Starting phenix.real_space_refine on Sun Aug 24 08:19:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qeo_18374/08_2025/8qeo_18374_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qeo_18374/08_2025/8qeo_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/cci-nas-00/data/ceres_data/8qeo_18374/08_2025/8qeo_18374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qeo_18374/08_2025/8qeo_18374.map" model { file = "/net/cci-nas-00/data/ceres_data/8qeo_18374/08_2025/8qeo_18374_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qeo_18374/08_2025/8qeo_18374_neut.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'ASN:plan1': 1, 'ARG: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: 4.41, per 1000 atoms: 0.24 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 - 3.00 Amino acid : True - 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: 1.74 Conformation dependent library (CDL) restraints added in 867.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 1.26 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: 5.74 Time building geometry restraints manager: 2.26 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: 0.00 - 1.35: 24327 1.35 - 2.70: 591 2.70 - 4.04: 73 4.04 - 5.39: 17 5.39 - 6.74: 3 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 3.040 nonbonded pdb=" OG SER A 748 " pdb=" OE1 GLU A 749 " model vdw 2.129 3.040 nonbonded pdb=" N GLU A 907 " pdb=" OE1 GLU A 907 " model vdw 2.142 3.120 nonbonded pdb=" O ASN B 164 " pdb=" OG1 THR B 165 " model vdw 2.193 3.040 nonbonded pdb=" ND2 ASN A 40 " pdb=" OE1 GLU A 44 " model vdw 2.196 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 12.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 23.830 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.830 ------------------------------------------------------------------------------- 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 : 0.005 0.442 18477 Z= 0.218 Angle : 0.527 6.742 25017 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 : 6.34 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A 499 TYR 0.013 0.002 TYR A 189 PHE 0.014 0.001 PHE A1621 TRP 0.009 0.001 TRP A 102 HIS 0.002 0.001 HIS A1997 Details of bonding type rmsd covalent geometry : bond 0.00375 (18471) covalent geometry : angle 0.52714 (25011) SS BOND : bond 0.00469 ( 3) SS BOND : angle 0.84264 ( 6) hydrogen bonds : bond 0.14593 ( 707) hydrogen bonds : angle 6.39669 ( 1905) metal coordination : bond 0.31224 ( 3) *********************** 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 to be fit. rotamer outliers: 54 poor density : 419 time to evaluate : 0.712 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: 0.1485 time to fit residues: 104.6771 Evaluate side-chains 275 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 252 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 216 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.0020 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 ASN A 492 HIS A 596 ASN A 611 ASN A 809 ASN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1126 HIS ** A1747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1778 ASN A2184 GLN ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN B 136 ASN ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.132460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.110676 restraints weight = 39734.707| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.99 r_work: 0.3584 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18477 Z= 0.198 Angle : 0.633 9.815 25017 Z= 0.338 Chirality : 0.047 0.212 2793 Planarity : 0.004 0.060 3254 Dihedral : 6.678 85.641 2477 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.72 % Favored : 92.15 % Rotamer: Outliers : 2.85 % Allowed : 11.05 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.18), residues: 2255 helix: 0.92 (0.20), residues: 668 sheet: -1.39 (0.24), residues: 417 loop : -1.69 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1281 TYR 0.025 0.002 TYR A 580 PHE 0.030 0.002 PHE A1966 TRP 0.013 0.002 TRP A1264 HIS 0.010 0.001 HIS A2041 Details of bonding type rmsd covalent geometry : bond 0.00461 (18471) covalent geometry : angle 0.63334 (25011) SS BOND : bond 0.00372 ( 3) SS BOND : angle 0.69221 ( 6) hydrogen bonds : bond 0.04826 ( 707) hydrogen bonds : angle 5.31325 ( 1905) metal coordination : bond 0.02661 ( 3) *********************** 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 328 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 270 time to evaluate : 0.716 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 251 SER cc_start: 0.8444 (p) cc_final: 0.8103 (m) REVERT: A 289 MET cc_start: 0.8587 (mmm) cc_final: 0.8326 (mmm) REVERT: A 315 THR cc_start: 0.8046 (OUTLIER) cc_final: 0.7800 (t) REVERT: A 463 LYS cc_start: 0.8105 (mtpp) cc_final: 0.7759 (ttmm) REVERT: A 510 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8605 (pt0) REVERT: A 603 TYR cc_start: 0.7606 (m-80) cc_final: 0.7305 (m-80) REVERT: A 640 ILE cc_start: 0.8579 (pt) cc_final: 0.8327 (pt) REVERT: A 741 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8484 (tt0) REVERT: A 900 PHE cc_start: 0.7539 (m-80) cc_final: 0.7003 (m-80) REVERT: A 985 MET cc_start: 0.6668 (mmp) cc_final: 0.5057 (ptt) REVERT: A 1066 ILE cc_start: 0.4272 (OUTLIER) cc_final: 0.3929 (mm) REVERT: A 1125 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8087 (ttmm) REVERT: A 1332 MET cc_start: 0.6763 (mtm) cc_final: 0.6562 (mtm) REVERT: A 1387 HIS cc_start: 0.7594 (OUTLIER) cc_final: 0.7385 (m90) REVERT: A 1433 LEU cc_start: 0.6691 (tp) cc_final: 0.6426 (tp) REVERT: A 1503 LYS cc_start: 0.8630 (mptt) cc_final: 0.8423 (mptt) REVERT: A 1787 LYS cc_start: -0.0068 (tppt) cc_final: -0.0790 (mmtt) REVERT: A 2147 ASN cc_start: 0.5337 (t0) cc_final: 0.4707 (m110) REVERT: A 2149 PHE cc_start: 0.7886 (m-80) cc_final: 0.7275 (m-80) REVERT: B 91 LYS cc_start: 0.8381 (tppp) cc_final: 0.7943 (tptm) REVERT: B 141 GLN cc_start: 0.5495 (pp30) cc_final: 0.4885 (pp30) outliers start: 58 outliers final: 34 residues processed: 314 average time/residue: 0.1499 time to fit residues: 72.4901 Evaluate side-chains 263 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 223 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 315 THR 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 521 SER Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain A residue 575 ARG 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 980 ASN Chi-restraints excluded: chain A residue 983 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 1066 ILE Chi-restraints excluded: chain A residue 1125 LYS Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1283 GLU Chi-restraints excluded: chain A residue 1303 ILE 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 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 2032 THR 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 93 optimal weight: 1.9990 chunk 174 optimal weight: 0.0170 chunk 189 optimal weight: 0.8980 chunk 210 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 86 optimal weight: 0.0470 chunk 96 optimal weight: 6.9990 chunk 197 optimal weight: 0.2980 chunk 154 optimal weight: 0.9980 chunk 204 optimal weight: 0.0980 chunk 3 optimal weight: 2.9990 overall best weight: 0.2716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2184 GLN ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.134543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.113409 restraints weight = 40081.101| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.21 r_work: 0.3612 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18477 Z= 0.121 Angle : 0.561 10.292 25017 Z= 0.301 Chirality : 0.044 0.210 2793 Planarity : 0.004 0.043 3254 Dihedral : 6.113 80.952 2465 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.18 % Favored : 92.64 % Rotamer: Outliers : 3.00 % Allowed : 12.03 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.18), residues: 2255 helix: 1.30 (0.21), residues: 668 sheet: -1.38 (0.25), residues: 389 loop : -1.60 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1296 TYR 0.016 0.001 TYR A 580 PHE 0.018 0.001 PHE A1262 TRP 0.017 0.001 TRP A1264 HIS 0.008 0.001 HIS A 924 Details of bonding type rmsd covalent geometry : bond 0.00263 (18471) covalent geometry : angle 0.56123 (25011) SS BOND : bond 0.01741 ( 3) SS BOND : angle 1.07903 ( 6) hydrogen bonds : bond 0.03844 ( 707) hydrogen bonds : angle 4.94795 ( 1905) metal coordination : bond 0.00129 ( 3) *********************** 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 318 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 257 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 SER cc_start: 0.8447 (p) cc_final: 0.8189 (m) REVERT: A 315 THR cc_start: 0.7985 (OUTLIER) cc_final: 0.7774 (t) REVERT: A 463 LYS cc_start: 0.8125 (mtpp) cc_final: 0.7788 (ttmm) REVERT: A 510 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8512 (pt0) REVERT: A 516 MET cc_start: 0.8608 (mtp) cc_final: 0.8315 (mtp) REVERT: A 566 ILE cc_start: 0.6331 (OUTLIER) cc_final: 0.5677 (pt) REVERT: A 603 TYR cc_start: 0.7483 (m-80) cc_final: 0.7197 (m-80) REVERT: A 741 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8335 (tt0) REVERT: A 815 LEU cc_start: 0.5524 (tp) cc_final: 0.5260 (tp) REVERT: A 900 PHE cc_start: 0.7549 (m-80) cc_final: 0.6867 (m-80) REVERT: A 964 PHE cc_start: 0.6357 (m-80) cc_final: 0.5567 (m-80) REVERT: A 982 SER cc_start: 0.8488 (t) cc_final: 0.8183 (p) REVERT: A 985 MET cc_start: 0.6725 (mmp) cc_final: 0.5045 (ptt) REVERT: A 1125 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8257 (ttmm) REVERT: A 1157 PHE cc_start: 0.7351 (m-80) cc_final: 0.7019 (m-10) REVERT: A 1332 MET cc_start: 0.6876 (mtm) cc_final: 0.6556 (mtm) REVERT: A 1526 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8515 (mt) REVERT: A 1787 LYS cc_start: -0.0808 (tppt) cc_final: -0.1271 (mmtt) REVERT: A 1884 LYS cc_start: 0.5072 (ptpp) cc_final: 0.4486 (mtmt) REVERT: A 2079 TRP cc_start: 0.8265 (m100) cc_final: 0.7973 (m100) REVERT: A 2147 ASN cc_start: 0.5326 (t0) cc_final: 0.4781 (m110) REVERT: A 2149 PHE cc_start: 0.7782 (m-80) cc_final: 0.7180 (m-80) REVERT: B 78 ASP cc_start: 0.6530 (t0) cc_final: 0.6321 (t0) REVERT: B 91 LYS cc_start: 0.8354 (tppp) cc_final: 0.7949 (tptm) REVERT: B 121 ARG cc_start: 0.6864 (tmt170) cc_final: 0.6630 (ttp80) REVERT: B 158 GLU cc_start: 0.7731 (mp0) cc_final: 0.7459 (mp0) outliers start: 61 outliers final: 37 residues processed: 309 average time/residue: 0.1469 time to fit residues: 69.3705 Evaluate side-chains 268 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 510 GLN 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 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 1032 ILE Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1125 LYS Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1297 SER 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 1462 TYR Chi-restraints excluded: chain A residue 1526 ILE Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1612 ILE Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1661 TYR 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 2059 ILE 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 4 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 171 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 225 optimal weight: 9.9990 chunk 216 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 GLN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1589 ASN A1744 ASN A1934 ASN ** A2143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.132587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.110962 restraints weight = 39983.129| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.17 r_work: 0.3576 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18477 Z= 0.174 Angle : 0.597 9.762 25017 Z= 0.318 Chirality : 0.045 0.196 2793 Planarity : 0.004 0.042 3254 Dihedral : 6.000 86.826 2454 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.72 % Favored : 92.15 % Rotamer: Outliers : 3.68 % Allowed : 12.97 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.18), residues: 2255 helix: 1.13 (0.20), residues: 668 sheet: -1.47 (0.24), residues: 430 loop : -1.62 (0.18), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1281 TYR 0.016 0.002 TYR A1531 PHE 0.019 0.002 PHE A1966 TRP 0.023 0.002 TRP A1264 HIS 0.008 0.001 HIS A 924 Details of bonding type rmsd covalent geometry : bond 0.00406 (18471) covalent geometry : angle 0.59662 (25011) SS BOND : bond 0.00137 ( 3) SS BOND : angle 1.61647 ( 6) hydrogen bonds : bond 0.04300 ( 707) hydrogen bonds : angle 5.08157 ( 1905) metal coordination : bond 0.00328 ( 3) *********************** 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 314 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 239 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 SER cc_start: 0.8448 (p) cc_final: 0.8135 (m) REVERT: A 315 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7821 (t) REVERT: A 321 MET cc_start: 0.8334 (mmt) cc_final: 0.7789 (mmt) REVERT: A 463 LYS cc_start: 0.8117 (mtpp) cc_final: 0.7692 (ttpp) REVERT: A 566 ILE cc_start: 0.6573 (OUTLIER) cc_final: 0.5958 (pt) REVERT: A 603 TYR cc_start: 0.7516 (m-80) cc_final: 0.7200 (m-80) REVERT: A 741 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8194 (mt0) REVERT: A 815 LEU cc_start: 0.5508 (tp) cc_final: 0.5241 (tp) REVERT: A 900 PHE cc_start: 0.7659 (m-80) cc_final: 0.6760 (m-80) REVERT: A 964 PHE cc_start: 0.6516 (m-80) cc_final: 0.5600 (m-80) REVERT: A 985 MET cc_start: 0.6777 (mmp) cc_final: 0.5032 (ptt) REVERT: A 1125 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8267 (ttmm) REVERT: A 1157 PHE cc_start: 0.7423 (m-80) cc_final: 0.7202 (m-10) REVERT: A 1312 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7231 (mm) REVERT: A 1332 MET cc_start: 0.6818 (mtm) cc_final: 0.6525 (mtm) REVERT: A 1433 LEU cc_start: 0.6849 (tp) cc_final: 0.6628 (tp) REVERT: A 1526 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8512 (mt) REVERT: A 1787 LYS cc_start: -0.0617 (tppt) cc_final: -0.2137 (mptt) REVERT: A 1976 LYS cc_start: 0.7643 (mttt) cc_final: 0.7070 (mmmt) REVERT: A 2147 ASN cc_start: 0.5672 (t0) cc_final: 0.5000 (m-40) REVERT: B 78 ASP cc_start: 0.7035 (t0) cc_final: 0.6812 (t0) REVERT: B 91 LYS cc_start: 0.8371 (tppp) cc_final: 0.7980 (tptm) REVERT: B 105 MET cc_start: 0.5031 (tpt) cc_final: 0.4793 (tpt) REVERT: B 141 GLN cc_start: 0.6724 (pm20) cc_final: 0.5971 (pp30) outliers start: 75 outliers final: 49 residues processed: 294 average time/residue: 0.1391 time to fit residues: 63.6917 Evaluate side-chains 276 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 221 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 277 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 315 THR 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 393 SER 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 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 723 ILE Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain A residue 878 LEU 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 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 1125 LYS Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1297 SER 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 1526 ILE Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1612 ILE Chi-restraints excluded: chain A residue 1649 VAL 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 2059 ILE Chi-restraints excluded: chain A residue 2112 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 155 optimal weight: 0.9980 chunk 205 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 225 optimal weight: 0.4980 chunk 121 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 210 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 99 optimal weight: 0.0270 chunk 161 optimal weight: 0.7980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 GLN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1654 ASN A1997 HIS A2143 ASN ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.133067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.111180 restraints weight = 39903.474| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.26 r_work: 0.3587 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18477 Z= 0.144 Angle : 0.567 10.439 25017 Z= 0.302 Chirality : 0.044 0.191 2793 Planarity : 0.004 0.042 3254 Dihedral : 5.641 57.761 2451 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.49 % Favored : 92.37 % Rotamer: Outliers : 3.68 % Allowed : 14.00 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.18), residues: 2255 helix: 1.23 (0.21), residues: 665 sheet: -1.41 (0.24), residues: 429 loop : -1.62 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1241 TYR 0.020 0.002 TYR A1330 PHE 0.023 0.001 PHE A2129 TRP 0.018 0.001 TRP A1264 HIS 0.006 0.001 HIS A 924 Details of bonding type rmsd covalent geometry : bond 0.00331 (18471) covalent geometry : angle 0.56670 (25011) SS BOND : bond 0.00327 ( 3) SS BOND : angle 1.13909 ( 6) hydrogen bonds : bond 0.03973 ( 707) hydrogen bonds : angle 4.93059 ( 1905) metal coordination : bond 0.00228 ( 3) *********************** 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 309 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 234 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 SER cc_start: 0.8460 (p) cc_final: 0.8127 (m) REVERT: A 321 MET cc_start: 0.8277 (mmt) cc_final: 0.7787 (mmt) REVERT: A 463 LYS cc_start: 0.8096 (mtpp) cc_final: 0.7667 (ttpp) REVERT: A 566 ILE cc_start: 0.6534 (OUTLIER) cc_final: 0.5917 (pt) REVERT: A 603 TYR cc_start: 0.7479 (m-80) cc_final: 0.7164 (m-80) REVERT: A 741 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8439 (mt0) REVERT: A 815 LEU cc_start: 0.5544 (tp) cc_final: 0.5273 (tp) REVERT: A 900 PHE cc_start: 0.7617 (m-80) cc_final: 0.6823 (m-80) REVERT: A 964 PHE cc_start: 0.6637 (m-80) cc_final: 0.5700 (m-80) REVERT: A 985 MET cc_start: 0.6870 (mmp) cc_final: 0.5060 (ptt) REVERT: A 1125 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8246 (ttmm) REVERT: A 1157 PHE cc_start: 0.7498 (m-80) cc_final: 0.7198 (m-10) REVERT: A 1332 MET cc_start: 0.6855 (mtm) cc_final: 0.6548 (mtm) REVERT: A 1433 LEU cc_start: 0.6824 (tp) cc_final: 0.6563 (tp) REVERT: A 1464 PHE cc_start: 0.8518 (t80) cc_final: 0.8249 (t80) REVERT: A 1471 GLU cc_start: 0.6909 (mp0) cc_final: 0.6352 (mp0) REVERT: A 1526 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8494 (mt) REVERT: A 1787 LYS cc_start: 0.0304 (tppt) cc_final: -0.3345 (tptp) REVERT: A 1884 LYS cc_start: 0.4986 (pttt) cc_final: 0.4646 (ptpt) REVERT: A 1986 GLN cc_start: 0.6283 (mm-40) cc_final: 0.5996 (mm110) REVERT: A 2147 ASN cc_start: 0.5646 (t0) cc_final: 0.4977 (m-40) REVERT: A 2150 TYR cc_start: 0.7962 (t80) cc_final: 0.7565 (t80) REVERT: B 91 LYS cc_start: 0.8398 (tppp) cc_final: 0.7999 (tptm) REVERT: B 99 ARG cc_start: 0.6572 (tpp80) cc_final: 0.6359 (tpp80) REVERT: B 158 GLU cc_start: 0.7561 (mp0) cc_final: 0.7289 (mp0) outliers start: 75 outliers final: 57 residues processed: 288 average time/residue: 0.1299 time to fit residues: 57.7789 Evaluate side-chains 280 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 219 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 277 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 339 ASP 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 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 1066 ILE Chi-restraints excluded: chain A residue 1125 LYS Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1297 SER 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 1526 ILE Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1612 ILE Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1661 TYR 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 1992 ILE Chi-restraints excluded: chain A residue 2025 MET Chi-restraints excluded: chain A residue 2041 HIS Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain A residue 2112 ASN Chi-restraints excluded: chain A residue 2143 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 86 optimal weight: 0.7980 chunk 183 optimal weight: 0.0870 chunk 19 optimal weight: 0.9990 chunk 164 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1441 ASN A1934 ASN A2026 GLN ** A2143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.132923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.110933 restraints weight = 39761.851| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.27 r_work: 0.3585 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18477 Z= 0.159 Angle : 0.578 9.194 25017 Z= 0.308 Chirality : 0.045 0.191 2793 Planarity : 0.004 0.043 3254 Dihedral : 5.691 58.042 2451 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.58 % Favored : 92.28 % Rotamer: Outliers : 3.68 % Allowed : 14.39 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.18), residues: 2255 helix: 1.20 (0.21), residues: 667 sheet: -1.45 (0.24), residues: 438 loop : -1.64 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1281 TYR 0.019 0.002 TYR A1531 PHE 0.019 0.002 PHE A2129 TRP 0.025 0.002 TRP A1264 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd covalent geometry : bond 0.00371 (18471) covalent geometry : angle 0.57774 (25011) SS BOND : bond 0.00287 ( 3) SS BOND : angle 0.96452 ( 6) hydrogen bonds : bond 0.04084 ( 707) hydrogen bonds : angle 4.94647 ( 1905) metal coordination : bond 0.00292 ( 3) *********************** 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 307 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 232 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 PHE cc_start: 0.6898 (OUTLIER) cc_final: 0.5410 (t80) REVERT: A 251 SER cc_start: 0.8467 (p) cc_final: 0.8098 (m) REVERT: A 270 ASP cc_start: 0.7203 (t0) cc_final: 0.6995 (m-30) REVERT: A 315 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7814 (t) REVERT: A 321 MET cc_start: 0.8308 (mmt) cc_final: 0.7908 (mmt) REVERT: A 463 LYS cc_start: 0.8109 (mtpp) cc_final: 0.7684 (ttpp) REVERT: A 566 ILE cc_start: 0.6583 (OUTLIER) cc_final: 0.5993 (pt) REVERT: A 603 TYR cc_start: 0.7471 (m-80) cc_final: 0.7162 (m-80) REVERT: A 815 LEU cc_start: 0.5553 (tp) cc_final: 0.5281 (tp) REVERT: A 858 GLU cc_start: 0.7272 (tt0) cc_final: 0.6998 (tt0) REVERT: A 900 PHE cc_start: 0.7700 (m-80) cc_final: 0.6754 (m-80) REVERT: A 964 PHE cc_start: 0.6517 (m-80) cc_final: 0.5521 (m-80) REVERT: A 985 MET cc_start: 0.6914 (mmp) cc_final: 0.5053 (ptt) REVERT: A 1125 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8249 (ttmm) REVERT: A 1433 LEU cc_start: 0.6852 (tp) cc_final: 0.6514 (tp) REVERT: A 1464 PHE cc_start: 0.8552 (t80) cc_final: 0.8255 (t80) REVERT: A 1471 GLU cc_start: 0.6863 (mp0) cc_final: 0.6391 (mp0) REVERT: A 1526 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8488 (mt) REVERT: A 1787 LYS cc_start: 0.0814 (tppt) cc_final: -0.3177 (tptp) REVERT: A 1986 GLN cc_start: 0.6385 (mm-40) cc_final: 0.6129 (mm110) REVERT: B 91 LYS cc_start: 0.8407 (tppp) cc_final: 0.7988 (tptm) REVERT: B 99 ARG cc_start: 0.6493 (tpp80) cc_final: 0.6257 (tpp80) REVERT: B 158 GLU cc_start: 0.7568 (mp0) cc_final: 0.7302 (mp0) outliers start: 75 outliers final: 57 residues processed: 285 average time/residue: 0.1304 time to fit residues: 58.0206 Evaluate side-chains 275 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 213 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 243 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 339 ASP 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 393 SER 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 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 787 ILE 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 980 ASN Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1125 LYS Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1297 SER 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 1526 ILE Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1612 ILE Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1661 TYR 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 1992 ILE Chi-restraints excluded: chain A residue 2005 MET Chi-restraints excluded: chain A residue 2041 HIS Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain A residue 2112 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 130 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 GLN A 553 GLN A 781 ASN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2026 GLN ** A2143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.130986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.109834 restraints weight = 39918.241| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.17 r_work: 0.3549 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 18477 Z= 0.238 Angle : 0.656 9.453 25017 Z= 0.350 Chirality : 0.047 0.292 2793 Planarity : 0.004 0.046 3254 Dihedral : 6.025 58.808 2451 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.91 % Favored : 90.95 % Rotamer: Outliers : 3.98 % Allowed : 15.08 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.18), residues: 2255 helix: 0.90 (0.20), residues: 667 sheet: -1.57 (0.24), residues: 433 loop : -1.78 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1281 TYR 0.022 0.002 TYR A2148 PHE 0.024 0.002 PHE A1621 TRP 0.028 0.002 TRP A1264 HIS 0.010 0.001 HIS A 924 Details of bonding type rmsd covalent geometry : bond 0.00561 (18471) covalent geometry : angle 0.65561 (25011) SS BOND : bond 0.00453 ( 3) SS BOND : angle 1.23651 ( 6) hydrogen bonds : bond 0.04817 ( 707) hydrogen bonds : angle 5.23368 ( 1905) metal coordination : bond 0.00477 ( 3) *********************** 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 313 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 232 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 SER cc_start: 0.8452 (p) cc_final: 0.8064 (m) REVERT: A 270 ASP cc_start: 0.7339 (t0) cc_final: 0.7044 (m-30) REVERT: A 315 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7870 (t) REVERT: A 321 MET cc_start: 0.8332 (mmt) cc_final: 0.7854 (mmt) REVERT: A 463 LYS cc_start: 0.8169 (mtpp) cc_final: 0.7742 (ttpp) REVERT: A 603 TYR cc_start: 0.7619 (m-80) cc_final: 0.7288 (m-80) REVERT: A 815 LEU cc_start: 0.5746 (tp) cc_final: 0.5499 (tp) REVERT: A 858 GLU cc_start: 0.7316 (tt0) cc_final: 0.6891 (tt0) REVERT: A 964 PHE cc_start: 0.6679 (m-80) cc_final: 0.5641 (m-80) REVERT: A 1312 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7255 (mm) REVERT: A 1433 LEU cc_start: 0.6930 (tp) cc_final: 0.6497 (tp) REVERT: A 1462 TYR cc_start: 0.6770 (t80) cc_final: 0.6270 (t80) REVERT: A 1464 PHE cc_start: 0.8604 (t80) cc_final: 0.8271 (t80) REVERT: A 1471 GLU cc_start: 0.6873 (mp0) cc_final: 0.6273 (mp0) REVERT: A 1526 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8519 (mt) REVERT: A 1884 LYS cc_start: 0.4910 (pttt) cc_final: 0.4453 (ptpt) REVERT: A 1986 GLN cc_start: 0.6464 (mm-40) cc_final: 0.6262 (mm110) REVERT: B 91 LYS cc_start: 0.8374 (tppp) cc_final: 0.8141 (tppt) REVERT: B 99 ARG cc_start: 0.6568 (tpp80) cc_final: 0.6317 (tpp80) REVERT: B 158 GLU cc_start: 0.7642 (mp0) cc_final: 0.7369 (mp0) outliers start: 81 outliers final: 62 residues processed: 291 average time/residue: 0.1241 time to fit residues: 56.2308 Evaluate side-chains 284 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 219 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 124 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 315 THR 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 393 SER 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 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 781 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 980 ASN Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1125 LYS Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1297 SER 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 1478 SER Chi-restraints excluded: chain A residue 1492 VAL Chi-restraints excluded: chain A residue 1526 ILE Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1612 ILE Chi-restraints excluded: chain A residue 1649 VAL 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 1992 ILE Chi-restraints excluded: chain A residue 2005 MET Chi-restraints excluded: chain A residue 2041 HIS Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain A residue 2112 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 37 optimal weight: 0.7980 chunk 179 optimal weight: 0.6980 chunk 143 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 69 optimal weight: 0.4980 chunk 166 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 198 optimal weight: 0.0470 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 GLN A 553 GLN ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1441 ASN A2026 GLN ** A2143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.133258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.111354 restraints weight = 39687.166| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.15 r_work: 0.3604 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18477 Z= 0.138 Angle : 0.591 9.842 25017 Z= 0.312 Chirality : 0.045 0.256 2793 Planarity : 0.004 0.043 3254 Dihedral : 5.827 58.904 2451 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.32 % Favored : 92.55 % Rotamer: Outliers : 3.14 % Allowed : 16.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.18), residues: 2255 helix: 1.14 (0.21), residues: 668 sheet: -1.44 (0.24), residues: 429 loop : -1.69 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1281 TYR 0.020 0.002 TYR A1531 PHE 0.019 0.002 PHE A2129 TRP 0.010 0.001 TRP A1948 HIS 0.012 0.001 HIS A 924 Details of bonding type rmsd covalent geometry : bond 0.00319 (18471) covalent geometry : angle 0.59052 (25011) SS BOND : bond 0.00265 ( 3) SS BOND : angle 1.01721 ( 6) hydrogen bonds : bond 0.04003 ( 707) hydrogen bonds : angle 5.00174 ( 1905) metal coordination : bond 0.00260 ( 3) *********************** 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 287 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 223 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 PHE cc_start: 0.6895 (OUTLIER) cc_final: 0.5300 (t80) REVERT: A 289 MET cc_start: 0.8646 (mmm) cc_final: 0.8440 (mmm) REVERT: A 315 THR cc_start: 0.8069 (OUTLIER) cc_final: 0.7821 (t) REVERT: A 321 MET cc_start: 0.8242 (mmt) cc_final: 0.7894 (mmt) REVERT: A 463 LYS cc_start: 0.8074 (mtpp) cc_final: 0.7691 (ttpp) REVERT: A 603 TYR cc_start: 0.7510 (m-80) cc_final: 0.7203 (m-80) REVERT: A 878 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6585 (pp) REVERT: A 900 PHE cc_start: 0.7602 (m-80) cc_final: 0.7082 (m-80) REVERT: A 985 MET cc_start: 0.7140 (mmm) cc_final: 0.5573 (ptt) REVERT: A 1433 LEU cc_start: 0.6839 (tp) cc_final: 0.6397 (tp) REVERT: A 1462 TYR cc_start: 0.6643 (t80) cc_final: 0.6356 (t80) REVERT: A 1464 PHE cc_start: 0.8575 (t80) cc_final: 0.8215 (t80) REVERT: A 1471 GLU cc_start: 0.6839 (mp0) cc_final: 0.6286 (mp0) REVERT: A 1526 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8465 (mt) REVERT: A 1812 ASP cc_start: 0.5432 (p0) cc_final: 0.5151 (p0) REVERT: A 1955 MET cc_start: 0.6592 (tpp) cc_final: 0.6145 (tpp) REVERT: A 2147 ASN cc_start: 0.5699 (t0) cc_final: 0.4974 (m-40) REVERT: B 91 LYS cc_start: 0.8333 (tppp) cc_final: 0.8117 (tppt) REVERT: B 158 GLU cc_start: 0.7655 (mp0) cc_final: 0.7341 (mp0) outliers start: 64 outliers final: 51 residues processed: 271 average time/residue: 0.1156 time to fit residues: 49.1782 Evaluate side-chains 271 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 216 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 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 302 GLU Chi-restraints excluded: chain A residue 315 THR 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 393 SER 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 571 ARG Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain A residue 578 ILE 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 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 980 ASN Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1194 THR Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1297 SER Chi-restraints excluded: chain A residue 1305 THR 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 1478 SER Chi-restraints excluded: chain A residue 1526 ILE Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1612 ILE Chi-restraints excluded: chain A residue 1649 VAL 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 1992 ILE Chi-restraints excluded: chain A residue 2041 HIS Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain A residue 2112 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 134 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 223 optimal weight: 3.9990 chunk 212 optimal weight: 0.6980 chunk 49 optimal weight: 0.0570 chunk 97 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 120 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 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 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1986 GLN A2026 GLN ** A2143 ASN ** 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 = 0.4116 r_free = 0.4116 target = 0.133756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.112714 restraints weight = 39428.133| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.04 r_work: 0.3613 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18477 Z= 0.131 Angle : 0.581 9.331 25017 Z= 0.307 Chirality : 0.044 0.241 2793 Planarity : 0.004 0.044 3254 Dihedral : 5.694 58.412 2451 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.72 % Favored : 92.15 % Rotamer: Outliers : 3.19 % Allowed : 16.75 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.18), residues: 2255 helix: 1.26 (0.21), residues: 668 sheet: -1.40 (0.24), residues: 420 loop : -1.67 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1241 TYR 0.021 0.002 TYR A1837 PHE 0.016 0.002 PHE A 446 TRP 0.012 0.001 TRP A1948 HIS 0.014 0.001 HIS A 924 Details of bonding type rmsd covalent geometry : bond 0.00300 (18471) covalent geometry : angle 0.58075 (25011) SS BOND : bond 0.00323 ( 3) SS BOND : angle 0.93962 ( 6) hydrogen bonds : bond 0.03879 ( 707) hydrogen bonds : angle 4.90980 ( 1905) metal coordination : bond 0.00173 ( 3) *********************** 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 294 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 229 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 PHE cc_start: 0.6883 (OUTLIER) cc_final: 0.5403 (t80) REVERT: A 251 SER cc_start: 0.8410 (p) cc_final: 0.8005 (m) REVERT: A 315 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7801 (t) REVERT: A 321 MET cc_start: 0.8239 (mmt) cc_final: 0.7869 (mmt) REVERT: A 438 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7544 (mm-30) REVERT: A 463 LYS cc_start: 0.8022 (mtpp) cc_final: 0.7705 (ttpp) REVERT: A 603 TYR cc_start: 0.7465 (m-80) cc_final: 0.7158 (m-80) REVERT: A 656 ASP cc_start: 0.7700 (p0) cc_final: 0.7465 (p0) REVERT: A 878 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6674 (pp) REVERT: A 900 PHE cc_start: 0.7530 (m-80) cc_final: 0.7034 (m-80) REVERT: A 985 MET cc_start: 0.7128 (mmm) cc_final: 0.5451 (ptt) REVERT: A 1170 TRP cc_start: 0.6892 (m-10) cc_final: 0.6652 (m-10) REVERT: A 1433 LEU cc_start: 0.6788 (tp) cc_final: 0.6418 (tp) REVERT: A 1464 PHE cc_start: 0.8560 (t80) cc_final: 0.8125 (t80) REVERT: A 1471 GLU cc_start: 0.6823 (mp0) cc_final: 0.6251 (mp0) REVERT: A 1526 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8453 (mt) REVERT: A 1955 MET cc_start: 0.6543 (tpp) cc_final: 0.6132 (tpp) REVERT: A 2147 ASN cc_start: 0.5677 (t0) cc_final: 0.4885 (m-40) REVERT: B 91 LYS cc_start: 0.8302 (tppp) cc_final: 0.8066 (tppt) REVERT: B 158 GLU cc_start: 0.7611 (mp0) cc_final: 0.7302 (mp0) outliers start: 65 outliers final: 50 residues processed: 276 average time/residue: 0.1254 time to fit residues: 54.3415 Evaluate side-chains 271 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 217 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 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 302 GLU Chi-restraints excluded: chain A residue 315 THR 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 393 SER 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 571 ARG Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 787 ILE 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 980 ASN Chi-restraints excluded: chain A residue 1032 ILE 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 1297 SER Chi-restraints excluded: chain A residue 1305 THR 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 1526 ILE Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1612 ILE Chi-restraints excluded: chain A residue 1649 VAL 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 1946 VAL Chi-restraints excluded: chain A residue 1992 ILE Chi-restraints excluded: chain A residue 2041 HIS Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain A residue 2112 ASN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 134 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 139 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 225 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 75 optimal weight: 0.0270 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1459 ASN A1986 GLN A2026 GLN A2063 ASN ** A2143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.132626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.111273 restraints weight = 39507.387| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.20 r_work: 0.3583 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18477 Z= 0.164 Angle : 0.612 10.586 25017 Z= 0.324 Chirality : 0.046 0.239 2793 Planarity : 0.004 0.044 3254 Dihedral : 5.773 58.607 2451 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.76 % Favored : 92.06 % Rotamer: Outliers : 3.05 % Allowed : 17.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.18), residues: 2255 helix: 1.21 (0.21), residues: 668 sheet: -1.38 (0.24), residues: 427 loop : -1.71 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1281 TYR 0.018 0.002 TYR A1531 PHE 0.027 0.002 PHE A1157 TRP 0.010 0.001 TRP A1948 HIS 0.014 0.001 HIS A 924 Details of bonding type rmsd covalent geometry : bond 0.00383 (18471) covalent geometry : angle 0.61222 (25011) SS BOND : bond 0.00277 ( 3) SS BOND : angle 0.79294 ( 6) hydrogen bonds : bond 0.04138 ( 707) hydrogen bonds : angle 4.98328 ( 1905) metal coordination : bond 0.00294 ( 3) ********************** 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 287 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 225 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 PHE cc_start: 0.6921 (OUTLIER) cc_final: 0.5373 (t80) REVERT: A 270 ASP cc_start: 0.7416 (t0) cc_final: 0.7183 (m-30) REVERT: A 315 THR cc_start: 0.8101 (OUTLIER) cc_final: 0.7854 (t) REVERT: A 321 MET cc_start: 0.8291 (mmt) cc_final: 0.7917 (mmt) REVERT: A 438 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7642 (mm-30) REVERT: A 448 MET cc_start: 0.7990 (tpp) cc_final: 0.7762 (mtp) REVERT: A 463 LYS cc_start: 0.8015 (mtpp) cc_final: 0.7691 (ttpp) REVERT: A 603 TYR cc_start: 0.7525 (m-80) cc_final: 0.7215 (m-80) REVERT: A 656 ASP cc_start: 0.7827 (p0) cc_final: 0.7582 (p0) REVERT: A 858 GLU cc_start: 0.7018 (tt0) cc_final: 0.6809 (tt0) REVERT: A 878 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6692 (pp) REVERT: A 900 PHE cc_start: 0.7634 (m-80) cc_final: 0.7054 (m-80) REVERT: A 964 PHE cc_start: 0.6662 (m-80) cc_final: 0.5710 (m-80) REVERT: A 985 MET cc_start: 0.7075 (mmm) cc_final: 0.5363 (ptt) REVERT: A 1170 TRP cc_start: 0.7047 (m-10) cc_final: 0.6821 (m-10) REVERT: A 1230 PHE cc_start: 0.7586 (m-80) cc_final: 0.7330 (m-80) REVERT: A 1433 LEU cc_start: 0.6971 (tp) cc_final: 0.6598 (tp) REVERT: A 1464 PHE cc_start: 0.8561 (t80) cc_final: 0.8139 (t80) REVERT: A 1471 GLU cc_start: 0.6842 (mp0) cc_final: 0.6276 (mp0) REVERT: A 1526 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8459 (mt) REVERT: A 1588 MET cc_start: 0.7652 (mmt) cc_final: 0.7295 (mmp) REVERT: A 1955 MET cc_start: 0.6628 (tpp) cc_final: 0.6300 (tpp) REVERT: A 1956 HIS cc_start: 0.7775 (m170) cc_final: 0.7429 (m170) REVERT: A 2147 ASN cc_start: 0.5762 (t0) cc_final: 0.4977 (m-40) REVERT: B 91 LYS cc_start: 0.8233 (tppp) cc_final: 0.7993 (tppt) REVERT: B 158 GLU cc_start: 0.7588 (mp0) cc_final: 0.7284 (mp0) outliers start: 62 outliers final: 54 residues processed: 271 average time/residue: 0.1361 time to fit residues: 58.1143 Evaluate side-chains 276 residues out of total 2049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 218 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 243 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 315 THR 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 393 SER 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 571 ARG Chi-restraints excluded: chain A residue 575 ARG Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 787 ILE 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 980 ASN Chi-restraints excluded: chain A residue 1032 ILE 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 1295 THR Chi-restraints excluded: chain A residue 1297 SER Chi-restraints excluded: chain A residue 1305 THR 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 1526 ILE Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1569 MET Chi-restraints excluded: chain A residue 1612 ILE Chi-restraints excluded: chain A residue 1649 VAL 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 1946 VAL Chi-restraints excluded: chain A residue 2041 HIS Chi-restraints excluded: chain A residue 2059 ILE Chi-restraints excluded: chain A residue 2063 ASN Chi-restraints excluded: chain A residue 2112 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 103 optimal weight: 0.0670 chunk 57 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 186 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 224 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1986 GLN A2026 GLN A2063 ASN ** A2143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.133407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.111996 restraints weight = 39562.733| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.22 r_work: 0.3603 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18477 Z= 0.138 Angle : 0.599 10.140 25017 Z= 0.317 Chirality : 0.045 0.220 2793 Planarity : 0.004 0.044 3254 Dihedral : 5.701 57.935 2451 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.89 % Favored : 91.93 % Rotamer: Outliers : 3.19 % Allowed : 17.19 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.18), residues: 2255 helix: 1.28 (0.21), residues: 668 sheet: -1.38 (0.24), residues: 423 loop : -1.68 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1241 TYR 0.024 0.002 TYR A1837 PHE 0.022 0.002 PHE A1157 TRP 0.011 0.001 TRP A1948 HIS 0.018 0.001 HIS A 924 Details of bonding type rmsd covalent geometry : bond 0.00317 (18471) covalent geometry : angle 0.59914 (25011) SS BOND : bond 0.00259 ( 3) SS BOND : angle 0.82615 ( 6) hydrogen bonds : bond 0.03928 ( 707) hydrogen bonds : angle 4.89717 ( 1905) metal coordination : bond 0.00235 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5903.50 seconds wall clock time: 101 minutes 42.47 seconds (6102.47 seconds total)