Starting phenix.real_space_refine on Sun Dec 10 03:48:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qfs_18383/12_2023/8qfs_18383_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qfs_18383/12_2023/8qfs_18383.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qfs_18383/12_2023/8qfs_18383_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qfs_18383/12_2023/8qfs_18383_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qfs_18383/12_2023/8qfs_18383_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qfs_18383/12_2023/8qfs_18383.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qfs_18383/12_2023/8qfs_18383.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qfs_18383/12_2023/8qfs_18383_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qfs_18383/12_2023/8qfs_18383_updated.pdb" } resolution = 2.7 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= 0.006 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: 6 Type Number sf(0) Gaussians P 64 5.49 5 Mg 1 5.21 5 S 37 5.16 5 C 8204 2.51 5 N 2265 2.21 5 O 2723 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 22": "OD1" <-> "OD2" Residue "C PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C ASP 208": "OD1" <-> "OD2" Residue "C GLU 216": "OE1" <-> "OE2" Residue "C GLU 233": "OE1" <-> "OE2" Residue "C ASP 371": "OD1" <-> "OD2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 6": "OE1" <-> "OE2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 449": "OD1" <-> "OD2" Residue "A PHE 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 569": "OD1" <-> "OD2" Residue "A GLU 590": "OE1" <-> "OE2" Residue "A GLU 623": "OE1" <-> "OE2" Residue "A PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 697": "OE1" <-> "OE2" Residue "A GLU 698": "OE1" <-> "OE2" Residue "A GLU 701": "OE1" <-> "OE2" Residue "A ASP 735": "OD1" <-> "OD2" Residue "A GLU 763": "OE1" <-> "OE2" Residue "A ASP 768": "OD1" <-> "OD2" Residue "A ASP 807": "OD1" <-> "OD2" Residue "A TYR 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 854": "OE1" <-> "OE2" Residue "A TYR 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 909": "OD1" <-> "OD2" Residue "A GLU 915": "OE1" <-> "OE2" Residue "A PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 932": "OE1" <-> "OE2" Residue "A GLU 947": "OE1" <-> "OE2" Residue "A GLU 997": "OE1" <-> "OE2" Residue "A PHE 1002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1007": "OE1" <-> "OE2" Residue "A TYR 1008": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1010": "OE1" <-> "OE2" Residue "A PHE 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1020": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1362": "OE1" <-> "OE2" Residue "A PHE 1364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1365": "OE1" <-> "OE2" Residue "A TYR 1368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1402": "OE1" <-> "OE2" Residue "A PHE 1421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1508": "NH1" <-> "NH2" Residue "A TYR 1525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1565": "OE1" <-> "OE2" Residue "A ASP 1571": "OD1" <-> "OD2" Residue "A PHE 1572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1605": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13294 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 2937 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 20, 'TRANS': 372} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 80 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 1309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1309 Classifications: {'RNA': 61} Modifications used: {'p5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 5, 'rna3p': 6, 'rna3p_pur': 21, 'rna3p_pyr': 20} Link IDs: {'rna2p': 13, 'rna3p': 47} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 9015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 9015 Classifications: {'peptide': 1183} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 42, 'TRANS': 1140} Chain breaks: 14 Unresolved non-hydrogen bonds: 482 Unresolved non-hydrogen angles: 588 Unresolved non-hydrogen dihedrals: 401 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 4, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 32, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 301 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.02, per 1000 atoms: 0.60 Number of scatterers: 13294 At special positions: 0 Unit cell: (109.714, 122.718, 142.222, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 37 16.00 P 64 15.00 Mg 1 11.99 O 2723 8.00 N 2265 7.00 C 8204 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: 6.62 Conformation dependent library (CDL) restraints added in 2.4 seconds 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2982 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 4 sheets defined 61.7% alpha, 6.1% beta 21 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 7.22 Creating SS restraints... Processing helix chain 'C' and resid 25 through 39 Processing helix chain 'C' and resid 47 through 50 No H-bonds generated for 'chain 'C' and resid 47 through 50' Processing helix chain 'C' and resid 54 through 59 Processing helix chain 'C' and resid 86 through 98 removed outlier: 3.518A pdb=" N VAL C 89 " --> pdb=" O ALA C 86 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LYS C 90 " --> pdb=" O ASP C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 125 Processing helix chain 'C' and resid 144 through 161 removed outlier: 3.694A pdb=" N TYR C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 180 Processing helix chain 'C' and resid 183 through 199 removed outlier: 4.167A pdb=" N LYS C 188 " --> pdb=" O GLU C 184 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE C 189 " --> pdb=" O TRP C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'A' and resid 4 through 14 Processing helix chain 'A' and resid 18 through 33 Processing helix chain 'A' and resid 41 through 47 removed outlier: 4.048A pdb=" N TYR A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 87 Processing helix chain 'A' and resid 105 through 124 Processing helix chain 'A' and resid 127 through 139 Proline residue: A 135 - end of helix removed outlier: 4.779A pdb=" N LYS A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 154 removed outlier: 3.744A pdb=" N ASN A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 190 through 204 removed outlier: 4.506A pdb=" N LEU A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Proline residue: A 196 - end of helix Processing helix chain 'A' and resid 230 through 243 removed outlier: 3.981A pdb=" N GLU A 234 " --> pdb=" O LYS A 230 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N THR A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LYS A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 266 Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 294 through 309 Processing helix chain 'A' and resid 318 through 338 Processing helix chain 'A' and resid 389 through 410 Processing helix chain 'A' and resid 413 through 427 Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'A' and resid 445 through 465 removed outlier: 4.135A pdb=" N GLN A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) Proline residue: A 460 - end of helix removed outlier: 3.568A pdb=" N LEU A 465 " --> pdb=" O HIS A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 478 removed outlier: 3.570A pdb=" N LYS A 471 " --> pdb=" O PRO A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 488 No H-bonds generated for 'chain 'A' and resid 485 through 488' Processing helix chain 'A' and resid 492 through 498 Processing helix chain 'A' and resid 502 through 546 removed outlier: 3.867A pdb=" N CYS A 509 " --> pdb=" O GLN A 505 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS A 510 " --> pdb=" O VAL A 506 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ASP A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N SER A 512 " --> pdb=" O SER A 508 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN A 546 " --> pdb=" O ALA A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 606 removed outlier: 3.670A pdb=" N ARG A 578 " --> pdb=" O TYR A 574 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 638 removed outlier: 3.937A pdb=" N THR A 631 " --> pdb=" O LYS A 627 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) Proline residue: A 634 - end of helix Processing helix chain 'A' and resid 642 through 654 removed outlier: 3.960A pdb=" N SER A 650 " --> pdb=" O THR A 646 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 651 " --> pdb=" O ARG A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 706 removed outlier: 4.020A pdb=" N VAL A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N SER A 669 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU A 670 " --> pdb=" O ASP A 666 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYS A 671 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N SER A 672 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLY A 673 " --> pdb=" O SER A 669 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 719 removed outlier: 3.985A pdb=" N GLN A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 728 Processing helix chain 'A' and resid 730 through 740 Processing helix chain 'A' and resid 742 through 749 Processing helix chain 'A' and resid 752 through 758 removed outlier: 3.944A pdb=" N GLN A 757 " --> pdb=" O GLU A 753 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 758 " --> pdb=" O VAL A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 769 No H-bonds generated for 'chain 'A' and resid 767 through 769' Processing helix chain 'A' and resid 780 through 805 Processing helix chain 'A' and resid 822 through 843 Processing helix chain 'A' and resid 849 through 862 Proline residue: A 861 - end of helix Processing helix chain 'A' and resid 885 through 896 Processing helix chain 'A' and resid 910 through 925 Processing helix chain 'A' and resid 935 through 954 removed outlier: 4.339A pdb=" N GLY A 954 " --> pdb=" O LYS A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 977 Processing helix chain 'A' and resid 984 through 1012 Processing helix chain 'A' and resid 1020 through 1038 Processing helix chain 'A' and resid 1242 through 1258 Proline residue: A1257 - end of helix Processing helix chain 'A' and resid 1277 through 1287 Processing helix chain 'A' and resid 1297 through 1311 Processing helix chain 'A' and resid 1328 through 1348 Processing helix chain 'A' and resid 1355 through 1368 Processing helix chain 'A' and resid 1389 through 1408 Processing helix chain 'A' and resid 1412 through 1420 Processing helix chain 'A' and resid 1425 through 1439 Proline residue: A1434 - end of helix Processing helix chain 'A' and resid 1501 through 1510 removed outlier: 3.593A pdb=" N PHE A1505 " --> pdb=" O ILE A1501 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N HIS A1509 " --> pdb=" O PHE A1505 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LYS A1510 " --> pdb=" O GLU A1506 " (cutoff:3.500A) Processing helix chain 'A' and resid 1517 through 1527 Processing helix chain 'A' and resid 1533 through 1553 Proline residue: A1548 - end of helix removed outlier: 4.510A pdb=" N LYS A1552 " --> pdb=" O PRO A1548 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A1553 " --> pdb=" O HIS A1549 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1564 No H-bonds generated for 'chain 'A' and resid 1561 through 1564' Processing helix chain 'A' and resid 1569 through 1617 removed outlier: 3.669A pdb=" N ASP A1582 " --> pdb=" O ARG A1578 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU A1583 " --> pdb=" O ILE A1579 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER A1584 " --> pdb=" O ILE A1580 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LYS A1585 " --> pdb=" O ASN A1581 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A1602 " --> pdb=" O ARG A1598 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 170 through 172 removed outlier: 9.163A pdb=" N VAL C 171 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL C 133 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA C 102 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N PHE C 134 " --> pdb=" O ALA C 102 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU C 104 " --> pdb=" O PHE C 134 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASN C 136 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL C 106 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 212 through 214 Processing sheet with id= C, first strand: chain 'C' and resid 217 through 221 removed outlier: 3.647A pdb=" N ASP C 217 " --> pdb=" O THR C 229 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR C 226 " --> pdb=" O LEU C 279 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 340 through 343 removed outlier: 6.464A pdb=" N GLU C 308 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N VAL C 389 " --> pdb=" O GLU C 308 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TYR C 310 " --> pdb=" O GLY C 387 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLY C 387 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE C 377 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ALA C 386 " --> pdb=" O PHE C 375 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N PHE C 375 " --> pdb=" O ALA C 386 " (cutoff:3.500A) 710 hydrogen bonds defined for protein. 2079 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 56 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 5.31 Time building geometry restraints manager: 6.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2100 1.29 - 1.42: 3513 1.42 - 1.55: 7846 1.55 - 1.68: 130 1.68 - 1.81: 64 Bond restraints: 13653 Sorted by residual: bond pdb=" C4 5MU B 54 " pdb=" C5 5MU B 54 " ideal model delta sigma weight residual 1.802 1.447 0.355 2.00e-02 2.50e+03 3.15e+02 bond pdb=" N1 5MU B 54 " pdb=" C6 5MU B 54 " ideal model delta sigma weight residual 1.635 1.371 0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" N3 5MU B 54 " pdb=" C4 5MU B 54 " ideal model delta sigma weight residual 1.182 1.378 -0.196 2.00e-02 2.50e+03 9.63e+01 bond pdb=" C5 5MU B 54 " pdb=" C6 5MU B 54 " ideal model delta sigma weight residual 1.155 1.342 -0.187 2.00e-02 2.50e+03 8.77e+01 bond pdb=" CG PRO A1295 " pdb=" CD PRO A1295 " ideal model delta sigma weight residual 1.503 1.279 0.224 3.40e-02 8.65e+02 4.33e+01 ... (remaining 13648 not shown) Histogram of bond angle deviations from ideal: 89.39 - 99.85: 5 99.85 - 110.31: 3353 110.31 - 120.77: 11379 120.77 - 131.23: 4030 131.23 - 141.68: 33 Bond angle restraints: 18800 Sorted by residual: angle pdb=" CA PRO A1295 " pdb=" N PRO A1295 " pdb=" CD PRO A1295 " ideal model delta sigma weight residual 112.00 94.51 17.49 1.40e+00 5.10e-01 1.56e+02 angle pdb=" N PRO A1295 " pdb=" CD PRO A1295 " pdb=" CG PRO A1295 " ideal model delta sigma weight residual 103.20 89.39 13.81 1.50e+00 4.44e-01 8.47e+01 angle pdb=" C6 5MU B 54 " pdb=" C5 5MU B 54 " pdb=" C5M 5MU B 54 " ideal model delta sigma weight residual 106.09 123.13 -17.04 3.00e+00 1.11e-01 3.23e+01 angle pdb=" CA PRO A1295 " pdb=" CB PRO A1295 " pdb=" CG PRO A1295 " ideal model delta sigma weight residual 104.50 94.99 9.51 1.90e+00 2.77e-01 2.51e+01 angle pdb=" N3 5MU B 54 " pdb=" C4 5MU B 54 " pdb=" O4 5MU B 54 " ideal model delta sigma weight residual 107.56 120.41 -12.85 3.00e+00 1.11e-01 1.84e+01 ... (remaining 18795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 7865 35.09 - 70.18: 395 70.18 - 105.27: 50 105.27 - 140.36: 2 140.36 - 175.45: 5 Dihedral angle restraints: 8317 sinusoidal: 3721 harmonic: 4596 Sorted by residual: dihedral pdb=" O4' C B 17 " pdb=" C1' C B 17 " pdb=" N1 C B 17 " pdb=" C2 C B 17 " ideal model delta sinusoidal sigma weight residual 232.00 56.55 175.45 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' C B 75 " pdb=" C1' C B 75 " pdb=" N1 C B 75 " pdb=" C2 C B 75 " ideal model delta sinusoidal sigma weight residual 232.00 71.64 160.36 1 1.70e+01 3.46e-03 6.45e+01 dihedral pdb=" C8 GTP C 402 " pdb=" C1* GTP C 402 " pdb=" N9 GTP C 402 " pdb=" O4* GTP C 402 " ideal model delta sinusoidal sigma weight residual 104.59 -55.45 160.05 1 2.00e+01 2.50e-03 4.66e+01 ... (remaining 8314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2027 0.068 - 0.136: 180 0.136 - 0.204: 5 0.204 - 0.271: 2 0.271 - 0.339: 1 Chirality restraints: 2215 Sorted by residual: chirality pdb=" CA PRO A1295 " pdb=" N PRO A1295 " pdb=" C PRO A1295 " pdb=" CB PRO A1295 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C1' C B 74 " pdb=" O4' C B 74 " pdb=" C2' C B 74 " pdb=" N1 C B 74 " both_signs ideal model delta sigma weight residual False 2.47 2.23 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C3' G B 70 " pdb=" C4' G B 70 " pdb=" O3' G B 70 " pdb=" C2' G B 70 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2212 not shown) Planarity restraints: 2185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MU B 54 " 0.025 2.00e-02 2.50e+03 5.55e-01 6.93e+03 pdb=" C4' 5MU B 54 " 0.431 2.00e-02 2.50e+03 pdb=" O4' 5MU B 54 " 0.599 2.00e-02 2.50e+03 pdb=" C3' 5MU B 54 " -0.584 2.00e-02 2.50e+03 pdb=" O3' 5MU B 54 " -0.547 2.00e-02 2.50e+03 pdb=" C2' 5MU B 54 " -0.217 2.00e-02 2.50e+03 pdb=" O2' 5MU B 54 " 0.892 2.00e-02 2.50e+03 pdb=" C1' 5MU B 54 " 0.232 2.00e-02 2.50e+03 pdb=" N1 5MU B 54 " -0.831 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' H2U B 20 " -0.027 2.00e-02 2.50e+03 5.29e-01 6.29e+03 pdb=" C4' H2U B 20 " -0.418 2.00e-02 2.50e+03 pdb=" O4' H2U B 20 " -0.529 2.00e-02 2.50e+03 pdb=" C3' H2U B 20 " 0.578 2.00e-02 2.50e+03 pdb=" O3' H2U B 20 " 0.513 2.00e-02 2.50e+03 pdb=" C2' H2U B 20 " 0.224 2.00e-02 2.50e+03 pdb=" O2' H2U B 20 " -0.871 2.00e-02 2.50e+03 pdb=" C1' H2U B 20 " -0.241 2.00e-02 2.50e+03 pdb=" N1 H2U B 20 " 0.772 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' H2U B 16 " 0.006 2.00e-02 2.50e+03 5.12e-01 5.89e+03 pdb=" C4' H2U B 16 " -0.409 2.00e-02 2.50e+03 pdb=" O4' H2U B 16 " -0.556 2.00e-02 2.50e+03 pdb=" C3' H2U B 16 " 0.581 2.00e-02 2.50e+03 pdb=" O3' H2U B 16 " 0.445 2.00e-02 2.50e+03 pdb=" C2' H2U B 16 " 0.251 2.00e-02 2.50e+03 pdb=" O2' H2U B 16 " -0.811 2.00e-02 2.50e+03 pdb=" C1' H2U B 16 " -0.254 2.00e-02 2.50e+03 pdb=" N1 H2U B 16 " 0.748 2.00e-02 2.50e+03 ... (remaining 2182 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 122 2.55 - 3.14: 10226 3.14 - 3.73: 22876 3.73 - 4.31: 30549 4.31 - 4.90: 49051 Nonbonded interactions: 112824 Sorted by model distance: nonbonded pdb="MG MG C 401 " pdb=" O2B GTP C 402 " model vdw 1.966 2.170 nonbonded pdb=" OG1 THR C 26 " pdb="MG MG C 401 " model vdw 2.037 2.170 nonbonded pdb=" OG1 THR C 62 " pdb="MG MG C 401 " model vdw 2.062 2.170 nonbonded pdb="MG MG C 401 " pdb=" O1G GTP C 402 " model vdw 2.068 2.170 nonbonded pdb=" O SER A 253 " pdb=" OG SER A 256 " model vdw 2.149 2.440 ... (remaining 112819 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: 8.660 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: 22.290 Check model and map are aligned: 0.190 Set scattering table: 0.140 Process input model: 45.670 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 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:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 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 : 0.006 0.355 13653 Z= 0.378 Angle : 0.650 17.492 18800 Z= 0.317 Chirality : 0.039 0.339 2215 Planarity : 0.021 0.555 2185 Dihedral : 19.927 175.454 5335 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.11 % Favored : 96.83 % Rotamer: Outliers : 4.62 % Allowed : 19.22 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.82 (0.22), residues: 1544 helix: 2.23 (0.17), residues: 990 sheet: -0.59 (0.45), residues: 121 loop : -0.66 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 498 HIS 0.008 0.001 HIS A 124 PHE 0.012 0.001 PHE A 526 TYR 0.011 0.001 TYR A 466 ARG 0.008 0.000 ARG A1003 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 66 time to evaluate : 1.551 Fit side-chains outliers start: 57 outliers final: 46 residues processed: 119 average time/residue: 0.8445 time to fit residues: 115.7850 Evaluate side-chains 110 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 64 time to evaluate : 1.541 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 44 residues processed: 2 average time/residue: 0.1189 time to fit residues: 2.4912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.0970 chunk 123 optimal weight: 20.0000 chunk 68 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 160 GLN C 252 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.0641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 13653 Z= 0.390 Angle : 0.778 17.955 18800 Z= 0.418 Chirality : 0.043 0.268 2215 Planarity : 0.006 0.142 2185 Dihedral : 18.214 179.025 2605 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.63 % Favored : 96.24 % Rotamer: Outliers : 6.41 % Allowed : 17.52 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.80 (0.22), residues: 1544 helix: 2.18 (0.16), residues: 992 sheet: -0.43 (0.47), residues: 110 loop : -0.65 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 438 HIS 0.010 0.001 HIS A 113 PHE 0.021 0.002 PHE A 599 TYR 0.018 0.002 TYR A 815 ARG 0.003 0.000 ARG C 378 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 66 time to evaluate : 1.439 Fit side-chains outliers start: 79 outliers final: 53 residues processed: 134 average time/residue: 0.8830 time to fit residues: 135.4954 Evaluate side-chains 119 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 66 time to evaluate : 1.499 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 48 residues processed: 5 average time/residue: 0.3431 time to fit residues: 4.2843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 123 optimal weight: 20.0000 chunk 100 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 160 optimal weight: 0.6980 chunk 132 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 160 GLN C 252 GLN A 323 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.0643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13653 Z= 0.308 Angle : 0.734 16.894 18800 Z= 0.400 Chirality : 0.041 0.236 2215 Planarity : 0.006 0.136 2185 Dihedral : 18.146 178.358 2605 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.57 % Rotamer: Outliers : 6.89 % Allowed : 16.95 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.85 (0.22), residues: 1544 helix: 2.23 (0.16), residues: 990 sheet: -0.41 (0.47), residues: 110 loop : -0.67 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 438 HIS 0.010 0.001 HIS A 113 PHE 0.016 0.002 PHE A 599 TYR 0.016 0.002 TYR A 838 ARG 0.002 0.000 ARG C 378 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 69 time to evaluate : 1.466 Fit side-chains outliers start: 85 outliers final: 54 residues processed: 144 average time/residue: 0.9030 time to fit residues: 148.6984 Evaluate side-chains 120 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 66 time to evaluate : 1.481 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 50 residues processed: 4 average time/residue: 0.3953 time to fit residues: 3.8608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 0.8980 chunk 111 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 chunk 99 optimal weight: 0.0020 chunk 148 optimal weight: 0.9990 chunk 157 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.0546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13653 Z= 0.161 Angle : 0.673 12.418 18800 Z= 0.376 Chirality : 0.038 0.223 2215 Planarity : 0.006 0.122 2185 Dihedral : 18.100 178.339 2605 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.11 % Favored : 96.83 % Rotamer: Outliers : 5.92 % Allowed : 18.73 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 2.00 (0.22), residues: 1544 helix: 2.43 (0.17), residues: 990 sheet: -0.57 (0.45), residues: 121 loop : -0.75 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 498 HIS 0.008 0.001 HIS A 113 PHE 0.011 0.001 PHE A 526 TYR 0.014 0.001 TYR A 838 ARG 0.002 0.000 ARG A1003 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 67 time to evaluate : 1.581 Fit side-chains outliers start: 73 outliers final: 51 residues processed: 132 average time/residue: 0.8526 time to fit residues: 129.6914 Evaluate side-chains 116 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 65 time to evaluate : 1.587 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 48 residues processed: 3 average time/residue: 0.2387 time to fit residues: 2.9992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 160 GLN C 252 GLN A 675 ASN A 679 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.101 13653 Z= 0.504 Angle : 0.803 17.982 18800 Z= 0.430 Chirality : 0.046 0.255 2215 Planarity : 0.006 0.146 2185 Dihedral : 18.231 179.501 2605 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.95 % Favored : 95.92 % Rotamer: Outliers : 6.08 % Allowed : 18.57 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.69 (0.22), residues: 1544 helix: 2.11 (0.16), residues: 991 sheet: -0.51 (0.47), residues: 112 loop : -0.73 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 438 HIS 0.012 0.001 HIS A 113 PHE 0.026 0.002 PHE A 599 TYR 0.019 0.002 TYR A 198 ARG 0.004 0.000 ARG C 378 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 66 time to evaluate : 1.470 Fit side-chains outliers start: 75 outliers final: 51 residues processed: 132 average time/residue: 0.9495 time to fit residues: 142.9668 Evaluate side-chains 118 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 67 time to evaluate : 1.362 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 48 residues processed: 3 average time/residue: 0.5097 time to fit residues: 3.8664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 0.5980 chunk 141 optimal weight: 20.0000 chunk 31 optimal weight: 0.0770 chunk 92 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 157 optimal weight: 0.5980 chunk 130 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 GLN C 252 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.0711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13653 Z= 0.168 Angle : 0.686 12.279 18800 Z= 0.380 Chirality : 0.038 0.226 2215 Planarity : 0.006 0.124 2185 Dihedral : 18.025 179.717 2605 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.85 % Favored : 97.02 % Rotamer: Outliers : 5.27 % Allowed : 19.63 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.98 (0.22), residues: 1544 helix: 2.42 (0.16), residues: 986 sheet: -0.60 (0.46), residues: 119 loop : -0.73 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 498 HIS 0.008 0.001 HIS A 113 PHE 0.013 0.001 PHE A 820 TYR 0.016 0.001 TYR A 198 ARG 0.002 0.000 ARG C 378 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 69 time to evaluate : 1.407 Fit side-chains outliers start: 65 outliers final: 48 residues processed: 129 average time/residue: 0.9027 time to fit residues: 133.2192 Evaluate side-chains 112 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 64 time to evaluate : 1.464 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 46 residues processed: 2 average time/residue: 0.2180 time to fit residues: 2.5979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 157 optimal weight: 0.0570 chunk 98 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 GLN C 252 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13653 Z= 0.205 Angle : 0.702 13.490 18800 Z= 0.384 Chirality : 0.039 0.227 2215 Planarity : 0.006 0.126 2185 Dihedral : 17.907 177.557 2605 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.37 % Favored : 96.50 % Rotamer: Outliers : 4.87 % Allowed : 20.11 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 2.00 (0.22), residues: 1544 helix: 2.45 (0.16), residues: 989 sheet: -0.59 (0.45), residues: 119 loop : -0.77 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 438 HIS 0.008 0.001 HIS A 113 PHE 0.013 0.001 PHE A 599 TYR 0.016 0.001 TYR A 838 ARG 0.001 0.000 ARG C 378 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 68 time to evaluate : 1.356 Fit side-chains outliers start: 60 outliers final: 47 residues processed: 125 average time/residue: 0.9701 time to fit residues: 137.5248 Evaluate side-chains 112 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 65 time to evaluate : 1.598 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 47 residues processed: 1 average time/residue: 0.2973 time to fit residues: 2.4871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 0.0020 chunk 107 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 123 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 GLN C 252 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 13653 Z= 0.334 Angle : 0.748 12.909 18800 Z= 0.404 Chirality : 0.042 0.238 2215 Planarity : 0.006 0.132 2185 Dihedral : 17.990 179.581 2605 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.69 % Favored : 96.18 % Rotamer: Outliers : 5.03 % Allowed : 19.63 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.94 (0.22), residues: 1544 helix: 2.35 (0.16), residues: 986 sheet: -0.39 (0.47), residues: 110 loop : -0.71 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 438 HIS 0.010 0.001 HIS A 113 PHE 0.019 0.002 PHE A 599 TYR 0.018 0.002 TYR A 838 ARG 0.004 0.000 ARG A1003 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 65 time to evaluate : 1.536 Fit side-chains outliers start: 62 outliers final: 51 residues processed: 120 average time/residue: 0.9843 time to fit residues: 134.2444 Evaluate side-chains 117 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 66 time to evaluate : 1.572 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 47 residues processed: 4 average time/residue: 0.4015 time to fit residues: 4.1184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.0770 chunk 146 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 114 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 138 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 GLN C 252 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13653 Z= 0.282 Angle : 0.722 12.711 18800 Z= 0.394 Chirality : 0.041 0.232 2215 Planarity : 0.006 0.130 2185 Dihedral : 17.947 179.328 2605 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.56 % Favored : 96.31 % Rotamer: Outliers : 4.54 % Allowed : 20.03 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.97 (0.22), residues: 1544 helix: 2.40 (0.16), residues: 982 sheet: -0.39 (0.47), residues: 110 loop : -0.75 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 438 HIS 0.010 0.001 HIS A 113 PHE 0.016 0.002 PHE A 599 TYR 0.017 0.001 TYR A 838 ARG 0.004 0.000 ARG A1003 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 65 time to evaluate : 1.367 Fit side-chains outliers start: 56 outliers final: 50 residues processed: 119 average time/residue: 0.9960 time to fit residues: 134.4885 Evaluate side-chains 115 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 65 time to evaluate : 1.523 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 49 residues processed: 1 average time/residue: 0.1239 time to fit residues: 2.2332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 129 optimal weight: 20.0000 chunk 13 optimal weight: 0.5980 chunk 99 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 GLN C 252 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13653 Z= 0.238 Angle : 0.712 12.514 18800 Z= 0.388 Chirality : 0.040 0.227 2215 Planarity : 0.006 0.128 2185 Dihedral : 17.904 178.302 2605 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.24 % Favored : 96.63 % Rotamer: Outliers : 4.38 % Allowed : 20.36 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 2.00 (0.22), residues: 1544 helix: 2.47 (0.16), residues: 980 sheet: -0.55 (0.45), residues: 119 loop : -0.80 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 438 HIS 0.009 0.001 HIS A 113 PHE 0.014 0.001 PHE A 599 TYR 0.017 0.001 TYR A 838 ARG 0.005 0.000 ARG A1003 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 65 time to evaluate : 1.687 Fit side-chains outliers start: 54 outliers final: 49 residues processed: 118 average time/residue: 1.0058 time to fit residues: 135.0811 Evaluate side-chains 114 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 65 time to evaluate : 1.465 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 49 residues processed: 0 time to fit residues: 2.0013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 129 optimal weight: 30.0000 chunk 54 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 16 optimal weight: 0.0670 chunk 23 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 GLN C 252 GLN A 995 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.119521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.090088 restraints weight = 22344.324| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.41 r_work: 0.2847 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13653 Z= 0.203 Angle : 0.693 12.442 18800 Z= 0.382 Chirality : 0.039 0.225 2215 Planarity : 0.006 0.126 2185 Dihedral : 17.849 177.890 2605 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.24 % Favored : 96.63 % Rotamer: Outliers : 4.38 % Allowed : 20.36 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 2.04 (0.22), residues: 1544 helix: 2.48 (0.16), residues: 986 sheet: -0.54 (0.45), residues: 119 loop : -0.77 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 498 HIS 0.009 0.001 HIS A 113 PHE 0.013 0.001 PHE A 599 TYR 0.015 0.001 TYR A 838 ARG 0.003 0.000 ARG A1003 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3701.34 seconds wall clock time: 68 minutes 21.59 seconds (4101.59 seconds total)