Starting phenix.real_space_refine on Sat Mar 16 01:07:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qfs_18383/03_2024/8qfs_18383_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qfs_18383/03_2024/8qfs_18383.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qfs_18383/03_2024/8qfs_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_18383/03_2024/8qfs_18383_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qfs_18383/03_2024/8qfs_18383_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qfs_18383/03_2024/8qfs_18383.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qfs_18383/03_2024/8qfs_18383.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qfs_18383/03_2024/8qfs_18383_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qfs_18383/03_2024/8qfs_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-dev-5265/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: 8.16, per 1000 atoms: 0.61 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: 6.01 Conformation dependent library (CDL) restraints added in 2.0 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: 7.37 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: 5.32 Time building geometry restraints manager: 6.44 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: 7882 35.09 - 70.18: 406 70.18 - 105.27: 50 105.27 - 140.36: 2 140.36 - 175.45: 5 Dihedral angle restraints: 8345 sinusoidal: 3749 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 8342 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: 6.820 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: 0.010 Extract box with map and model: 22.050 Check model and map are aligned: 0.210 Set scattering table: 0.150 Process input model: 44.520 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:13.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.320 ------------------------------------------------------------------------------- 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 : 20.053 175.454 5363 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 : 1.492 Fit side-chains REVERT: A 1535 ASN cc_start: 0.7974 (OUTLIER) cc_final: 0.7737 (p0) outliers start: 57 outliers final: 46 residues processed: 119 average time/residue: 0.8510 time to fit residues: 116.5725 Evaluate side-chains 111 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 64 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 391 LYS Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 804 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1254 TYR Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1402 GLU Chi-restraints excluded: chain A residue 1406 SER Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1535 ASN Chi-restraints excluded: chain A residue 1604 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 8.9990 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: 10.0000 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 95 optimal weight: 0.0770 chunk 148 optimal weight: 5.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- 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: 0.8754 moved from start: 0.0633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 13653 Z= 0.388 Angle : 0.779 17.787 18800 Z= 0.418 Chirality : 0.043 0.264 2215 Planarity : 0.006 0.143 2185 Dihedral : 18.999 179.283 2707 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.63 % Favored : 96.24 % Rotamer: Outliers : 4.95 % Allowed : 18.65 % Favored : 76.40 % 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: 1.78 (0.22), residues: 1544 helix: 2.15 (0.16), residues: 996 sheet: -0.41 (0.46), residues: 112 loop : -0.67 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 438 HIS 0.011 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 127 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 66 time to evaluate : 1.252 Fit side-chains REVERT: C 231 ARG cc_start: 0.9323 (OUTLIER) cc_final: 0.7473 (ttm170) REVERT: A 1421 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.7779 (p90) outliers start: 61 outliers final: 35 residues processed: 117 average time/residue: 0.9137 time to fit residues: 122.1152 Evaluate side-chains 102 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 65 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1254 TYR Chi-restraints excluded: chain A residue 1406 SER Chi-restraints excluded: chain A residue 1421 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1511 ILE Chi-restraints excluded: chain A residue 1535 ASN 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: 2.9990 chunk 123 optimal weight: 20.0000 chunk 100 optimal weight: 0.0970 chunk 40 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 147 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 A 679 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 13653 Z= 0.469 Angle : 0.811 20.747 18800 Z= 0.435 Chirality : 0.045 0.251 2215 Planarity : 0.006 0.144 2185 Dihedral : 18.859 179.736 2676 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.69 % Favored : 96.18 % Rotamer: Outliers : 5.68 % Allowed : 17.84 % Favored : 76.48 % 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: 1.61 (0.22), residues: 1544 helix: 2.03 (0.16), residues: 990 sheet: -0.37 (0.47), residues: 112 loop : -0.77 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 438 HIS 0.012 0.001 HIS A 113 PHE 0.023 0.002 PHE A 599 TYR 0.020 0.002 TYR A 815 ARG 0.004 0.000 ARG C 231 *********************** 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 139 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 69 time to evaluate : 1.507 Fit side-chains REVERT: C 209 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8471 (mmtp) REVERT: C 231 ARG cc_start: 0.9347 (OUTLIER) cc_final: 0.7543 (ttm170) REVERT: A 144 MET cc_start: 0.9502 (mmp) cc_final: 0.9286 (mmm) REVERT: A 987 THR cc_start: 0.6119 (OUTLIER) cc_final: 0.5906 (p) REVERT: A 1358 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8096 (ptp-110) REVERT: A 1421 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.7963 (p90) REVERT: A 1613 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8496 (t0) outliers start: 70 outliers final: 36 residues processed: 128 average time/residue: 0.9563 time to fit residues: 138.5241 Evaluate side-chains 106 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 64 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1358 ARG Chi-restraints excluded: chain A residue 1421 PHE Chi-restraints excluded: chain A residue 1511 ILE Chi-restraints excluded: chain A residue 1613 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 148 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 141 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 A 675 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.0683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13653 Z= 0.196 Angle : 0.690 12.332 18800 Z= 0.383 Chirality : 0.039 0.228 2215 Planarity : 0.006 0.125 2185 Dihedral : 18.563 178.406 2667 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.37 % Favored : 96.50 % Rotamer: Outliers : 4.30 % Allowed : 19.38 % Favored : 76.32 % 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: 1.93 (0.22), residues: 1544 helix: 2.38 (0.16), residues: 985 sheet: -0.54 (0.45), residues: 121 loop : -0.77 (0.31), residues: 438 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 0.011 0.001 PHE A 820 TYR 0.015 0.001 TYR A 838 ARG 0.002 0.000 ARG C 378 *********************** 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 118 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 65 time to evaluate : 1.694 Fit side-chains REVERT: C 124 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.7513 (ttm-80) REVERT: C 209 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8441 (mmtp) REVERT: A 144 MET cc_start: 0.9480 (mmp) cc_final: 0.9269 (mmm) REVERT: A 865 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.7693 (tmm) REVERT: A 987 THR cc_start: 0.6302 (OUTLIER) cc_final: 0.6097 (p) REVERT: A 1358 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7919 (ptp-110) REVERT: A 1421 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.7885 (p90) outliers start: 53 outliers final: 25 residues processed: 113 average time/residue: 0.9322 time to fit residues: 119.8116 Evaluate side-chains 95 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 64 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 865 MET Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1358 ARG Chi-restraints excluded: chain A residue 1421 PHE Chi-restraints excluded: chain A residue 1423 THR 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: 3.9990 chunk 2 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 108 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 141 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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: 0.8759 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 13653 Z= 0.383 Angle : 0.751 14.337 18800 Z= 0.408 Chirality : 0.043 0.243 2215 Planarity : 0.006 0.139 2185 Dihedral : 18.549 179.188 2650 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.08 % Favored : 95.79 % Rotamer: Outliers : 4.62 % Allowed : 19.46 % Favored : 75.91 % 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: 1.84 (0.22), residues: 1544 helix: 2.24 (0.16), residues: 989 sheet: -0.35 (0.46), residues: 112 loop : -0.70 (0.31), residues: 443 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 0.019 0.002 TYR A 838 ARG 0.003 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 122 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 65 time to evaluate : 1.607 Fit side-chains REVERT: C 124 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.7536 (ttm-80) REVERT: C 209 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8436 (mmtp) REVERT: A 144 MET cc_start: 0.9486 (mmp) cc_final: 0.9265 (mmm) REVERT: A 865 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.7600 (tmm) REVERT: A 987 THR cc_start: 0.6263 (OUTLIER) cc_final: 0.6056 (p) REVERT: A 1358 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7979 (ptp-110) REVERT: A 1421 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.7943 (p90) outliers start: 57 outliers final: 33 residues processed: 114 average time/residue: 0.9581 time to fit residues: 124.5833 Evaluate side-chains 104 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 65 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 865 MET Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1358 ARG Chi-restraints excluded: chain A residue 1421 PHE Chi-restraints excluded: chain A residue 1511 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 130 optimal weight: 30.0000 chunk 73 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8719 moved from start: 0.0788 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= 0.221 Angle : 0.704 12.542 18800 Z= 0.385 Chirality : 0.039 0.227 2215 Planarity : 0.006 0.128 2185 Dihedral : 18.387 179.663 2648 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.17 % Favored : 96.70 % Rotamer: Outliers : 4.22 % Allowed : 20.03 % Favored : 75.75 % 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: 2.40 (0.16), residues: 985 sheet: -0.38 (0.46), residues: 112 loop : -0.70 (0.31), residues: 447 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 0.013 0.001 PHE A 599 TYR 0.015 0.001 TYR A 838 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 118 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 66 time to evaluate : 1.414 Fit side-chains REVERT: C 124 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.7513 (ttm-80) REVERT: C 209 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8433 (mmtp) REVERT: A 144 MET cc_start: 0.9478 (mmp) cc_final: 0.9262 (mmm) REVERT: A 865 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.7764 (tmm) REVERT: A 1358 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7949 (ptp-110) REVERT: A 1421 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.7900 (p90) outliers start: 52 outliers final: 32 residues processed: 114 average time/residue: 0.9656 time to fit residues: 124.5780 Evaluate side-chains 104 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 67 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 865 MET Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1254 TYR Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1358 ARG Chi-restraints excluded: chain A residue 1421 PHE Chi-restraints excluded: chain A residue 1423 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 88 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 97 optimal weight: 0.3980 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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: 0.8760 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 : 0.006 0.077 13653 Z= 0.395 Angle : 0.765 14.380 18800 Z= 0.412 Chirality : 0.043 0.243 2215 Planarity : 0.006 0.138 2185 Dihedral : 18.474 179.098 2647 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.08 % Favored : 95.79 % Rotamer: Outliers : 4.54 % Allowed : 20.19 % 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: 1.85 (0.22), residues: 1544 helix: 2.25 (0.16), residues: 987 sheet: -0.36 (0.46), residues: 112 loop : -0.71 (0.30), residues: 445 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 0.022 0.002 PHE A 599 TYR 0.019 0.002 TYR A 838 ARG 0.003 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 125 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 69 time to evaluate : 1.368 Fit side-chains REVERT: C 124 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.7537 (ttm-80) REVERT: C 209 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8434 (mmtp) REVERT: A 144 MET cc_start: 0.9485 (mmp) cc_final: 0.9267 (mmm) REVERT: A 865 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.7716 (tmt) REVERT: A 1023 ASN cc_start: 0.8513 (m110) cc_final: 0.7809 (t0) REVERT: A 1358 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7972 (ptp-110) REVERT: A 1421 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.7965 (p90) outliers start: 56 outliers final: 36 residues processed: 118 average time/residue: 0.8990 time to fit residues: 121.2118 Evaluate side-chains 107 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 66 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 865 MET Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1358 ARG Chi-restraints excluded: chain A residue 1421 PHE Chi-restraints excluded: chain A residue 1511 ILE 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: 0.7980 chunk 47 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 0.0970 chunk 107 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 123 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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: 0.8715 moved from start: 0.0869 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= 0.209 Angle : 0.700 12.308 18800 Z= 0.384 Chirality : 0.039 0.226 2215 Planarity : 0.006 0.125 2185 Dihedral : 18.290 178.390 2647 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.17 % Favored : 96.70 % Rotamer: Outliers : 3.73 % Allowed : 20.76 % Favored : 75.51 % 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: 2.02 (0.22), residues: 1544 helix: 2.43 (0.16), residues: 984 sheet: -0.40 (0.46), residues: 112 loop : -0.71 (0.31), residues: 448 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 0.012 0.001 PHE A 599 TYR 0.016 0.001 TYR A 838 ARG 0.002 0.000 ARG C 378 *********************** 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 111 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 65 time to evaluate : 1.553 Fit side-chains REVERT: C 124 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.7530 (ttm-80) REVERT: C 209 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8439 (mmtp) REVERT: A 144 MET cc_start: 0.9460 (mmp) cc_final: 0.9249 (mmm) REVERT: A 865 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.7762 (tmm) REVERT: A 1358 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7930 (ptp-110) REVERT: A 1421 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.7829 (p90) outliers start: 46 outliers final: 34 residues processed: 107 average time/residue: 1.0070 time to fit residues: 123.1743 Evaluate side-chains 106 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 67 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 865 MET Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1258 VAL Chi-restraints excluded: chain A residue 1358 ARG Chi-restraints excluded: chain A residue 1421 PHE Chi-restraints excluded: chain A residue 1511 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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: 0.8763 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 13653 Z= 0.424 Angle : 0.774 14.843 18800 Z= 0.416 Chirality : 0.044 0.245 2215 Planarity : 0.006 0.136 2185 Dihedral : 18.426 179.292 2647 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.02 % Favored : 95.85 % Rotamer: Outliers : 4.22 % Allowed : 20.68 % 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: 1.84 (0.22), residues: 1544 helix: 2.24 (0.16), residues: 988 sheet: -0.35 (0.46), residues: 112 loop : -0.71 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 438 HIS 0.011 0.001 HIS A 113 PHE 0.023 0.002 PHE A 599 TYR 0.020 0.002 TYR A 815 ARG 0.004 0.000 ARG C 378 *********************** 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 120 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 68 time to evaluate : 1.544 Fit side-chains REVERT: C 124 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.7535 (ttm-80) REVERT: C 209 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8472 (mmtp) REVERT: A 144 MET cc_start: 0.9483 (mmp) cc_final: 0.9262 (mmm) REVERT: A 865 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.7673 (tmt) REVERT: A 1358 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7973 (ptp-110) REVERT: A 1421 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.7982 (p90) outliers start: 52 outliers final: 37 residues processed: 114 average time/residue: 0.9059 time to fit residues: 117.4850 Evaluate side-chains 109 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 67 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 865 MET Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1358 ARG Chi-restraints excluded: chain A residue 1421 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1511 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 129 optimal weight: 20.0000 chunk 13 optimal weight: 0.2980 chunk 99 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 999 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 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 : 0.003 0.042 13653 Z= 0.224 Angle : 0.704 12.496 18800 Z= 0.386 Chirality : 0.039 0.225 2215 Planarity : 0.006 0.127 2185 Dihedral : 18.297 178.487 2647 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.24 % Favored : 96.63 % Rotamer: Outliers : 3.41 % Allowed : 21.57 % 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: 1.94 (0.22), residues: 1544 helix: 2.39 (0.16), residues: 984 sheet: -0.55 (0.45), residues: 121 loop : -0.77 (0.31), 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 0.016 0.001 TYR A 838 ARG 0.002 0.000 ARG C 378 ********************** 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 108 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 66 time to evaluate : 1.567 Fit side-chains REVERT: C 124 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.7517 (ttm-80) REVERT: C 209 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8429 (mmtp) REVERT: A 144 MET cc_start: 0.9460 (mmp) cc_final: 0.9251 (mmm) REVERT: A 865 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.7762 (tmm) REVERT: A 1358 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7932 (ptp-110) REVERT: A 1421 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.7851 (p90) outliers start: 42 outliers final: 34 residues processed: 103 average time/residue: 1.0160 time to fit residues: 117.5444 Evaluate side-chains 105 residues out of total 1381 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 66 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 220 SER Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 306 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 687 GLN Chi-restraints excluded: chain A residue 706 LYS Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 865 MET Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1358 ARG Chi-restraints excluded: chain A residue 1421 PHE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1511 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.4980 chunk 39 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 129 optimal weight: 30.0000 chunk 54 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 999 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.118828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.087026 restraints weight = 22310.196| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.42 r_work: 0.2846 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13653 Z= 0.235 Angle : 0.705 12.578 18800 Z= 0.387 Chirality : 0.039 0.227 2215 Planarity : 0.006 0.127 2185 Dihedral : 18.227 178.116 2647 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.63 % Favored : 96.24 % Rotamer: Outliers : 3.41 % Allowed : 21.57 % 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: 2.41 (0.16), residues: 986 sheet: -0.35 (0.46), residues: 112 loop : -0.74 (0.31), residues: 446 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 0.015 0.002 PHE A 599 TYR 0.017 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: 3569.95 seconds wall clock time: 64 minutes 56.31 seconds (3896.31 seconds total)