Starting phenix.real_space_refine on Mon Jul 22 12:27:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qeo_18374/07_2024/8qeo_18374_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qeo_18374/07_2024/8qeo_18374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qeo_18374/07_2024/8qeo_18374.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qeo_18374/07_2024/8qeo_18374.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qeo_18374/07_2024/8qeo_18374_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qeo_18374/07_2024/8qeo_18374_neut.cif" } resolution = 3.26 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= 0.014 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 58 5.16 5 C 11543 2.51 5 N 2875 2.21 5 O 3649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 910": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1899": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2030": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 18126 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 17176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2146, 17176 Classifications: {'peptide': 2146} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 2, 'PTRANS': 46, 'TRANS': 2097} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 949 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 10, 'TRANS': 110} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5669 SG CYS A 698 30.811 52.975 158.551 1.00 14.16 S Time building chain proxies: 11.34, per 1000 atoms: 0.63 Number of scatterers: 18126 At special positions: 0 Unit cell: (129.83, 112.442, 239.954, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 58 16.00 O 3649 8.00 N 2875 7.00 C 11543 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 160 " distance=2.02 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 148 " distance=2.03 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: 7.00 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2800 " pdb="ZN ZN A2800 " - pdb=" ND1 HIS A 653 " pdb="ZN ZN A2800 " - pdb=" SG CYS A 698 " pdb="ZN ZN A2800 " - pdb=" NE2 HIS A 757 " 4510 Ramachandran restraints generated. 2255 Oldfield, 0 Emsley, 2255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4280 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 31 sheets defined 33.7% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.912A pdb=" N LYS A 11 " --> pdb=" O LYS A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 36 removed outlier: 3.823A pdb=" N ILE A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 63 Processing helix chain 'A' and resid 68 through 89 Processing helix chain 'A' and resid 108 through 121 removed outlier: 3.921A pdb=" N VAL A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 158 removed outlier: 3.700A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 163 through 166 Processing helix chain 'A' and resid 167 through 197 removed outlier: 3.503A pdb=" N PHE A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 218 through 235 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.968A pdb=" N LEU A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 280 removed outlier: 3.549A pdb=" N LEU A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 324 Processing helix chain 'A' and resid 332 through 337 removed outlier: 3.638A pdb=" N MET A 337 " --> pdb=" O GLU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 352 removed outlier: 3.626A pdb=" N SER A 352 " --> pdb=" O SER A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 393 through 420 Proline residue: A 416 - end of helix removed outlier: 3.993A pdb=" N GLU A 420 " --> pdb=" O PRO A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 439 Processing helix chain 'A' and resid 443 through 450 Processing helix chain 'A' and resid 451 through 456 removed outlier: 4.997A pdb=" N LEU A 454 " --> pdb=" O GLY A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 469 Processing helix chain 'A' and resid 471 through 484 Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 512 through 520 removed outlier: 3.788A pdb=" N TRP A 520 " --> pdb=" O MET A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 544 through 548 removed outlier: 3.655A pdb=" N ASP A 547 " --> pdb=" O GLY A 544 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASN A 548 " --> pdb=" O GLU A 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 544 through 548' Processing helix chain 'A' and resid 558 through 564 Processing helix chain 'A' and resid 587 through 601 removed outlier: 3.632A pdb=" N THR A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 604 No H-bonds generated for 'chain 'A' and resid 602 through 604' Processing helix chain 'A' and resid 667 through 683 Processing helix chain 'A' and resid 706 through 709 Processing helix chain 'A' and resid 710 through 720 Processing helix chain 'A' and resid 722 through 727 Processing helix chain 'A' and resid 731 through 733 No H-bonds generated for 'chain 'A' and resid 731 through 733' Processing helix chain 'A' and resid 764 through 774 Processing helix chain 'A' and resid 793 through 809 removed outlier: 3.568A pdb=" N ASN A 809 " --> pdb=" O ARG A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 839 Processing helix chain 'A' and resid 850 through 876 Processing helix chain 'A' and resid 885 through 889 removed outlier: 3.801A pdb=" N ILE A 889 " --> pdb=" O PHE A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 932 removed outlier: 3.723A pdb=" N THR A 926 " --> pdb=" O ALA A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 936 Processing helix chain 'A' and resid 957 through 966 Processing helix chain 'A' and resid 978 through 994 Processing helix chain 'A' and resid 1005 through 1017 Processing helix chain 'A' and resid 1056 through 1061 Processing helix chain 'A' and resid 1075 through 1080 removed outlier: 3.526A pdb=" N THR A1080 " --> pdb=" O THR A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1133 removed outlier: 3.991A pdb=" N VAL A1120 " --> pdb=" O LYS A1116 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A1131 " --> pdb=" O VAL A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1255 removed outlier: 3.654A pdb=" N ARG A1255 " --> pdb=" O LEU A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1311 Processing helix chain 'A' and resid 1432 through 1439 Processing helix chain 'A' and resid 1439 through 1450 Processing helix chain 'A' and resid 1558 through 1572 Processing helix chain 'A' and resid 1585 through 1589 Processing helix chain 'A' and resid 1590 through 1594 removed outlier: 3.986A pdb=" N PHE A1594 " --> pdb=" O LYS A1591 " (cutoff:3.500A) Processing helix chain 'A' and resid 1679 through 1682 Processing helix chain 'A' and resid 1684 through 1688 Processing helix chain 'A' and resid 1791 through 1799 Processing helix chain 'A' and resid 1867 through 1871 Processing helix chain 'A' and resid 1889 through 1893 removed outlier: 3.968A pdb=" N VAL A1893 " --> pdb=" O GLN A1890 " (cutoff:3.500A) Processing helix chain 'A' and resid 2061 through 2065 removed outlier: 3.855A pdb=" N ASN A2064 " --> pdb=" O ASN A2061 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 79 through 84 removed outlier: 4.247A pdb=" N VAL B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 92 removed outlier: 3.687A pdb=" N VAL B 90 " --> pdb=" O PHE B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 107 Processing helix chain 'B' and resid 123 through 132 removed outlier: 3.520A pdb=" N CYS B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 139 removed outlier: 3.954A pdb=" N PHE B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 151 removed outlier: 5.922A pdb=" N CYS B 148 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLU B 149 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA2, first strand: chain 'A' and resid 237 through 239 removed outlier: 6.117A pdb=" N LEU A 98 " --> pdb=" O ASN A 128 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N PHE A 130 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE A 100 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASN A 97 " --> pdb=" O MET A 283 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU A 285 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N HIS A 99 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 389 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 388 " --> pdb=" O LYS A 374 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 291 Processing sheet with id=AA4, first strand: chain 'A' and resid 578 through 579 removed outlier: 6.117A pdb=" N ILE A 578 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N THR A 649 " --> pdb=" O ILE A 578 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 578 through 579 removed outlier: 6.117A pdb=" N ILE A 578 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N THR A 649 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N CYS A 698 " --> pdb=" O GLY A 652 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE A 735 " --> pdb=" O PHE A 780 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE A 780 " --> pdb=" O ILE A 735 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N TYR A 777 " --> pdb=" O LYS A 790 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 606 through 608 Processing sheet with id=AA7, first strand: chain 'A' and resid 744 through 746 Processing sheet with id=AA8, first strand: chain 'A' and resid 1161 through 1162 removed outlier: 7.890A pdb=" N ASN A1335 " --> pdb=" O LEU A1312 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR A1314 " --> pdb=" O ASN A1335 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLU A1337 " --> pdb=" O TYR A1314 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE A1316 " --> pdb=" O GLU A1337 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A1338 " --> pdb=" O SER A1392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1167 through 1168 removed outlier: 6.180A pdb=" N GLU A1168 " --> pdb=" O PHE A1230 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N TRP A1232 " --> pdb=" O GLU A1168 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN A1227 " --> pdb=" O TYR A1282 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR A1282 " --> pdb=" O ASN A1227 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL A1229 " --> pdb=" O PRO A1280 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ALA A1231 " --> pdb=" O LEU A1278 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU A1278 " --> pdb=" O ALA A1231 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLU A1233 " --> pdb=" O THR A1276 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1220 through 1221 removed outlier: 6.412A pdb=" N MET A1220 " --> pdb=" O ILE A1299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 1325 through 1326 removed outlier: 6.714A pdb=" N LEU A1325 " --> pdb=" O ASP A1347 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TRP A1344 " --> pdb=" O PHE A1401 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N SER A1403 " --> pdb=" O VAL A1418 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A1418 " --> pdb=" O SER A1403 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N THR A1405 " --> pdb=" O ILE A1416 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE A1416 " --> pdb=" O THR A1405 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N SER A1407 " --> pdb=" O ALA A1414 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ALA A1414 " --> pdb=" O SER A1407 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1460 through 1464 removed outlier: 3.501A pdb=" N TYR A1509 " --> pdb=" O VAL A1595 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1514 through 1521 removed outlier: 4.426A pdb=" N VAL A1516 " --> pdb=" O THR A1528 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR A1528 " --> pdb=" O VAL A1516 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL A1518 " --> pdb=" O ILE A1526 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE A1526 " --> pdb=" O VAL A1518 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR A1520 " --> pdb=" O VAL A1524 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A1524 " --> pdb=" O THR A1520 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASN A1525 " --> pdb=" O LEU A1544 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU A1544 " --> pdb=" O ASN A1525 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR A1543 " --> pdb=" O LEU A1552 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU A1552 " --> pdb=" O THR A1543 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP A1607 " --> pdb=" O LEU A1552 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N SER A1554 " --> pdb=" O ASP A1607 " (cutoff:3.500A) removed outlier: 11.149A pdb=" N ASN A1609 " --> pdb=" O SER A1554 " (cutoff:3.500A) removed outlier: 11.112A pdb=" N HIS A1556 " --> pdb=" O ASN A1609 " (cutoff:3.500A) removed outlier: 11.123A pdb=" N ILE A1611 " --> pdb=" O HIS A1556 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1619 through 1620 removed outlier: 4.720A pdb=" N TYR A1648 " --> pdb=" O ASN A1654 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ASN A1654 " --> pdb=" O TYR A1648 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL A1691 " --> pdb=" O ILE A1718 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1674 through 1677 removed outlier: 6.205A pdb=" N ILE A1674 " --> pdb=" O ASN A1703 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N THR A1705 " --> pdb=" O ILE A1674 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N PHE A1676 " --> pdb=" O THR A1705 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE A1729 " --> pdb=" O SER A1781 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ASN A1783 " --> pdb=" O ILE A1729 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A1731 " --> pdb=" O ASN A1783 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1814 through 1818 Processing sheet with id=AB8, first strand: chain 'A' and resid 1834 through 1837 Processing sheet with id=AB9, first strand: chain 'A' and resid 1855 through 1857 removed outlier: 3.525A pdb=" N TYR A1864 " --> pdb=" O VAL A1857 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1877 through 1880 Processing sheet with id=AC2, first strand: chain 'A' and resid 1897 through 1901 removed outlier: 3.720A pdb=" N GLU A1921 " --> pdb=" O ALA A1909 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1927 through 1931 Processing sheet with id=AC4, first strand: chain 'A' and resid 1949 through 1950 Processing sheet with id=AC5, first strand: chain 'A' and resid 1968 through 1972 Processing sheet with id=AC6, first strand: chain 'A' and resid 1988 through 1992 Processing sheet with id=AC7, first strand: chain 'A' and resid 2008 through 2012 Processing sheet with id=AC8, first strand: chain 'A' and resid 2028 through 2032 removed outlier: 3.856A pdb=" N GLU A2052 " --> pdb=" O ALA A2040 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 2058 through 2060 Processing sheet with id=AD1, first strand: chain 'A' and resid 2078 through 2081 Processing sheet with id=AD2, first strand: chain 'A' and resid 2100 through 2104 Processing sheet with id=AD3, first strand: chain 'A' and resid 2120 through 2124 Processing sheet with id=AD4, first strand: chain 'A' and resid 2160 through 2164 707 hydrogen bonds defined for protein. 1905 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.39 Time building geometry restraints manager: 7.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5937 1.34 - 1.46: 3914 1.46 - 1.58: 8522 1.58 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 18471 Sorted by residual: bond pdb=" C ALA B 107 " pdb=" O ALA B 107 " ideal model delta sigma weight residual 1.235 1.244 -0.009 4.70e-03 4.53e+04 3.45e+00 bond pdb=" CB ASP A 480 " pdb=" CG ASP A 480 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.16e+00 bond pdb=" C PHE A1908 " pdb=" N ALA A1909 " ideal model delta sigma weight residual 1.325 1.308 0.017 1.58e-02 4.01e+03 1.14e+00 bond pdb=" CA LEU A1200 " pdb=" CB LEU A1200 " ideal model delta sigma weight residual 1.541 1.529 0.012 1.20e-02 6.94e+03 1.07e+00 bond pdb=" CA ILE A1345 " pdb=" C ILE A1345 " ideal model delta sigma weight residual 1.527 1.518 0.009 8.50e-03 1.38e+04 1.06e+00 ... (remaining 18466 not shown) Histogram of bond angle deviations from ideal: 99.90 - 106.72: 325 106.72 - 113.54: 10067 113.54 - 120.36: 6932 120.36 - 127.18: 7577 127.18 - 134.00: 110 Bond angle restraints: 25011 Sorted by residual: angle pdb=" C ASP A1915 " pdb=" CA ASP A1915 " pdb=" CB ASP A1915 " ideal model delta sigma weight residual 116.34 110.62 5.72 1.40e+00 5.10e-01 1.67e+01 angle pdb=" N PHE A1187 " pdb=" CA PHE A1187 " pdb=" CB PHE A1187 " ideal model delta sigma weight residual 114.17 109.84 4.33 1.14e+00 7.69e-01 1.44e+01 angle pdb=" C ASN A1385 " pdb=" CA ASN A1385 " pdb=" CB ASN A1385 " ideal model delta sigma weight residual 116.54 112.23 4.31 1.15e+00 7.56e-01 1.40e+01 angle pdb=" N LEU A1200 " pdb=" CA LEU A1200 " pdb=" CB LEU A1200 " ideal model delta sigma weight residual 114.17 110.10 4.07 1.14e+00 7.69e-01 1.28e+01 angle pdb=" CA GLY A1904 " pdb=" C GLY A1904 " pdb=" N PHE A1905 " ideal model delta sigma weight residual 115.30 117.66 -2.36 8.20e-01 1.49e+00 8.31e+00 ... (remaining 25006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 10508 17.87 - 35.73: 443 35.73 - 53.60: 103 53.60 - 71.46: 17 71.46 - 89.33: 4 Dihedral angle restraints: 11075 sinusoidal: 4417 harmonic: 6658 Sorted by residual: dihedral pdb=" CA SER A1671 " pdb=" C SER A1671 " pdb=" N THR A1672 " pdb=" CA THR A1672 " ideal model delta harmonic sigma weight residual 180.00 -156.91 -23.09 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA ALA B 107 " pdb=" C ALA B 107 " pdb=" N PRO B 108 " pdb=" CA PRO B 108 " ideal model delta harmonic sigma weight residual 180.00 159.87 20.13 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA TYR A1661 " pdb=" C TYR A1661 " pdb=" N ASP A1662 " pdb=" CA ASP A1662 " ideal model delta harmonic sigma weight residual -180.00 -160.21 -19.79 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 11072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1760 0.031 - 0.063: 685 0.063 - 0.094: 179 0.094 - 0.126: 135 0.126 - 0.157: 34 Chirality restraints: 2793 Sorted by residual: chirality pdb=" CA ILE A1460 " pdb=" N ILE A1460 " pdb=" C ILE A1460 " pdb=" CB ILE A1460 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" CA ILE A1415 " pdb=" N ILE A1415 " pdb=" C ILE A1415 " pdb=" CB ILE A1415 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA ILE A 578 " pdb=" N ILE A 578 " pdb=" C ILE A 578 " pdb=" CB ILE A 578 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.67e-01 ... (remaining 2790 not shown) Planarity restraints: 3254 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A1279 " 0.028 5.00e-02 4.00e+02 4.19e-02 2.82e+00 pdb=" N PRO A1280 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A1280 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1280 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 142 " 0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO B 143 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 143 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 143 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 117 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.34e+00 pdb=" N PRO B 118 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 118 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 118 " -0.021 5.00e-02 4.00e+02 ... (remaining 3251 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 215 2.59 - 3.17: 16650 3.17 - 3.75: 27053 3.75 - 4.32: 40429 4.32 - 4.90: 65722 Nonbonded interactions: 150069 Sorted by model distance: nonbonded pdb=" O GLU A 299 " pdb=" OG SER A 300 " model vdw 2.018 2.440 nonbonded pdb=" OG SER A 748 " pdb=" OE1 GLU A 749 " model vdw 2.129 2.440 nonbonded pdb=" N GLU A 907 " pdb=" OE1 GLU A 907 " model vdw 2.142 2.520 nonbonded pdb=" O ASN B 164 " pdb=" OG1 THR B 165 " model vdw 2.193 2.440 nonbonded pdb=" ND2 ASN A 40 " pdb=" OE1 GLU A 44 " model vdw 2.196 2.520 ... (remaining 150064 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: 15.980 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 59.330 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 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 : 0.004 0.037 18471 Z= 0.242 Angle : 0.527 6.742 25011 Z= 0.306 Chirality : 0.043 0.157 2793 Planarity : 0.003 0.042 3254 Dihedral : 11.102 89.330 6786 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.60 % Favored : 91.26 % Rotamer: Outliers : 2.65 % Allowed : 5.89 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.18), residues: 2255 helix: 0.68 (0.21), residues: 659 sheet: -1.34 (0.26), residues: 388 loop : -1.71 (0.18), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 102 HIS 0.002 0.001 HIS A1997 PHE 0.014 0.001 PHE A1621 TYR 0.013 0.002 TYR A 189 ARG 0.003 0.000 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4510 Ramachandran restraints generated. 2255 Oldfield, 0 Emsley, 2255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4510 Ramachandran restraints generated. 2255 Oldfield, 0 Emsley, 2255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 419 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 SER cc_start: 0.7937 (OUTLIER) cc_final: 0.7381 (m) REVERT: A 575 ARG cc_start: 0.4998 (OUTLIER) cc_final: 0.4223 (pmt-80) REVERT: A 603 TYR cc_start: 0.6666 (m-80) cc_final: 0.6417 (m-80) REVERT: A 900 PHE cc_start: 0.7954 (m-80) cc_final: 0.7545 (m-80) REVERT: A 985 MET cc_start: 0.6392 (mmp) cc_final: 0.4966 (ptt) REVERT: A 1007 VAL cc_start: 0.4595 (OUTLIER) cc_final: 0.4238 (t) REVERT: A 1234 THR cc_start: 0.6725 (p) cc_final: 0.6491 (p) REVERT: A 1244 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7540 (tm-30) REVERT: A 1387 HIS cc_start: 0.7496 (OUTLIER) cc_final: 0.7258 (m90) REVERT: A 1448 ASP cc_start: 0.7401 (m-30) cc_final: 0.7170 (m-30) REVERT: A 1526 ILE cc_start: 0.8343 (mp) cc_final: 0.8084 (mt) REVERT: A 1770 VAL cc_start: 0.8064 (OUTLIER) cc_final: 0.7774 (t) REVERT: B 77 GLU cc_start: 0.7199 (tt0) cc_final: 0.6985 (tt0) REVERT: B 91 LYS cc_start: 0.8744 (tppp) cc_final: 0.8344 (tptm) REVERT: B 105 MET cc_start: 0.4803 (tpt) cc_final: 0.4597 (tpt) outliers start: 54 outliers final: 17 residues processed: 463 average time/residue: 0.3348 time to fit residues: 235.7902 Evaluate side-chains 275 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 252 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain A residue 1387 HIS Chi-restraints excluded: chain A residue 1490 ASP Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1711 ASN Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1770 VAL Chi-restraints excluded: chain A residue 1835 LEU Chi-restraints excluded: chain A residue 1864 TYR Chi-restraints excluded: chain B residue 160 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 190 optimal weight: 0.7980 chunk 171 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 107 optimal weight: 0.4980 chunk 131 optimal weight: 0.5980 chunk 205 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 490 ASN A 492 HIS A 596 ASN A 611 ASN A 809 ASN A 835 GLN ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1778 ASN B 85 GLN B 136 ASN ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 18471 Z= 0.243 Angle : 0.593 8.918 25011 Z= 0.316 Chirality : 0.046 0.211 2793 Planarity : 0.004 0.040 3254 Dihedral : 6.597 85.851 2477 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.27 % Favored : 92.59 % Rotamer: Outliers : 3.24 % Allowed : 10.95 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.18), residues: 2255 helix: 1.12 (0.21), residues: 666 sheet: -1.29 (0.25), residues: 399 loop : -1.61 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1264 HIS 0.009 0.001 HIS A2041 PHE 0.030 0.002 PHE A1966 TYR 0.023 0.002 TYR A 580 ARG 0.005 0.001 ARG A1228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4510 Ramachandran restraints generated. 2255 Oldfield, 0 Emsley, 2255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4510 Ramachandran restraints generated. 2255 Oldfield, 0 Emsley, 2255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 270 time to evaluate : 1.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 SER cc_start: 0.7902 (OUTLIER) cc_final: 0.7373 (m) REVERT: A 289 MET cc_start: 0.8353 (mmm) cc_final: 0.8135 (mmm) REVERT: A 510 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8543 (pt0) REVERT: A 603 TYR cc_start: 0.6649 (m-80) cc_final: 0.6382 (m-80) REVERT: A 640 ILE cc_start: 0.8518 (pt) cc_final: 0.8289 (pt) REVERT: A 741 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: A 985 MET cc_start: 0.6460 (mmp) cc_final: 0.4987 (ptt) REVERT: A 1007 VAL cc_start: 0.4452 (OUTLIER) cc_final: 0.4211 (t) REVERT: A 1234 THR cc_start: 0.6631 (p) cc_final: 0.6398 (p) REVERT: A 1242 SER cc_start: 0.8383 (p) cc_final: 0.8172 (p) REVERT: A 1387 HIS cc_start: 0.7462 (OUTLIER) cc_final: 0.7252 (m90) REVERT: A 1787 LYS cc_start: -0.0739 (tppt) cc_final: -0.0990 (tppt) REVERT: A 1955 MET cc_start: 0.6751 (tpt) cc_final: 0.6444 (tpt) REVERT: A 2149 PHE cc_start: 0.7420 (m-80) cc_final: 0.7106 (m-80) REVERT: B 91 LYS cc_start: 0.8581 (tppp) cc_final: 0.8203 (tptm) REVERT: B 141 GLN cc_start: 0.5584 (pp30) cc_final: 0.5265 (pp30) outliers start: 66 outliers final: 37 residues processed: 319 average time/residue: 0.3026 time to fit residues: 147.6484 Evaluate side-chains 271 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 229 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1283 GLU Chi-restraints excluded: chain A residue 1313 SER Chi-restraints excluded: chain A residue 1374 THR Chi-restraints excluded: chain A residue 1387 HIS Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1711 ASN Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1770 VAL Chi-restraints excluded: chain A residue 1774 LYS Chi-restraints excluded: chain A residue 1790 VAL Chi-restraints excluded: chain A residue 1835 LEU Chi-restraints excluded: chain A residue 1864 TYR Chi-restraints excluded: chain A residue 1941 ASN Chi-restraints excluded: chain A residue 2032 THR Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain B residue 109 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 114 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 56 optimal weight: 0.3980 chunk 205 optimal weight: 0.0570 chunk 222 optimal weight: 0.9980 chunk 183 optimal weight: 0.3980 chunk 203 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18471 Z= 0.193 Angle : 0.557 9.980 25011 Z= 0.297 Chirality : 0.044 0.202 2793 Planarity : 0.003 0.043 3254 Dihedral : 6.278 85.002 2469 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.49 % Favored : 92.37 % Rotamer: Outliers : 3.00 % Allowed : 12.38 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.18), residues: 2255 helix: 1.28 (0.21), residues: 669 sheet: -1.20 (0.25), residues: 404 loop : -1.58 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1948 HIS 0.007 0.001 HIS A 924 PHE 0.021 0.002 PHE A 964 TYR 0.014 0.001 TYR A 580 ARG 0.004 0.000 ARG A1281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4510 Ramachandran restraints generated. 2255 Oldfield, 0 Emsley, 2255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4510 Ramachandran restraints generated. 2255 Oldfield, 0 Emsley, 2255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 252 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.8314 (mmm) cc_final: 0.8059 (mmm) REVERT: A 566 ILE cc_start: 0.6188 (OUTLIER) cc_final: 0.5955 (pt) REVERT: A 603 TYR cc_start: 0.6581 (m-80) cc_final: 0.6317 (m-80) REVERT: A 640 ILE cc_start: 0.8545 (pt) cc_final: 0.8331 (pt) REVERT: A 741 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: A 900 PHE cc_start: 0.7395 (m-80) cc_final: 0.7182 (m-80) REVERT: A 985 MET cc_start: 0.6509 (mmp) cc_final: 0.4970 (ptt) REVERT: A 1007 VAL cc_start: 0.4228 (OUTLIER) cc_final: 0.3985 (t) REVERT: A 1124 PHE cc_start: 0.6887 (m-80) cc_final: 0.6563 (m-80) REVERT: A 1242 SER cc_start: 0.8374 (p) cc_final: 0.8146 (p) REVERT: A 2079 TRP cc_start: 0.7882 (m100) cc_final: 0.7637 (m100) REVERT: A 2149 PHE cc_start: 0.7333 (m-80) cc_final: 0.7107 (m-80) REVERT: B 91 LYS cc_start: 0.8553 (tppp) cc_final: 0.8223 (tptm) REVERT: B 105 MET cc_start: 0.4959 (tpt) cc_final: 0.4419 (tpt) outliers start: 61 outliers final: 42 residues processed: 303 average time/residue: 0.2977 time to fit residues: 138.4296 Evaluate side-chains 279 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 234 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 896 PHE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1313 SER Chi-restraints excluded: chain A residue 1329 GLN Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1374 THR Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1711 ASN Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1770 VAL Chi-restraints excluded: chain A residue 1774 LYS Chi-restraints excluded: chain A residue 1790 VAL Chi-restraints excluded: chain A residue 1835 LEU Chi-restraints excluded: chain A residue 1864 TYR Chi-restraints excluded: chain A residue 1941 ASN Chi-restraints excluded: chain A residue 2032 THR Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain A residue 2125 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 134 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 203 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 206 optimal weight: 0.5980 chunk 218 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 195 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1762 GLN A1997 HIS A2041 HIS B 136 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 18471 Z= 0.248 Angle : 0.587 9.002 25011 Z= 0.311 Chirality : 0.045 0.193 2793 Planarity : 0.004 0.040 3254 Dihedral : 5.947 57.909 2459 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.94 % Favored : 91.93 % Rotamer: Outliers : 4.08 % Allowed : 12.92 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.18), residues: 2255 helix: 1.28 (0.21), residues: 659 sheet: -1.21 (0.25), residues: 411 loop : -1.61 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 102 HIS 0.017 0.002 HIS A2041 PHE 0.019 0.002 PHE A1621 TYR 0.019 0.002 TYR A1531 ARG 0.003 0.000 ARG B 121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4510 Ramachandran restraints generated. 2255 Oldfield, 0 Emsley, 2255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4510 Ramachandran restraints generated. 2255 Oldfield, 0 Emsley, 2255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 251 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 MET cc_start: 0.7837 (mmt) cc_final: 0.7411 (mmt) REVERT: A 516 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8165 (mtp) REVERT: A 546 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.7406 (m-30) REVERT: A 640 ILE cc_start: 0.8557 (pt) cc_final: 0.8198 (pt) REVERT: A 741 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8326 (mt0) REVERT: A 815 LEU cc_start: 0.5103 (tp) cc_final: 0.4898 (tp) REVERT: A 900 PHE cc_start: 0.7675 (m-80) cc_final: 0.7392 (m-80) REVERT: A 964 PHE cc_start: 0.6060 (m-80) cc_final: 0.5304 (m-80) REVERT: A 985 MET cc_start: 0.6503 (mmp) cc_final: 0.4922 (ptt) REVERT: A 1124 PHE cc_start: 0.6943 (m-80) cc_final: 0.6607 (m-80) REVERT: A 1157 PHE cc_start: 0.7181 (m-80) cc_final: 0.6776 (m-10) REVERT: A 1168 GLU cc_start: 0.6580 (mp0) cc_final: 0.6084 (mp0) REVERT: A 1242 SER cc_start: 0.8395 (p) cc_final: 0.8162 (p) REVERT: A 1278 LEU cc_start: 0.6414 (mp) cc_final: 0.5878 (pp) REVERT: A 1464 PHE cc_start: 0.8175 (t80) cc_final: 0.7970 (t80) REVERT: A 1786 ASP cc_start: 0.6803 (OUTLIER) cc_final: 0.6097 (t70) REVERT: A 1787 LYS cc_start: -0.1762 (mmtt) cc_final: -0.3425 (mmtm) REVERT: A 1976 LYS cc_start: 0.7027 (mtpt) cc_final: 0.6760 (mmmt) REVERT: A 2079 TRP cc_start: 0.7970 (m100) cc_final: 0.7489 (m100) REVERT: A 2149 PHE cc_start: 0.7408 (m-80) cc_final: 0.7193 (m-80) REVERT: B 91 LYS cc_start: 0.8535 (tppp) cc_final: 0.8195 (tptm) REVERT: B 105 MET cc_start: 0.5143 (tpt) cc_final: 0.4846 (tpt) outliers start: 83 outliers final: 51 residues processed: 318 average time/residue: 0.2843 time to fit residues: 141.9268 Evaluate side-chains 283 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 228 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1313 SER Chi-restraints excluded: chain A residue 1329 GLN Chi-restraints excluded: chain A residue 1335 ASN Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1374 THR Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1711 ASN Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1770 VAL Chi-restraints excluded: chain A residue 1774 LYS Chi-restraints excluded: chain A residue 1786 ASP Chi-restraints excluded: chain A residue 1835 LEU Chi-restraints excluded: chain A residue 1864 TYR Chi-restraints excluded: chain A residue 1941 ASN Chi-restraints excluded: chain A residue 1991 SER Chi-restraints excluded: chain A residue 2032 THR Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 134 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 181 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 196 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1329 GLN ** A1589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1744 ASN ** A2125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 18471 Z= 0.330 Angle : 0.631 10.095 25011 Z= 0.335 Chirality : 0.046 0.197 2793 Planarity : 0.004 0.043 3254 Dihedral : 6.181 59.790 2458 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.56 % Favored : 91.31 % Rotamer: Outliers : 4.08 % Allowed : 14.93 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.18), residues: 2255 helix: 1.02 (0.21), residues: 663 sheet: -1.36 (0.24), residues: 423 loop : -1.74 (0.18), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 102 HIS 0.007 0.001 HIS A2041 PHE 0.025 0.002 PHE A2129 TYR 0.017 0.002 TYR A1330 ARG 0.003 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4510 Ramachandran restraints generated. 2255 Oldfield, 0 Emsley, 2255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4510 Ramachandran restraints generated. 2255 Oldfield, 0 Emsley, 2255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 240 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.8400 (mmm) cc_final: 0.8130 (mmm) REVERT: A 321 MET cc_start: 0.7905 (mmt) cc_final: 0.7490 (mmt) REVERT: A 516 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8173 (mtp) REVERT: A 546 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.7296 (m-30) REVERT: A 580 TYR cc_start: 0.6714 (OUTLIER) cc_final: 0.6510 (t80) REVERT: A 640 ILE cc_start: 0.8588 (pt) cc_final: 0.8226 (pt) REVERT: A 878 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6674 (pp) REVERT: A 900 PHE cc_start: 0.7791 (m-80) cc_final: 0.7447 (m-80) REVERT: A 964 PHE cc_start: 0.6091 (m-80) cc_final: 0.5247 (m-80) REVERT: A 985 MET cc_start: 0.6596 (mmp) cc_final: 0.4913 (ptt) REVERT: A 1124 PHE cc_start: 0.7027 (m-80) cc_final: 0.6670 (m-80) REVERT: A 1242 SER cc_start: 0.8432 (p) cc_final: 0.8206 (p) REVERT: A 1312 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6636 (mm) REVERT: A 1462 TYR cc_start: 0.6591 (t80) cc_final: 0.6232 (t80) REVERT: A 1786 ASP cc_start: 0.6947 (OUTLIER) cc_final: 0.6119 (t0) REVERT: A 1787 LYS cc_start: -0.0264 (mmtt) cc_final: -0.2756 (tptt) REVERT: A 1986 GLN cc_start: 0.5234 (mm110) cc_final: 0.4930 (mm110) REVERT: B 91 LYS cc_start: 0.8647 (tppp) cc_final: 0.8274 (tptm) outliers start: 83 outliers final: 59 residues processed: 302 average time/residue: 0.2970 time to fit residues: 140.4125 Evaluate side-chains 283 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 218 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain A residue 580 TYR Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 876 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 PHE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1275 ILE Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1329 GLN Chi-restraints excluded: chain A residue 1335 ASN Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1374 THR Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1711 ASN Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1770 VAL Chi-restraints excluded: chain A residue 1774 LYS Chi-restraints excluded: chain A residue 1786 ASP Chi-restraints excluded: chain A residue 1835 LEU Chi-restraints excluded: chain A residue 1864 TYR Chi-restraints excluded: chain A residue 1941 ASN Chi-restraints excluded: chain A residue 1991 SER Chi-restraints excluded: chain A residue 1992 ILE Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain A residue 2147 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 73 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 18 optimal weight: 0.6980 chunk 72 optimal weight: 0.3980 chunk 114 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 18471 Z= 0.246 Angle : 0.589 9.237 25011 Z= 0.314 Chirality : 0.045 0.192 2793 Planarity : 0.004 0.043 3254 Dihedral : 5.981 57.917 2457 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.03 % Favored : 91.84 % Rotamer: Outliers : 4.08 % Allowed : 15.57 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.18), residues: 2255 helix: 1.10 (0.21), residues: 665 sheet: -1.32 (0.24), residues: 430 loop : -1.71 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 102 HIS 0.006 0.001 HIS A2041 PHE 0.020 0.002 PHE A2129 TYR 0.030 0.002 TYR A1330 ARG 0.003 0.000 ARG A1281 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4510 Ramachandran restraints generated. 2255 Oldfield, 0 Emsley, 2255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4510 Ramachandran restraints generated. 2255 Oldfield, 0 Emsley, 2255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 232 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 MET cc_start: 0.7865 (mmt) cc_final: 0.7480 (mmt) REVERT: A 516 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8142 (mtp) REVERT: A 546 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.7297 (m-30) REVERT: A 566 ILE cc_start: 0.6303 (OUTLIER) cc_final: 0.6075 (pt) REVERT: A 640 ILE cc_start: 0.8623 (pt) cc_final: 0.8284 (pt) REVERT: A 741 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8333 (mt0) REVERT: A 926 THR cc_start: 0.7916 (m) cc_final: 0.7616 (p) REVERT: A 964 PHE cc_start: 0.6015 (m-80) cc_final: 0.5186 (m-80) REVERT: A 985 MET cc_start: 0.6664 (mmp) cc_final: 0.4936 (ptt) REVERT: A 1526 ILE cc_start: 0.8137 (mm) cc_final: 0.7790 (mt) REVERT: A 1774 LYS cc_start: 0.7010 (OUTLIER) cc_final: 0.6790 (tmtt) REVERT: A 1786 ASP cc_start: 0.6585 (OUTLIER) cc_final: 0.6269 (p0) REVERT: A 1986 GLN cc_start: 0.5356 (mm110) cc_final: 0.5125 (mm110) REVERT: B 91 LYS cc_start: 0.8627 (tppp) cc_final: 0.8281 (tptm) outliers start: 83 outliers final: 60 residues processed: 297 average time/residue: 0.2900 time to fit residues: 135.1619 Evaluate side-chains 285 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 219 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 896 PHE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1275 ILE Chi-restraints excluded: chain A residue 1284 ASP Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1313 SER Chi-restraints excluded: chain A residue 1335 ASN Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1374 THR Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1534 ASP Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1711 ASN Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1770 VAL Chi-restraints excluded: chain A residue 1774 LYS Chi-restraints excluded: chain A residue 1786 ASP Chi-restraints excluded: chain A residue 1835 LEU Chi-restraints excluded: chain A residue 1864 TYR Chi-restraints excluded: chain A residue 1941 ASN Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 1991 SER Chi-restraints excluded: chain A residue 1992 ILE Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain A residue 2147 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 210 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 124 optimal weight: 0.4980 chunk 159 optimal weight: 0.5980 chunk 123 optimal weight: 0.5980 chunk 184 optimal weight: 0.0020 chunk 122 optimal weight: 5.9990 chunk 217 optimal weight: 4.9990 chunk 136 optimal weight: 0.6980 chunk 132 optimal weight: 0.0470 chunk 100 optimal weight: 4.9990 overall best weight: 0.3486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1329 GLN A1632 GLN A2026 GLN ** A2125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18471 Z= 0.163 Angle : 0.541 8.492 25011 Z= 0.288 Chirality : 0.044 0.189 2793 Planarity : 0.003 0.045 3254 Dihedral : 5.707 59.900 2457 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.45 % Favored : 92.42 % Rotamer: Outliers : 3.29 % Allowed : 16.75 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.18), residues: 2255 helix: 1.34 (0.21), residues: 667 sheet: -1.25 (0.24), residues: 415 loop : -1.57 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1948 HIS 0.003 0.001 HIS A2041 PHE 0.028 0.001 PHE A1464 TYR 0.021 0.001 TYR A1837 ARG 0.003 0.000 ARG A1281 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4510 Ramachandran restraints generated. 2255 Oldfield, 0 Emsley, 2255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4510 Ramachandran restraints generated. 2255 Oldfield, 0 Emsley, 2255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 234 time to evaluate : 2.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 PHE cc_start: 0.6638 (OUTLIER) cc_final: 0.5341 (t80) REVERT: A 289 MET cc_start: 0.8234 (mmm) cc_final: 0.7943 (mmm) REVERT: A 321 MET cc_start: 0.7853 (mmt) cc_final: 0.7579 (mmt) REVERT: A 546 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.7237 (m-30) REVERT: A 566 ILE cc_start: 0.6422 (OUTLIER) cc_final: 0.6127 (pt) REVERT: A 640 ILE cc_start: 0.8521 (pt) cc_final: 0.8252 (pt) REVERT: A 741 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8255 (mt0) REVERT: A 926 THR cc_start: 0.7925 (m) cc_final: 0.7622 (p) REVERT: A 964 PHE cc_start: 0.5975 (m-80) cc_final: 0.5221 (m-80) REVERT: A 985 MET cc_start: 0.6611 (mmp) cc_final: 0.4911 (ptt) REVERT: A 1526 ILE cc_start: 0.8124 (mm) cc_final: 0.7808 (mt) REVERT: A 1588 MET cc_start: 0.6864 (mmt) cc_final: 0.6643 (mmp) REVERT: A 1738 ILE cc_start: 0.8099 (tt) cc_final: 0.7836 (tt) REVERT: A 1774 LYS cc_start: 0.6844 (OUTLIER) cc_final: 0.6561 (tmtt) REVERT: A 1955 MET cc_start: 0.6369 (tpp) cc_final: 0.5937 (tpp) REVERT: A 2017 PHE cc_start: 0.6816 (m-80) cc_final: 0.6582 (m-80) REVERT: B 91 LYS cc_start: 0.8601 (tppp) cc_final: 0.8239 (tptm) outliers start: 67 outliers final: 52 residues processed: 288 average time/residue: 0.3045 time to fit residues: 136.9311 Evaluate side-chains 273 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 216 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 896 PHE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1275 ILE Chi-restraints excluded: chain A residue 1284 ASP Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1313 SER Chi-restraints excluded: chain A residue 1329 GLN Chi-restraints excluded: chain A residue 1335 ASN Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1374 THR Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1661 TYR Chi-restraints excluded: chain A residue 1711 ASN Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1770 VAL Chi-restraints excluded: chain A residue 1774 LYS Chi-restraints excluded: chain A residue 1835 LEU Chi-restraints excluded: chain A residue 1864 TYR Chi-restraints excluded: chain A residue 1941 ASN Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 1992 ILE Chi-restraints excluded: chain A residue 2032 THR Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 134 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 chunk 198 optimal weight: 0.0060 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18471 Z= 0.187 Angle : 0.562 8.933 25011 Z= 0.296 Chirality : 0.044 0.196 2793 Planarity : 0.003 0.046 3254 Dihedral : 5.661 59.646 2457 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.41 % Favored : 92.42 % Rotamer: Outliers : 3.68 % Allowed : 16.50 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.18), residues: 2255 helix: 1.36 (0.21), residues: 663 sheet: -1.21 (0.25), residues: 411 loop : -1.51 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1948 HIS 0.010 0.001 HIS A 924 PHE 0.019 0.001 PHE A1908 TYR 0.020 0.001 TYR A1330 ARG 0.004 0.000 ARG A1281 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4510 Ramachandran restraints generated. 2255 Oldfield, 0 Emsley, 2255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4510 Ramachandran restraints generated. 2255 Oldfield, 0 Emsley, 2255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 226 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.6895 (OUTLIER) cc_final: 0.6638 (p0) REVERT: A 243 PHE cc_start: 0.6611 (OUTLIER) cc_final: 0.5345 (t80) REVERT: A 321 MET cc_start: 0.7871 (mmt) cc_final: 0.7602 (mmt) REVERT: A 546 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7251 (m-30) REVERT: A 566 ILE cc_start: 0.6435 (OUTLIER) cc_final: 0.6141 (pt) REVERT: A 640 ILE cc_start: 0.8524 (pt) cc_final: 0.8273 (pt) REVERT: A 741 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8335 (mt0) REVERT: A 926 THR cc_start: 0.7932 (m) cc_final: 0.7635 (p) REVERT: A 964 PHE cc_start: 0.5914 (m-80) cc_final: 0.5273 (m-80) REVERT: A 985 MET cc_start: 0.6619 (mmp) cc_final: 0.4907 (ptt) REVERT: A 1526 ILE cc_start: 0.8120 (mm) cc_final: 0.7778 (mt) REVERT: A 1738 ILE cc_start: 0.8094 (tt) cc_final: 0.7890 (tt) REVERT: A 1955 MET cc_start: 0.6372 (tpp) cc_final: 0.5952 (tpp) REVERT: A 2017 PHE cc_start: 0.6861 (m-80) cc_final: 0.6614 (m-80) REVERT: B 91 LYS cc_start: 0.8606 (tppp) cc_final: 0.8249 (tptm) outliers start: 75 outliers final: 60 residues processed: 282 average time/residue: 0.3115 time to fit residues: 137.0392 Evaluate side-chains 286 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 221 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 896 PHE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1275 ILE Chi-restraints excluded: chain A residue 1284 ASP Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1313 SER Chi-restraints excluded: chain A residue 1335 ASN Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1374 THR Chi-restraints excluded: chain A residue 1492 VAL Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1661 TYR Chi-restraints excluded: chain A residue 1711 ASN Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1770 VAL Chi-restraints excluded: chain A residue 1774 LYS Chi-restraints excluded: chain A residue 1835 LEU Chi-restraints excluded: chain A residue 1864 TYR Chi-restraints excluded: chain A residue 1941 ASN Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 1991 SER Chi-restraints excluded: chain A residue 1992 ILE Chi-restraints excluded: chain A residue 2025 MET Chi-restraints excluded: chain A residue 2032 THR Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 208 optimal weight: 0.5980 chunk 190 optimal weight: 0.1980 chunk 202 optimal weight: 0.2980 chunk 122 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 183 optimal weight: 0.1980 chunk 191 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 214 optimal weight: 0.0050 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1329 GLN A1335 ASN ** A1444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1762 GLN ** A1917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18471 Z= 0.152 Angle : 0.547 9.707 25011 Z= 0.287 Chirality : 0.043 0.203 2793 Planarity : 0.003 0.046 3254 Dihedral : 5.517 59.537 2457 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.87 % Favored : 92.95 % Rotamer: Outliers : 3.49 % Allowed : 16.94 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.18), residues: 2255 helix: 1.47 (0.21), residues: 662 sheet: -1.12 (0.25), residues: 406 loop : -1.45 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1948 HIS 0.009 0.001 HIS A 924 PHE 0.015 0.001 PHE A 446 TYR 0.022 0.001 TYR A1837 ARG 0.006 0.000 ARG A1296 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4510 Ramachandran restraints generated. 2255 Oldfield, 0 Emsley, 2255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4510 Ramachandran restraints generated. 2255 Oldfield, 0 Emsley, 2255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 234 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 PHE cc_start: 0.6573 (OUTLIER) cc_final: 0.5333 (t80) REVERT: A 321 MET cc_start: 0.7910 (mmt) cc_final: 0.7654 (mmt) REVERT: A 448 MET cc_start: 0.7065 (tpp) cc_final: 0.6838 (mtp) REVERT: A 546 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7255 (m-30) REVERT: A 566 ILE cc_start: 0.6408 (OUTLIER) cc_final: 0.6128 (pt) REVERT: A 640 ILE cc_start: 0.8493 (pt) cc_final: 0.8261 (pt) REVERT: A 741 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8317 (mt0) REVERT: A 926 THR cc_start: 0.7926 (m) cc_final: 0.7645 (p) REVERT: A 964 PHE cc_start: 0.5827 (m-80) cc_final: 0.5141 (m-80) REVERT: A 985 MET cc_start: 0.6545 (mmp) cc_final: 0.4868 (ptt) REVERT: A 1299 ILE cc_start: 0.7745 (mt) cc_final: 0.7521 (mt) REVERT: A 1526 ILE cc_start: 0.8031 (mm) cc_final: 0.7716 (mt) REVERT: A 1955 MET cc_start: 0.6316 (tpp) cc_final: 0.5607 (tpp) REVERT: B 91 LYS cc_start: 0.8581 (tppp) cc_final: 0.8225 (tptm) REVERT: B 135 MET cc_start: 0.5605 (OUTLIER) cc_final: 0.5104 (mmp) outliers start: 71 outliers final: 55 residues processed: 290 average time/residue: 0.2918 time to fit residues: 133.9234 Evaluate side-chains 275 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 215 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 896 PHE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1275 ILE Chi-restraints excluded: chain A residue 1284 ASP Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1313 SER Chi-restraints excluded: chain A residue 1329 GLN Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1374 THR Chi-restraints excluded: chain A residue 1492 VAL Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1661 TYR Chi-restraints excluded: chain A residue 1711 ASN Chi-restraints excluded: chain A residue 1770 VAL Chi-restraints excluded: chain A residue 1774 LYS Chi-restraints excluded: chain A residue 1835 LEU Chi-restraints excluded: chain A residue 1864 TYR Chi-restraints excluded: chain A residue 1941 ASN Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 1991 SER Chi-restraints excluded: chain A residue 2032 THR Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 131 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 225 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 179 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 781 ASN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1589 ASN ** A1917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18471 Z= 0.310 Angle : 0.643 11.569 25011 Z= 0.337 Chirality : 0.046 0.215 2793 Planarity : 0.004 0.045 3254 Dihedral : 5.674 59.895 2449 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.20 % Favored : 91.62 % Rotamer: Outliers : 3.14 % Allowed : 17.73 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.18), residues: 2255 helix: 1.14 (0.21), residues: 668 sheet: -1.16 (0.24), residues: 423 loop : -1.64 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1264 HIS 0.014 0.002 HIS A 924 PHE 0.029 0.002 PHE A1157 TYR 0.017 0.002 TYR A1698 ARG 0.003 0.000 ARG A1241 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4510 Ramachandran restraints generated. 2255 Oldfield, 0 Emsley, 2255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4510 Ramachandran restraints generated. 2255 Oldfield, 0 Emsley, 2255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 222 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 PHE cc_start: 0.6708 (OUTLIER) cc_final: 0.5395 (t80) REVERT: A 448 MET cc_start: 0.7027 (tpp) cc_final: 0.6760 (mtp) REVERT: A 546 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.7285 (m-30) REVERT: A 640 ILE cc_start: 0.8552 (pt) cc_final: 0.8258 (pt) REVERT: A 741 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8335 (mt0) REVERT: A 964 PHE cc_start: 0.5709 (m-80) cc_final: 0.5270 (m-80) REVERT: A 985 MET cc_start: 0.6649 (mmp) cc_final: 0.4862 (ptt) REVERT: A 1312 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6531 (mm) REVERT: A 1526 ILE cc_start: 0.8112 (mm) cc_final: 0.7776 (mt) REVERT: A 1738 ILE cc_start: 0.8093 (tt) cc_final: 0.7873 (tt) REVERT: A 1956 HIS cc_start: 0.6619 (m170) cc_final: 0.6413 (m170) REVERT: B 48 PHE cc_start: 0.6529 (m-10) cc_final: 0.6287 (m-10) REVERT: B 91 LYS cc_start: 0.8623 (tppp) cc_final: 0.8020 (mmtt) REVERT: B 105 MET cc_start: 0.5710 (tpt) cc_final: 0.5372 (tpt) outliers start: 64 outliers final: 49 residues processed: 275 average time/residue: 0.2913 time to fit residues: 126.8068 Evaluate side-chains 272 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 219 time to evaluate : 2.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 625 ASP Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 781 ASN Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 896 PHE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 980 ASN Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1135 VAL Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1275 ILE Chi-restraints excluded: chain A residue 1305 THR Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1313 SER Chi-restraints excluded: chain A residue 1348 VAL Chi-restraints excluded: chain A residue 1374 THR Chi-restraints excluded: chain A residue 1492 VAL Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1711 ASN Chi-restraints excluded: chain A residue 1770 VAL Chi-restraints excluded: chain A residue 1774 LYS Chi-restraints excluded: chain A residue 1835 LEU Chi-restraints excluded: chain A residue 1864 TYR Chi-restraints excluded: chain A residue 1946 VAL Chi-restraints excluded: chain A residue 1991 SER Chi-restraints excluded: chain A residue 2032 THR Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 135 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 54 optimal weight: 0.4980 chunk 165 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 179 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 184 optimal weight: 0.0870 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 157 optimal weight: 0.8980 chunk 10 optimal weight: 0.0980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1329 GLN A1723 ASN ** A1917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.133754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.112830 restraints weight = 39533.437| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.15 r_work: 0.3619 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18471 Z= 0.185 Angle : 0.596 10.945 25011 Z= 0.311 Chirality : 0.045 0.206 2793 Planarity : 0.004 0.045 3254 Dihedral : 5.536 57.085 2449 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.18 % Favored : 92.64 % Rotamer: Outliers : 2.85 % Allowed : 18.17 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.18), residues: 2255 helix: 1.30 (0.21), residues: 667 sheet: -1.18 (0.25), residues: 407 loop : -1.55 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 102 HIS 0.013 0.001 HIS A 924 PHE 0.041 0.002 PHE A1464 TYR 0.023 0.001 TYR A1837 ARG 0.003 0.000 ARG A1309 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4692.31 seconds wall clock time: 85 minutes 22.06 seconds (5122.06 seconds total)