processing helix chain 'A' and resid 999 through 1002 No H-bonds generated for 'chain 'A' and resid 999 through 1002' Processing helix chain 'A' and resid 1049 through 1051 No H-bonds generated for 'chain 'A' and resid 1049 through 1051' Processing helix chain 'A' and resid 1082 through 1088 Processing helix chain 'A' and resid 1100 through 1103 No H-bonds generated for 'chain 'A' and resid 1100 through 1103' Processing helix chain 'A' and resid 1105 through 1107 No H-bonds generated for 'chain 'A' and resid 1105 through 1107' Processing helix chain 'A' and resid 1121 through 1123 No H-bonds generated for 'chain 'A' and resid 1121 through 1123' Processing helix chain 'A' and resid 1128 through 1131 No H-bonds generated for 'chain 'A' and resid 1128 through 1131' Processing helix chain 'A' and resid 1413 through 1416 No H-bonds generated for 'chain 'A' and resid 1413 through 1416' Processing helix chain 'A' and resid 1427 through 1439 removed outlier: 4.032A pdb=" N SER A1439 " --> pdb=" O ILE A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1457 No H-bonds generated for 'chain 'A' and resid 1455 through 1457' Processing helix chain 'A' and resid 1572 through 1575 Processing helix chain 'A' and resid 1608 through 1613 Processing helix chain 'A' and resid 1618 through 1628 Processing helix chain 'A' and resid 1657 through 1659 No H-bonds generated for 'chain 'A' and resid 1657 through 1659' Processing helix chain 'A' and resid 1831 through 1833 No H-bonds generated for 'chain 'A' and resid 1831 through 1833' Processing helix chain 'A' and resid 1857 through 1860 No H-bonds generated for 'chain 'A' and resid 1857 through 1860' Processing helix chain 'A' and resid 1977 through 1980 No H-bonds generated for 'chain 'A' and resid 1977 through 1980' Processing helix chain 'A' and resid 1988 through 1994 Processing helix chain 'A' and resid 2072 through 2074 No H-bonds generated for 'chain 'A' and resid 2072 through 2074' Processing helix chain 'A' and resid 2085 through 2105 removed outlier: 3.661A pdb=" N ARG A2094 " --> pdb=" O PHE A2090 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LEU A2095 " --> pdb=" O ARG A2091 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE A2096 " --> pdb=" O SER A2092 " (cutoff:3.500A) Processing helix chain 'A' and resid 2130 through 2135 Processing helix chain 'A' and resid 2148 through 2160 Proline residue: A2153 - end of helix Processing helix chain 'A' and resid 2187 through 2189 No H-bonds generated for 'chain 'A' and resid 2187 through 2189' Processing helix chain 'B' and resid 28 through 41 Processing helix chain 'B' and resid 127 through 135 Proline residue: B 134 - end of helix Processing helix chain 'F' and resid 31 through 34 Processing helix chain 'F' and resid 39 through 44 Processing helix chain 'F' and resid 62 through 67 removed outlier: 4.056A pdb=" N ALA F 66 " --> pdb=" O ALA F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 296 Processing helix chain 'F' and resid 300 through 306 removed outlier: 3.825A pdb=" N PHE F 305 " --> pdb=" O VAL F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 321 removed outlier: 4.125A pdb=" N LYS F 320 " --> pdb=" O SER F 316 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU F 321 " --> pdb=" O GLU F 317 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 763 through 767 removed outlier: 6.605A pdb=" N PHE A 770 " --> pdb=" O ILE A 766 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE A1640 " --> pdb=" O PRO A1585 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N PHE A1662 " --> pdb=" O GLY A1641 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLN A1743 " --> pdb=" O ALA A1677 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR A1679 " --> pdb=" O ARG A1741 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG A1741 " --> pdb=" O TYR A1679 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP A1681 " --> pdb=" O SER A1739 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER A1739 " --> pdb=" O ASP A1681 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN A1683 " --> pdb=" O ARG A1737 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG A1737 " --> pdb=" O GLN A1683 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN A1685 " --> pdb=" O ILE A1735 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE A1735 " --> pdb=" O ASN A1685 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA A1687 " --> pdb=" O THR A1733 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR A1733 " --> pdb=" O ALA A1687 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ASN A1689 " --> pdb=" O PHE A1731 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N PHE A1731 " --> pdb=" O ASN A1689 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA A1691 " --> pdb=" O ILE A1729 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE A1729 " --> pdb=" O ALA A1691 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN A1728 " --> pdb=" O GLY A1771 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ILE A1789 " --> pdb=" O PRO A1816 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR A1847 " --> pdb=" O SER A1881 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE A1876 " --> pdb=" O PRO A1961 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ASN A1878 " --> pdb=" O VAL A1959 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL A1959 " --> pdb=" O ASN A1878 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ASN A1880 " --> pdb=" O GLY A1957 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLY A1957 " --> pdb=" O ASN A1880 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASN A1882 " --> pdb=" O ASN A1955 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ASN A1955 " --> pdb=" O ASN A1882 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU A1884 " --> pdb=" O THR A1953 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N THR A1953 " --> pdb=" O LEU A1884 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N THR A1886 " --> pdb=" O ASN A1951 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASN A1951 " --> pdb=" O THR A1886 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN A1951 " --> pdb=" O LYS A2016 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ASP A2034 " --> pdb=" O SER A2068 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA A2208 " --> pdb=" O THR A2069 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL A2287 " --> pdb=" O ALA A2274 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A2348 " --> pdb=" O THR A2334 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL A2336 " --> pdb=" O LEU A2346 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU A2346 " --> pdb=" O VAL A2336 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN A2351 " --> pdb=" O LYS A2379 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE A 205 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLN A 246 " --> pdb=" O GLN A 218 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL A 220 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS A 244 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL A 222 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY A 242 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN A 224 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU A 240 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ARG A 755 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR A 754 " --> pdb=" O ARG A 782 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 145 through 152 Processing sheet with id= C, first strand: chain 'A' and resid 264 through 270 Processing sheet with id= D, first strand: chain 'A' and resid 275 through 282 Processing sheet with id= E, first strand: chain 'A' and resid 291 through 293 removed outlier: 3.876A pdb=" N TYR A 447 " --> pdb=" O ASN A 442 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 425 through 428 removed outlier: 5.983A pdb=" N LEU A 503 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU A 347 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU A 505 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 11.775A pdb=" N VAL A 504 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N PHE A 464 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU A 460 " --> pdb=" O LEU A 508 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR A 467 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ILE A 318 " --> pdb=" O THR A 467 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 465 through 468 Processing sheet with id= H, first strand: chain 'A' and resid 486 through 489 Processing sheet with id= I, first strand: chain 'A' and resid 527 through 529 Processing sheet with id= J, first strand: chain 'A' and resid 717 through 720 Processing sheet with id= K, first strand: chain 'A' and resid 866 through 869 removed outlier: 3.727A pdb=" N ASP A1194 " --> pdb=" O GLN A1215 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS A1217 " --> pdb=" O ILE A1192 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE A1192 " --> pdb=" O LYS A1217 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1250 through 1254 Processing sheet with id= M, first strand: chain 'A' and resid 987 through 993 Processing sheet with id= N, first strand: chain 'A' and resid 1283 through 1291 Processing sheet with id= O, first strand: chain 'A' and resid 1313 through 1315 Processing sheet with id= P, first strand: chain 'A' and resid 1343 through 1348 Processing sheet with id= Q, first strand: chain 'A' and resid 1423 through 1426 removed outlier: 6.317A pdb=" N LEU A1510 " --> pdb=" O TYR A 857 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N TYR A 857 " --> pdb=" O LEU A1510 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 1739 through 1742 Processing sheet with id= S, first strand: chain 'A' and resid 1848 through 1853 Processing sheet with id= T, first strand: chain 'A' and resid 2027 through 2032 removed outlier: 6.386A pdb=" N GLU A2258 " --> pdb=" O LYS A2198 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE A2200 " --> pdb=" O ASP A2256 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASP A2256 " --> pdb=" O PHE A2200 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A2202 " --> pdb=" O ARG A2254 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG A2254 " --> pdb=" O LEU A2202 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 2044 through 2047 Processing sheet with id= V, first strand: chain 'A' and resid 2215 through 2217 Processing sheet with id= W, first strand: chain 'A' and resid 2276 through 2278 Processing sheet with id= X, first strand: chain 'B' and resid 97 through 99 Processing sheet with id= Y, first strand: chain 'B' and resid 55 through 59 removed outlier: 6.434A pdb=" N GLU B 141 " --> pdb=" O THR B 58 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 90 through 98 Processing sheet with id= AA, first strand: chain 'F' and resid 118 through 120 removed outlier: 3.778A pdb=" N ARG F 131 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 1363 through 1366 removed outlier: 3.671A pdb=" N THR D1375 " --> pdb=" O LEU D1364 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 1429 through 1434 removed outlier: 3.829A pdb=" N VAL D1419 " --> pdb=" O ARG D1431 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR D1395 " --> pdb=" O ILE D1386 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ASP D1388 " --> pdb=" O LEU D1393 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU D1393 " --> pdb=" O ASP D1388 " (cutoff:3.500A) 820 hydrogen bonds defined for protein. 2223 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: 12.85 Time building geometry restraints manager: 9.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7259 1.34 - 1.46: 4909 1.46 - 1.58: 10106 1.58 - 1.69: 6 1.69 - 1.81: 90 Bond restraints: 22370 Sorted by residual: bond pdb=" C1 LMN F 501 " pdb=" O5 LMN F 501 " ideal model delta sigma weight residual 1.403 1.563 -0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" C4 LMN F 501 " pdb=" O4 LMN F 501 " ideal model delta sigma weight residual 1.409 1.506 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" CCF LMN F 501 " pdb=" OBX LMN F 501 " ideal model delta sigma weight residual 1.410 1.499 -0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" CCS LMN F 501 " pdb=" OBZ LMN F 501 " ideal model delta sigma weight residual 1.394 1.482 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CCR LMN F 501 " pdb=" OBY LMN F 501 " ideal model delta sigma weight residual 1.393 1.475 -0.082 2.00e-02 2.50e+03 1.67e+01 ... (remaining 22365 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.85: 589 106.85 - 113.64: 11837 113.64 - 120.43: 8386 120.43 - 127.23: 9390 127.23 - 134.02: 162 Bond angle restraints: 30364 Sorted by residual: angle pdb=" N GLY A 759 " pdb=" CA GLY A 759 " pdb=" C GLY A 759 " ideal model delta sigma weight residual 110.96 115.20 -4.24 1.19e+00 7.06e-01 1.27e+01 angle pdb=" C4 LMN F 501 " pdb=" O4 LMN F 501 " pdb=" CCR LMN F 501 " ideal model delta sigma weight residual 120.22 109.89 10.33 3.00e+00 1.11e-01 1.19e+01 angle pdb=" N GLY A1152 " pdb=" CA GLY A1152 " pdb=" C GLY A1152 " ideal model delta sigma weight residual 112.73 116.83 -4.10 1.20e+00 6.94e-01 1.17e+01 angle pdb=" N VAL A 475 " pdb=" CA VAL A 475 " pdb=" C VAL A 475 " ideal model delta sigma weight residual 113.53 110.29 3.24 9.80e-01 1.04e+00 1.10e+01 angle pdb=" N VAL A1090 " pdb=" CA VAL A1090 " pdb=" C VAL A1090 " ideal model delta sigma weight residual 113.20 110.02 3.18 9.60e-01 1.09e+00 1.09e+01 ... (remaining 30359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.42: 13132 24.42 - 48.84: 219 48.84 - 73.26: 31 73.26 - 97.68: 18 97.68 - 122.10: 19 Dihedral angle restraints: 13419 sinusoidal: 5395 harmonic: 8024 Sorted by residual: dihedral pdb=" CCD LMN F 501 " pdb=" CCS LMN F 501 " pdb=" OBZ LMN F 501 " pdb=" OCB LMN F 501 " ideal model delta sinusoidal sigma weight residual 60.96 -176.94 -122.10 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" CCD LMN F 501 " pdb=" CCS LMN F 501 " pdb=" OBZ LMN F 501 " pdb=" CCW LMN F 501 " ideal model delta sinusoidal sigma weight residual -59.55 61.91 -121.46 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" CCC LMN F 501 " pdb=" CCR LMN F 501 " pdb=" OBY LMN F 501 " pdb=" O4 LMN F 501 " ideal model delta sinusoidal sigma weight residual 60.74 -179.75 -119.51 1 3.00e+01 1.11e-03 1.59e+01 ... (remaining 13416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2065 0.033 - 0.066: 835 0.066 - 0.099: 223 0.099 - 0.132: 177 0.132 - 0.164: 11 Chirality restraints: 3311 Sorted by residual: chirality pdb=" CCV LMN F 501 " pdb=" CCR LMN F 501 " pdb=" CCT LMN F 501 " pdb=" OAU LMN F 501 " both_signs ideal model delta sigma weight residual False 2.28 2.45 -0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" CCQ LMN F 501 " pdb=" CCF LMN F 501 " pdb=" CCH LMN F 501 " pdb=" OCB LMN F 501 " both_signs ideal model delta sigma weight residual False -2.61 -2.46 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CCW LMN F 501 " pdb=" CCS LMN F 501 " pdb=" CCU LMN F 501 " pdb=" OAV LMN F 501 " both_signs ideal model delta sigma weight residual False 2.30 2.45 -0.15 2.00e-01 2.50e+01 5.52e-01 ... (remaining 3308 not shown) Planarity restraints: 4017 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1639 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.59e+00 pdb=" C PHE A1639 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE A1639 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE A1640 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 176 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C SER A 176 " -0.028 2.00e-02 2.50e+03 pdb=" O SER A 176 " 0.011 2.00e-02 2.50e+03 pdb=" N MET A 177 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A1062 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO A1063 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A1063 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1063 " -0.022 5.00e-02 4.00e+02 ... (remaining 4014 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 304 2.65 - 3.21: 19272 3.21 - 3.77: 33438 3.77 - 4.34: 49874 4.34 - 4.90: 82244 Nonbonded interactions: 185132 Sorted by model distance: nonbonded pdb=" O LYS F 320 " pdb=" OG SER F 346 " model vdw 2.084 2.440 nonbonded pdb=" OG SER F 109 " pdb=" OD1 ASP F 141 " model vdw 2.180 2.440 nonbonded pdb=" O LEU A2156 " pdb=" OG1 THR A2160 " model vdw 2.213 2.440 nonbonded pdb=" OD2 ASP A2163 " pdb=" OG SER A2165 " model vdw 2.223 2.440 nonbonded pdb=" OH TYR A1048 " pdb=" O SER A1071 " model vdw 2.236 2.440 ... (remaining 185127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.960 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 63.580 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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 : 0.003 0.160 22370 Z= 0.214 Angle : 0.498 10.327 30364 Z= 0.268 Chirality : 0.044 0.164 3311 Planarity : 0.003 0.040 4017 Dihedral : 11.295 122.099 8297 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.87 % Allowed : 3.21 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.16), residues: 2744 helix: -0.43 (0.33), residues: 271 sheet: 0.31 (0.16), residues: 1075 loop : -0.48 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1996 HIS 0.004 0.001 HIS A1672 PHE 0.017 0.001 PHE A1009 TYR 0.013 0.001 TYR A1394 ARG 0.003 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 436 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 THR cc_start: 0.7538 (m) cc_final: 0.7298 (p) REVERT: B 47 GLN cc_start: 0.8458 (mp10) cc_final: 0.8229 (mp10) REVERT: B 166 LEU cc_start: 0.9165 (mt) cc_final: 0.8953 (mt) REVERT: D 1420 LYS cc_start: 0.8487 (mtpp) cc_final: 0.8250 (ttmm) outliers start: 21 outliers final: 6 residues processed: 450 average time/residue: 0.3482 time to fit residues: 242.7283 Evaluate side-chains 264 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 258 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1405 LEU Chi-restraints excluded: chain D residue 1416 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 231 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 214 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 248 optimal weight: 0.3980 overall best weight: 6.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 308 ASN A 734 GLN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 GLN ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1604 GLN A1787 ASN A1866 ASN ** A1984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN F 59 GLN F 122 GLN F 209 GLN D1396 ASN D1411 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.099 22370 Z= 0.590 Angle : 0.710 8.925 30364 Z= 0.367 Chirality : 0.051 0.280 3311 Planarity : 0.005 0.057 4017 Dihedral : 9.517 112.744 3151 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.65 % Favored : 94.31 % Rotamer: Outliers : 2.25 % Allowed : 8.00 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.75 (0.16), residues: 2744 helix: -1.25 (0.29), residues: 293 sheet: 0.05 (0.16), residues: 1081 loop : -0.69 (0.16), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A1996 HIS 0.010 0.002 HIS A2375 PHE 0.033 0.003 PHE A1480 TYR 0.030 0.002 TYR A1120 ARG 0.009 0.001 ARG D1431 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 256 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 THR cc_start: 0.7584 (m) cc_final: 0.7334 (p) REVERT: B 47 GLN cc_start: 0.8477 (mp10) cc_final: 0.8238 (mp10) outliers start: 54 outliers final: 41 residues processed: 287 average time/residue: 0.3344 time to fit residues: 155.1708 Evaluate side-chains 275 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 234 time to evaluate : 2.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1526 ASP Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1542 SER Chi-restraints excluded: chain A residue 1565 ASN Chi-restraints excluded: chain A residue 1785 THR Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2034 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain F residue 47 GLN Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 199 ASN Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1366 SER Chi-restraints excluded: chain D residue 1374 VAL Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1416 VAL Chi-restraints excluded: chain D residue 1422 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 138 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 169 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 249 optimal weight: 5.9990 chunk 269 optimal weight: 3.9990 chunk 221 optimal weight: 20.0000 chunk 247 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 199 optimal weight: 10.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A 330 ASN A 865 GLN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 GLN A1106 ASN ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1317 ASN A1485 ASN A2350 GLN B 143 GLN F 209 GLN D1385 ASN D1415 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22370 Z= 0.244 Angle : 0.541 7.734 30364 Z= 0.282 Chirality : 0.046 0.286 3311 Planarity : 0.004 0.043 4017 Dihedral : 8.178 105.216 3148 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.21 % Allowed : 9.95 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.61 (0.16), residues: 2744 helix: -0.85 (0.31), residues: 279 sheet: 0.07 (0.16), residues: 1078 loop : -0.60 (0.17), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1996 HIS 0.003 0.001 HIS A1672 PHE 0.019 0.001 PHE A1009 TYR 0.020 0.001 TYR D1395 ARG 0.005 0.000 ARG D1431 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 243 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6982 (m-30) REVERT: A 532 GLN cc_start: 0.6215 (mp10) cc_final: 0.5897 (mm-40) REVERT: B 25 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7789 (mtmt) REVERT: B 45 THR cc_start: 0.7559 (m) cc_final: 0.7307 (p) REVERT: B 101 TYR cc_start: 0.8351 (p90) cc_final: 0.7880 (p90) REVERT: B 112 ASP cc_start: 0.7505 (t70) cc_final: 0.6973 (t70) outliers start: 53 outliers final: 35 residues processed: 275 average time/residue: 0.3027 time to fit residues: 134.9963 Evaluate side-chains 269 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 233 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1526 ASP Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1542 SER Chi-restraints excluded: chain A residue 1565 ASN Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1943 THR Chi-restraints excluded: chain A residue 2034 ASP Chi-restraints excluded: chain A residue 2181 SER Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain F residue 199 ASN Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1366 SER Chi-restraints excluded: chain D residue 1367 VAL Chi-restraints excluded: chain D residue 1371 THR Chi-restraints excluded: chain D residue 1394 ILE Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1416 VAL Chi-restraints excluded: chain D residue 1422 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 246 optimal weight: 20.0000 chunk 187 optimal weight: 0.7980 chunk 129 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 250 optimal weight: 10.0000 chunk 264 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 237 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1317 ASN ** A1485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1874 ASN ** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN F 209 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 22370 Z= 0.424 Angle : 0.602 7.646 30364 Z= 0.314 Chirality : 0.047 0.287 3311 Planarity : 0.004 0.046 4017 Dihedral : 7.336 86.699 3148 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.87 % Allowed : 10.29 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.81 (0.16), residues: 2744 helix: -1.21 (0.29), residues: 298 sheet: -0.03 (0.16), residues: 1063 loop : -0.70 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1996 HIS 0.005 0.001 HIS A2375 PHE 0.021 0.002 PHE A1242 TYR 0.031 0.002 TYR D1395 ARG 0.004 0.001 ARG A1627 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 243 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 532 GLN cc_start: 0.6409 (mp10) cc_final: 0.6087 (mp10) REVERT: B 45 THR cc_start: 0.7667 (m) cc_final: 0.7420 (p) REVERT: B 112 ASP cc_start: 0.7384 (t70) cc_final: 0.7121 (t70) outliers start: 69 outliers final: 56 residues processed: 285 average time/residue: 0.3145 time to fit residues: 146.5916 Evaluate side-chains 285 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 229 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1442 ILE Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1542 SER Chi-restraints excluded: chain A residue 1560 ASP Chi-restraints excluded: chain A residue 1565 ASN Chi-restraints excluded: chain A residue 1785 THR Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1943 THR Chi-restraints excluded: chain A residue 2034 ASP Chi-restraints excluded: chain A residue 2181 SER Chi-restraints excluded: chain A residue 2288 LYS Chi-restraints excluded: chain A residue 2358 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain F residue 47 GLN Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 199 ASN Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1366 SER Chi-restraints excluded: chain D residue 1367 VAL Chi-restraints excluded: chain D residue 1371 THR Chi-restraints excluded: chain D residue 1374 VAL Chi-restraints excluded: chain D residue 1394 ILE Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1406 SER Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1416 VAL Chi-restraints excluded: chain D residue 1422 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 220 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 109 optimal weight: 0.3980 chunk 226 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 135 optimal weight: 0.9990 chunk 237 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1317 ASN ** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN F 209 GLN D1415 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22370 Z= 0.196 Angle : 0.521 7.875 30364 Z= 0.272 Chirality : 0.045 0.367 3311 Planarity : 0.003 0.043 4017 Dihedral : 6.567 82.567 3148 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.33 % Allowed : 11.66 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % 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: -0.65 (0.16), residues: 2744 helix: -0.88 (0.30), residues: 285 sheet: 0.02 (0.16), residues: 1072 loop : -0.61 (0.17), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1996 HIS 0.003 0.001 HIS A1672 PHE 0.018 0.001 PHE A1009 TYR 0.023 0.001 TYR D1395 ARG 0.006 0.000 ARG A2398 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 245 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 GLN cc_start: 0.6261 (mp10) cc_final: 0.6038 (mp10) REVERT: B 25 LYS cc_start: 0.8108 (mtmt) cc_final: 0.7621 (mtmt) REVERT: B 45 THR cc_start: 0.7631 (m) cc_final: 0.7379 (p) REVERT: B 101 TYR cc_start: 0.8427 (p90) cc_final: 0.8176 (p90) outliers start: 56 outliers final: 46 residues processed: 281 average time/residue: 0.3151 time to fit residues: 143.2745 Evaluate side-chains 271 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 225 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 807 SER Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1442 ILE Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1542 SER Chi-restraints excluded: chain A residue 1560 ASP Chi-restraints excluded: chain A residue 1565 ASN Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 2034 ASP Chi-restraints excluded: chain A residue 2181 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain F residue 47 GLN Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 199 ASN Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1366 SER Chi-restraints excluded: chain D residue 1367 VAL Chi-restraints excluded: chain D residue 1374 VAL Chi-restraints excluded: chain D residue 1390 THR Chi-restraints excluded: chain D residue 1394 ILE Chi-restraints excluded: chain D residue 1400 VAL Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1416 VAL Chi-restraints excluded: chain D residue 1422 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 89 optimal weight: 9.9990 chunk 238 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 265 optimal weight: 0.1980 chunk 220 optimal weight: 0.9980 chunk 122 optimal weight: 8.9990 chunk 22 optimal weight: 0.0040 chunk 87 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 overall best weight: 1.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1317 ASN A2136 ASN F 209 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22370 Z= 0.192 Angle : 0.510 7.787 30364 Z= 0.266 Chirality : 0.045 0.359 3311 Planarity : 0.003 0.039 4017 Dihedral : 6.188 80.845 3148 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.58 % Allowed : 12.00 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.16), residues: 2744 helix: -0.83 (0.30), residues: 281 sheet: 0.07 (0.16), residues: 1072 loop : -0.53 (0.17), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1996 HIS 0.004 0.001 HIS A1672 PHE 0.018 0.001 PHE A1009 TYR 0.030 0.001 TYR B 27 ARG 0.006 0.000 ARG A2398 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 231 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 532 GLN cc_start: 0.6194 (mp10) cc_final: 0.5986 (mp10) REVERT: B 45 THR cc_start: 0.7633 (m) cc_final: 0.7380 (p) REVERT: B 101 TYR cc_start: 0.8421 (p90) cc_final: 0.8180 (p90) outliers start: 62 outliers final: 49 residues processed: 274 average time/residue: 0.3416 time to fit residues: 153.4734 Evaluate side-chains 270 residues out of total 2401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 221 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain A residue 923 SER Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1442 ILE Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1542 SER Chi-restraints excluded: chain A residue 1560 ASP Chi-restraints excluded: chain A residue 1565 ASN Chi-restraints excluded: chain A residue 1568 THR Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 1811 LEU Chi-restraints excluded: chain A residue 1943 THR Chi-restraints excluded: chain A residue 2034 ASP Chi-restraints excluded: chain A residue 2181 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain F residue 47 GLN Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 199 ASN Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 386 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 1366 SER Chi-restraints excluded: chain D residue 1367 VAL Chi-restraints excluded: chain D residue 1371 THR Chi-restraints excluded: chain D residue 1374 VAL Chi-restraints excluded: chain D residue 1390 THR Chi-restraints excluded: chain D residue 1394 ILE Chi-restraints excluded: chain D residue 1410 LEU Chi-restraints excluded: chain D residue 1416 VAL Chi-restraints excluded: chain D residue 1422 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.3555 > 50: distance: 107 - 108: 16.833 distance: 108 - 109: 35.828 distance: 108 - 111: 14.925 distance: 109 - 110: 39.278 distance: 109 - 119: 46.435 distance: 110 - 143: 7.295 distance: 111 - 112: 3.878 distance: 112 - 113: 5.065 distance: 112 - 114: 4.435 distance: 113 - 115: 3.739 distance: 114 - 116: 3.037 distance: 119 - 120: 34.255 distance: 120 - 121: 35.099 distance: 120 - 123: 31.956 distance: 121 - 122: 20.412 distance: 121 - 124: 30.211 distance: 122 - 150: 34.331 distance: 124 - 125: 37.811 distance: 125 - 126: 41.997 distance: 125 - 128: 25.804 distance: 126 - 127: 45.318 distance: 126 - 131: 37.542 distance: 128 - 129: 11.638 distance: 128 - 130: 3.486 distance: 131 - 132: 21.261 distance: 132 - 133: 17.559 distance: 132 - 135: 10.385 distance: 133 - 134: 28.642 distance: 133 - 143: 14.951 distance: 135 - 136: 3.189 distance: 137 - 139: 5.539 distance: 138 - 140: 4.610 distance: 140 - 141: 3.345 distance: 141 - 142: 3.283 distance: 143 - 144: 21.702 distance: 144 - 145: 16.393 distance: 144 - 147: 8.261 distance: 145 - 146: 30.392 distance: 145 - 150: 27.687 distance: 147 - 148: 11.429 distance: 147 - 149: 5.286 distance: 150 - 151: 24.897 distance: 151 - 152: 3.981 distance: 151 - 154: 27.836 distance: 152 - 153: 25.068 distance: 152 - 155: 14.952 distance: 155 - 156: 11.484 distance: 156 - 157: 17.977 distance: 156 - 159: 11.488 distance: 157 - 158: 14.316 distance: 157 - 163: 14.844 distance: 159 - 160: 10.659 distance: 160 - 161: 5.602 distance: 160 - 162: 6.285 distance: 163 - 164: 23.675 distance: 164 - 165: 19.913 distance: 164 - 167: 18.573 distance: 165 - 166: 25.789 distance: 165 - 172: 31.715 distance: 167 - 168: 10.308 distance: 168 - 169: 9.563 distance: 169 - 170: 7.143 distance: 169 - 171: 3.437 distance: 172 - 173: 52.052 distance: 173 - 174: 46.590 distance: 174 - 175: 38.988 distance: 174 - 176: 17.154 distance: 176 - 177: 19.237 distance: 177 - 178: 12.403 distance: 177 - 180: 25.273 distance: 178 - 179: 24.744 distance: 178 - 188: 27.982 distance: 180 - 181: 10.366 distance: 181 - 182: 17.620 distance: 181 - 183: 8.048 distance: 182 - 184: 16.837 distance: 183 - 185: 16.741 distance: 184 - 186: 12.142 distance: 185 - 186: 17.273 distance: 186 - 187: 11.477