Starting phenix.real_space_refine (version: dev) on Mon Dec 12 23:54:26 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xjy_6724/12_2022/5xjy_6724.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xjy_6724/12_2022/5xjy_6724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xjy_6724/12_2022/5xjy_6724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xjy_6724/12_2022/5xjy_6724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xjy_6724/12_2022/5xjy_6724.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xjy_6724/12_2022/5xjy_6724.pdb" } resolution = 4.1 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 8": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 19": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 393": "NH1" <-> "NH2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 672": "NH1" <-> "NH2" Residue "A TYR 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 742": "NH1" <-> "NH2" Residue "A ARG 1336": "NH1" <-> "NH2" Residue "A TYR 1388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1417": "NH1" <-> "NH2" Residue "A ARG 1503": "NH1" <-> "NH2" Residue "A PHE 1535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1680": "NH1" <-> "NH2" Residue "A PHE 1721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1817": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 12785 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1901, 12626 Classifications: {'peptide': 1901} Incomplete info: {'truncation_to_alanine': 733} Link IDs: {'PTRANS': 89, 'TRANS': 1811} Chain breaks: 15 Unresolved chain link angles: 25 Unresolved non-hydrogen bonds: 2560 Unresolved non-hydrogen angles: 3266 Unresolved non-hydrogen dihedrals: 2133 Unresolved non-hydrogen chiralities: 254 Planarities with less than four sites: {'GLN:plan1': 28, 'ARG:plan': 40, 'TYR:plan': 21, 'ASN:plan1': 34, 'TRP:plan': 9, 'ASP:plan': 39, 'PHE:plan': 41, 'GLU:plan': 50, 'HIS:plan': 23} Unresolved non-hydrogen planarities: 1320 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 7.89, per 1000 atoms: 0.62 Number of scatterers: 12785 At special positions: 0 Unit cell: (101.91, 104.523, 220.805, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 2388 8.00 N 2245 7.00 C 8095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 81 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 309 " distance=2.02 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A1465 " - pdb=" SG CYS A1477 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " BMA B 3 " - " BMA B 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " BETA1-6 " BMA B 3 " - " BMA B 5 " NAG-ASN " NAG A2301 " - " ASN A 98 " " NAG A2302 " - " ASN A 400 " " NAG A2303 " - " ASN A 489 " " NAG A2304 " - " ASN A 521 " " NAG A2305 " - " ASN A1453 " " NAG B 1 " - " ASN A1504 " " NAG C 1 " - " ASN A1637 " Time building additional restraints: 5.89 Conformation dependent library (CDL) restraints added in 2.3 seconds 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3570 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 8 sheets defined 54.7% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 3 through 20 removed outlier: 4.017A pdb=" N LEU A 7 " --> pdb=" O CYS A 3 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 45 Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.538A pdb=" N ALA A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 117 removed outlier: 3.561A pdb=" N PHE A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 134 Processing helix chain 'A' and resid 200 through 210 removed outlier: 3.856A pdb=" N LEU A 206 " --> pdb=" O GLU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 227 removed outlier: 3.631A pdb=" N GLU A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 242 removed outlier: 3.713A pdb=" N MET A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Proline residue: A 238 - end of helix Processing helix chain 'A' and resid 251 through 275 removed outlier: 3.768A pdb=" N ALA A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 298 through 309 Processing helix chain 'A' and resid 353 through 365 Processing helix chain 'A' and resid 369 through 380 Proline residue: A 377 - end of helix removed outlier: 3.623A pdb=" N VAL A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 405 Processing helix chain 'A' and resid 410 through 427 removed outlier: 4.311A pdb=" N GLY A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TRP A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 418 " --> pdb=" O GLY A 414 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER A 420 " --> pdb=" O TRP A 416 " (cutoff:3.500A) Proline residue: A 421 - end of helix Processing helix chain 'A' and resid 430 through 440 Processing helix chain 'A' and resid 443 through 448 Processing helix chain 'A' and resid 448 through 455 Processing helix chain 'A' and resid 461 through 468 Processing helix chain 'A' and resid 483 through 502 removed outlier: 4.168A pdb=" N ASN A 489 " --> pdb=" O ARG A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 529 Processing helix chain 'A' and resid 592 through 609 removed outlier: 3.727A pdb=" N LEU A 596 " --> pdb=" O GLY A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 640 through 665 removed outlier: 4.343A pdb=" N ALA A 647 " --> pdb=" O PHE A 643 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TRP A 648 " --> pdb=" O MET A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 674 Processing helix chain 'A' and resid 677 through 706 removed outlier: 3.796A pdb=" N LEU A 681 " --> pdb=" O ASP A 677 " (cutoff:3.500A) Proline residue: A 692 - end of helix removed outlier: 3.528A pdb=" N LEU A 706 " --> pdb=" O VAL A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 736 removed outlier: 3.933A pdb=" N VAL A 718 " --> pdb=" O ASP A 714 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE A 719 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 759 removed outlier: 5.794A pdb=" N GLY A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE A 752 " --> pdb=" O ALA A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 765 Processing helix chain 'A' and resid 773 through 781 removed outlier: 3.966A pdb=" N LEU A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 797 removed outlier: 3.603A pdb=" N GLY A 790 " --> pdb=" O ALA A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 844 removed outlier: 3.588A pdb=" N SER A 824 " --> pdb=" O ASN A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 948 Processing helix chain 'A' and resid 964 through 968 removed outlier: 3.700A pdb=" N MET A 968 " --> pdb=" O ARG A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1002 Processing helix chain 'A' and resid 1006 through 1020 removed outlier: 3.698A pdb=" N ALA A1010 " --> pdb=" O LYS A1006 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU A1013 " --> pdb=" O LYS A1009 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A1014 " --> pdb=" O ALA A1010 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP A1018 " --> pdb=" O GLN A1014 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A1019 " --> pdb=" O MET A1015 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1028 Processing helix chain 'A' and resid 1037 through 1047 Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1066 through 1078 Processing helix chain 'A' and resid 1079 through 1081 No H-bonds generated for 'chain 'A' and resid 1079 through 1081' Processing helix chain 'A' and resid 1091 through 1097 Processing helix chain 'A' and resid 1114 through 1122 Processing helix chain 'A' and resid 1129 through 1137 removed outlier: 4.504A pdb=" N VAL A1135 " --> pdb=" O VAL A1131 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A1136 " --> pdb=" O LYS A1132 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A1137 " --> pdb=" O LYS A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1176 Processing helix chain 'A' and resid 1206 through 1212 removed outlier: 3.955A pdb=" N TYR A1210 " --> pdb=" O TYR A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1342 Processing helix chain 'A' and resid 1348 through 1366 Proline residue: A1354 - end of helix Processing helix chain 'A' and resid 1400 through 1409 removed outlier: 3.542A pdb=" N ALA A1407 " --> pdb=" O GLU A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1444 through 1453 Processing helix chain 'A' and resid 1504 through 1523 removed outlier: 3.636A pdb=" N LYS A1522 " --> pdb=" O ALA A1518 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN A1523 " --> pdb=" O LYS A1519 " (cutoff:3.500A) Processing helix chain 'A' and resid 1547 through 1561 Processing helix chain 'A' and resid 1569 through 1582 Processing helix chain 'A' and resid 1600 through 1618 removed outlier: 3.865A pdb=" N SER A1604 " --> pdb=" O HIS A1600 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A1606 " --> pdb=" O ILE A1602 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A1618 " --> pdb=" O LEU A1614 " (cutoff:3.500A) Processing helix chain 'A' and resid 1639 through 1665 removed outlier: 4.130A pdb=" N VAL A1657 " --> pdb=" O VAL A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1681 removed outlier: 4.186A pdb=" N PHE A1672 " --> pdb=" O VAL A1668 " (cutoff:3.500A) Processing helix chain 'A' and resid 1683 through 1691 removed outlier: 3.627A pdb=" N SER A1691 " --> pdb=" O LEU A1687 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1724 removed outlier: 4.241A pdb=" N VAL A1712 " --> pdb=" O CYS A1708 " (cutoff:3.500A) Proline residue: A1713 - end of helix Processing helix chain 'A' and resid 1735 through 1753 removed outlier: 4.205A pdb=" N LEU A1741 " --> pdb=" O VAL A1737 " (cutoff:3.500A) Proline residue: A1751 - end of helix Processing helix chain 'A' and resid 1765 through 1785 Processing helix chain 'A' and resid 1797 through 1803 Processing helix chain 'A' and resid 1804 through 1809 Processing helix chain 'A' and resid 1815 through 1838 Processing helix chain 'A' and resid 1850 through 1859 removed outlier: 3.947A pdb=" N PHE A1854 " --> pdb=" O GLY A1850 " (cutoff:3.500A) Processing helix chain 'A' and resid 1861 through 1874 removed outlier: 3.701A pdb=" N PHE A1874 " --> pdb=" O ILE A1870 " (cutoff:3.500A) Processing helix chain 'A' and resid 1953 through 1961 Processing helix chain 'A' and resid 2002 through 2013 Processing helix chain 'A' and resid 2019 through 2023 Processing helix chain 'A' and resid 2025 through 2030 Processing helix chain 'A' and resid 2048 through 2060 removed outlier: 3.567A pdb=" N LYS A2052 " --> pdb=" O GLY A2048 " (cutoff:3.500A) Processing helix chain 'A' and resid 2078 through 2093 Processing helix chain 'A' and resid 2103 through 2111 removed outlier: 3.579A pdb=" N CYS A2107 " --> pdb=" O SER A2103 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A2110 " --> pdb=" O GLU A2106 " (cutoff:3.500A) Processing helix chain 'A' and resid 2127 through 2135 Processing helix chain 'A' and resid 2142 through 2149 Processing helix chain 'A' and resid 2161 through 2170 removed outlier: 3.956A pdb=" N GLY A2165 " --> pdb=" O LEU A2161 " (cutoff:3.500A) Processing helix chain 'A' and resid 2192 through 2206 removed outlier: 3.901A pdb=" N GLN A2196 " --> pdb=" O SER A2192 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A2198 " --> pdb=" O LEU A2194 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS A2199 " --> pdb=" O SER A2195 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AA2, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.204A pdb=" N LEU A 158 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 166 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 384 through 385 removed outlier: 7.033A pdb=" N LEU A 384 " --> pdb=" O ILE A 536 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 617 through 621 removed outlier: 3.583A pdb=" N SER A1392 " --> pdb=" O PHE A1535 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 904 through 906 Processing sheet with id=AA6, first strand: chain 'A' and resid 977 through 978 removed outlier: 4.069A pdb=" N CYS A 978 " --> pdb=" O ILE A1055 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP A1057 " --> pdb=" O CYS A 978 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU A1056 " --> pdb=" O SER A1087 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1101 through 1104 removed outlier: 6.419A pdb=" N ILE A1101 " --> pdb=" O VAL A1112 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL A1112 " --> pdb=" O ILE A1101 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A1103 " --> pdb=" O CYS A1110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1183 through 1184 675 hydrogen bonds defined for protein. 1989 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: 5.15 Time building geometry restraints manager: 6.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4075 1.34 - 1.46: 3200 1.46 - 1.59: 5633 1.59 - 1.72: 0 1.72 - 1.84: 91 Bond restraints: 12999 Sorted by residual: bond pdb=" C LEU A1353 " pdb=" N PRO A1354 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.20e-02 6.94e+03 1.69e+01 bond pdb=" CB GLN A 621 " pdb=" CG GLN A 621 " ideal model delta sigma weight residual 1.520 1.429 0.091 3.00e-02 1.11e+03 9.24e+00 bond pdb=" CB PHE A1605 " pdb=" CG PHE A1605 " ideal model delta sigma weight residual 1.502 1.437 0.065 2.30e-02 1.89e+03 8.08e+00 bond pdb=" CB VAL A 399 " pdb=" CG1 VAL A 399 " ideal model delta sigma weight residual 1.521 1.434 0.087 3.30e-02 9.18e+02 6.95e+00 bond pdb=" CG MET A 61 " pdb=" SD MET A 61 " ideal model delta sigma weight residual 1.803 1.739 0.064 2.50e-02 1.60e+03 6.56e+00 ... (remaining 12994 not shown) Histogram of bond angle deviations from ideal: 91.91 - 101.15: 24 101.15 - 110.40: 3475 110.40 - 119.64: 7975 119.64 - 128.89: 6216 128.89 - 138.13: 103 Bond angle restraints: 17793 Sorted by residual: angle pdb=" C GLY A 926 " pdb=" N GLN A 927 " pdb=" CA GLN A 927 " ideal model delta sigma weight residual 121.54 133.77 -12.23 1.91e+00 2.74e-01 4.10e+01 angle pdb=" N GLN A 768 " pdb=" CA GLN A 768 " pdb=" CB GLN A 768 " ideal model delta sigma weight residual 114.17 107.20 6.97 1.14e+00 7.69e-01 3.74e+01 angle pdb=" N LEU A 759 " pdb=" CA LEU A 759 " pdb=" C LEU A 759 " ideal model delta sigma weight residual 109.81 122.50 -12.69 2.21e+00 2.05e-01 3.30e+01 angle pdb=" C TRP A1382 " pdb=" N MET A1383 " pdb=" CA MET A1383 " ideal model delta sigma weight residual 121.54 131.79 -10.25 1.91e+00 2.74e-01 2.88e+01 angle pdb=" CA LEU A1636 " pdb=" CB LEU A1636 " pdb=" CG LEU A1636 " ideal model delta sigma weight residual 116.30 134.69 -18.39 3.50e+00 8.16e-02 2.76e+01 ... (remaining 17788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.05: 7288 19.05 - 38.10: 318 38.10 - 57.14: 46 57.14 - 76.19: 9 76.19 - 95.24: 6 Dihedral angle restraints: 7667 sinusoidal: 2176 harmonic: 5491 Sorted by residual: dihedral pdb=" CA THR A 386 " pdb=" C THR A 386 " pdb=" N PRO A 387 " pdb=" CA PRO A 387 " ideal model delta harmonic sigma weight residual -180.00 -117.05 -62.95 0 5.00e+00 4.00e-02 1.59e+02 dihedral pdb=" CB CYS A 355 " pdb=" SG CYS A 355 " pdb=" SG CYS A 504 " pdb=" CB CYS A 504 " ideal model delta sinusoidal sigma weight residual 93.00 179.44 -86.44 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CB CYS A 75 " pdb=" SG CYS A 75 " pdb=" SG CYS A 309 " pdb=" CB CYS A 309 " ideal model delta sinusoidal sigma weight residual -86.00 -165.78 79.78 1 1.00e+01 1.00e-02 7.90e+01 ... (remaining 7664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1903 0.096 - 0.193: 246 0.193 - 0.289: 23 0.289 - 0.386: 6 0.386 - 0.482: 2 Chirality restraints: 2180 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A1637 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" CG LEU A 367 " pdb=" CB LEU A 367 " pdb=" CD1 LEU A 367 " pdb=" CD2 LEU A 367 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" CG LEU A1636 " pdb=" CB LEU A1636 " pdb=" CD1 LEU A1636 " pdb=" CD2 LEU A1636 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 2177 not shown) Planarity restraints: 2329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A1460 " -0.087 5.00e-02 4.00e+02 1.32e-01 2.78e+01 pdb=" N PRO A1461 " 0.228 5.00e-02 4.00e+02 pdb=" CA PRO A1461 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO A1461 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 386 " -0.075 5.00e-02 4.00e+02 1.12e-01 2.02e+01 pdb=" N PRO A 387 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO A 387 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 387 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1458 " 0.073 5.00e-02 4.00e+02 1.12e-01 1.99e+01 pdb=" N PRO A1459 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO A1459 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A1459 " 0.062 5.00e-02 4.00e+02 ... (remaining 2326 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1642 2.74 - 3.28: 13099 3.28 - 3.82: 20183 3.82 - 4.36: 22398 4.36 - 4.90: 36607 Nonbonded interactions: 93929 Sorted by model distance: nonbonded pdb=" O ASN A1451 " pdb=" OG1 THR A1455 " model vdw 2.200 2.440 nonbonded pdb=" O TRP A 12 " pdb=" OG1 THR A 16 " model vdw 2.206 2.440 nonbonded pdb=" O PRO A 641 " pdb=" OG1 THR A 645 " model vdw 2.231 2.440 nonbonded pdb=" O MET A1456 " pdb=" OG SER A1460 " model vdw 2.233 2.440 nonbonded pdb=" O ILE A1697 " pdb=" OG SER A1701 " model vdw 2.258 2.440 ... (remaining 93924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 8095 2.51 5 N 2245 2.21 5 O 2388 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue 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: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.050 Check model and map are aligned: 0.220 Convert atoms to be neutral: 0.120 Process input model: 39.080 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 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 : 0.010 0.095 12999 Z= 0.625 Angle : 1.293 18.386 17793 Z= 0.699 Chirality : 0.067 0.482 2180 Planarity : 0.009 0.132 2322 Dihedral : 12.177 95.239 4085 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.07 % Favored : 85.77 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.74 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.01 (0.13), residues: 1869 helix: -3.43 (0.11), residues: 936 sheet: -5.20 (0.28), residues: 116 loop : -4.46 (0.17), residues: 817 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 333 time to evaluate : 1.905 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 outliers start: 12 outliers final: 3 residues processed: 343 average time/residue: 0.2589 time to fit residues: 128.4245 Evaluate side-chains 210 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 207 time to evaluate : 1.563 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1131 time to fit residues: 2.7556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 5.9990 chunk 144 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 148 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 55 HIS A 78 ASN ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1380 GLN ** A1557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1607 ASN A1610 ASN ** A1611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1734 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 12999 Z= 0.252 Angle : 0.789 9.878 17793 Z= 0.418 Chirality : 0.049 0.666 2180 Planarity : 0.007 0.102 2322 Dihedral : 7.982 98.467 2049 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.02 % Favored : 88.98 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.49 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.53 (0.16), residues: 1869 helix: -1.79 (0.14), residues: 974 sheet: -5.18 (0.29), residues: 119 loop : -4.27 (0.18), residues: 776 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 279 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 282 average time/residue: 0.2010 time to fit residues: 86.6137 Evaluate side-chains 200 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 199 time to evaluate : 1.516 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1170 time to fit residues: 2.2503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 40.0000 chunk 53 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 172 optimal weight: 0.0370 chunk 186 optimal weight: 50.0000 chunk 153 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 overall best weight: 1.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1607 ASN ** A1611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1678 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 12999 Z= 0.253 Angle : 0.756 9.039 17793 Z= 0.395 Chirality : 0.048 0.570 2180 Planarity : 0.006 0.087 2322 Dihedral : 7.371 98.368 2049 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.25 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.18), residues: 1869 helix: -0.72 (0.15), residues: 982 sheet: -5.03 (0.32), residues: 113 loop : -4.18 (0.18), residues: 774 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 259 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 262 average time/residue: 0.2149 time to fit residues: 86.0687 Evaluate side-chains 198 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 196 time to evaluate : 1.570 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1164 time to fit residues: 2.4022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 0.9980 chunk 129 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 173 optimal weight: 0.0370 chunk 183 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 chunk 164 optimal weight: 50.0000 chunk 49 optimal weight: 0.6980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN ** A1557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1607 ASN A1611 ASN ** A1626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 12999 Z= 0.201 Angle : 0.718 13.071 17793 Z= 0.370 Chirality : 0.047 0.520 2180 Planarity : 0.005 0.081 2322 Dihedral : 6.980 98.205 2049 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.19), residues: 1869 helix: -0.08 (0.16), residues: 977 sheet: -4.80 (0.33), residues: 117 loop : -4.03 (0.19), residues: 775 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 265 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 266 average time/residue: 0.2016 time to fit residues: 83.9218 Evaluate side-chains 199 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.557 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 164 optimal weight: 40.0000 chunk 46 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1430 GLN A1443 GLN ** A1557 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 12999 Z= 0.202 Angle : 0.703 9.213 17793 Z= 0.360 Chirality : 0.046 0.480 2180 Planarity : 0.005 0.079 2322 Dihedral : 6.762 98.457 2049 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.19), residues: 1869 helix: 0.33 (0.17), residues: 981 sheet: -4.88 (0.36), residues: 99 loop : -3.94 (0.19), residues: 789 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.2247 time to fit residues: 88.5796 Evaluate side-chains 200 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.564 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 0.9990 chunk 165 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 183 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 15 optimal weight: 50.0000 chunk 60 optimal weight: 2.9990 chunk 96 optimal weight: 0.2980 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1686 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 12999 Z= 0.229 Angle : 0.721 15.094 17793 Z= 0.369 Chirality : 0.046 0.452 2180 Planarity : 0.005 0.080 2322 Dihedral : 6.665 98.514 2049 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.20), residues: 1869 helix: 0.53 (0.17), residues: 987 sheet: -4.73 (0.38), residues: 93 loop : -3.91 (0.19), residues: 789 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.2081 time to fit residues: 82.2074 Evaluate side-chains 205 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.627 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 104 optimal weight: 20.0000 chunk 134 optimal weight: 4.9990 chunk 154 optimal weight: 20.0000 chunk 102 optimal weight: 0.4980 chunk 183 optimal weight: 30.0000 chunk 114 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1611 ASN ** A1626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1678 GLN A1774 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.072 12999 Z= 0.404 Angle : 0.824 12.141 17793 Z= 0.429 Chirality : 0.051 0.447 2180 Planarity : 0.006 0.092 2322 Dihedral : 6.960 99.594 2049 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.80 % Favored : 86.20 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.20), residues: 1869 helix: 0.45 (0.17), residues: 990 sheet: -4.80 (0.39), residues: 95 loop : -3.95 (0.19), residues: 784 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.2069 time to fit residues: 80.6281 Evaluate side-chains 201 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.492 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 4.9990 chunk 109 optimal weight: 0.0270 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 143 optimal weight: 0.0270 chunk 166 optimal weight: 50.0000 chunk 175 optimal weight: 30.0000 overall best weight: 0.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1607 ASN A1610 ASN A1623 ASN A1626 HIS A1678 GLN A1774 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 12999 Z= 0.206 Angle : 0.726 11.240 17793 Z= 0.369 Chirality : 0.047 0.424 2180 Planarity : 0.005 0.075 2322 Dihedral : 6.700 98.156 2049 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.20), residues: 1869 helix: 0.76 (0.17), residues: 992 sheet: -4.68 (0.40), residues: 101 loop : -3.79 (0.20), residues: 776 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 256 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 257 average time/residue: 0.2149 time to fit residues: 85.2588 Evaluate side-chains 209 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.564 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 1.9990 chunk 170 optimal weight: 0.0670 chunk 175 optimal weight: 30.0000 chunk 102 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 154 optimal weight: 30.0000 chunk 161 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 180 optimal weight: 50.0000 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1610 ASN ** A1611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1623 ASN A1678 GLN A1774 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 12999 Z= 0.260 Angle : 0.747 16.447 17793 Z= 0.381 Chirality : 0.047 0.454 2180 Planarity : 0.005 0.094 2322 Dihedral : 6.665 99.129 2049 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.20), residues: 1869 helix: 0.82 (0.17), residues: 992 sheet: -4.64 (0.40), residues: 94 loop : -3.75 (0.20), residues: 783 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 246 average time/residue: 0.2094 time to fit residues: 79.8576 Evaluate side-chains 208 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.540 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 8.9990 chunk 85 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 189 optimal weight: 30.0000 chunk 174 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 15 optimal weight: 40.0000 chunk 116 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 119 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1623 ASN A1774 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 12999 Z= 0.310 Angle : 0.768 8.520 17793 Z= 0.397 Chirality : 0.049 0.443 2180 Planarity : 0.006 0.093 2322 Dihedral : 6.750 99.192 2049 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.36 % Favored : 87.64 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.25 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.20), residues: 1869 helix: 0.80 (0.17), residues: 992 sheet: -4.53 (0.42), residues: 93 loop : -3.75 (0.20), residues: 784 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 246 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 247 average time/residue: 0.2034 time to fit residues: 79.5306 Evaluate side-chains 208 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.501 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 0.7980 chunk 138 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 150 optimal weight: 0.0870 chunk 63 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1607 ASN A1623 ASN A1774 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.160527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.122885 restraints weight = 24037.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.122908 restraints weight = 20599.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.123510 restraints weight = 17935.071| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 12999 Z= 0.202 Angle : 0.737 12.054 17793 Z= 0.373 Chirality : 0.046 0.415 2180 Planarity : 0.005 0.091 2322 Dihedral : 6.587 98.313 2049 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.25 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.20), residues: 1869 helix: 0.98 (0.17), residues: 995 sheet: -4.51 (0.41), residues: 100 loop : -3.66 (0.20), residues: 774 =============================================================================== Job complete usr+sys time: 2503.50 seconds wall clock time: 46 minutes 8.16 seconds (2768.16 seconds total)