Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 15:56:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xjy_6724/04_2023/5xjy_6724.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xjy_6724/04_2023/5xjy_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_6724/04_2023/5xjy_6724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xjy_6724/04_2023/5xjy_6724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xjy_6724/04_2023/5xjy_6724.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xjy_6724/04_2023/5xjy_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 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. 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-1.21rc1-4938/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 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: 7.04, per 1000 atoms: 0.55 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: 5.69 Conformation dependent library (CDL) restraints added in 2.2 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: 0.89 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: 5.03 Time building geometry restraints manager: 6.09 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=" C1 NAG A2305 " pdb=" O5 NAG A2305 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.60e+00 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 ... (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 - 17.29: 7107 17.29 - 34.58: 389 34.58 - 51.87: 72 51.87 - 69.15: 7 69.15 - 86.44: 8 Dihedral angle restraints: 7583 sinusoidal: 2092 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 7580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1894 0.096 - 0.193: 253 0.193 - 0.289: 25 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 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: 0.330 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: 0.210 Set scattering table: 0.120 Process input model: 36.810 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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= 0.632 Angle : 1.309 18.386 17793 Z= 0.698 Chirality : 0.069 0.482 2180 Planarity : 0.009 0.132 2322 Dihedral : 12.023 80.392 4001 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.25 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 : 1.598 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: 0.2647 time to fit residues: 128.6268 Evaluate side-chains 210 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 207 time to evaluate : 1.464 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1130 time to fit residues: 2.6172 ------------------------------------------------------------------------------- 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: 0.7454 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 12999 Z= 0.245 Angle : 0.801 10.091 17793 Z= 0.416 Chirality : 0.050 0.786 2180 Planarity : 0.007 0.101 2322 Dihedral : 7.176 43.869 1965 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % 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: -4.46 (0.16), residues: 1869 helix: -1.71 (0.14), residues: 976 sheet: -5.17 (0.29), residues: 119 loop : -4.28 (0.18), residues: 774 *********************** 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 288 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 283 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 286 average time/residue: 0.2291 time to fit residues: 100.2028 Evaluate side-chains 203 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 202 time to evaluate : 1.604 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1218 time to fit residues: 2.3377 ------------------------------------------------------------------------------- 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: 1.9990 chunk 143 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 172 optimal weight: 0.0370 chunk 186 optimal weight: 40.0000 chunk 153 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- 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 ** A1626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1678 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3069 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= 0.257 Angle : 0.764 8.994 17793 Z= 0.395 Chirality : 0.048 0.564 2180 Planarity : 0.006 0.086 2322 Dihedral : 6.565 43.243 1965 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % 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: -3.52 (0.18), residues: 1869 helix: -0.69 (0.15), residues: 982 sheet: -5.03 (0.32), residues: 113 loop : -4.20 (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 268 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 263 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 266 average time/residue: 0.2223 time to fit residues: 90.2855 Evaluate side-chains 199 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 1.584 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1183 time to fit residues: 2.3215 ------------------------------------------------------------------------------- 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: 8.9990 chunk 129 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 173 optimal weight: 0.0020 chunk 183 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 chunk 164 optimal weight: 50.0000 chunk 49 optimal weight: 0.7980 overall best weight: 1.3190 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1611 ASN ** A1623 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: 0.7461 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 12999 Z= 0.227 Angle : 0.745 15.607 17793 Z= 0.378 Chirality : 0.047 0.465 2180 Planarity : 0.005 0.083 2322 Dihedral : 6.147 41.022 1965 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer Outliers : 0.21 % 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: -2.91 (0.19), residues: 1869 helix: -0.09 (0.16), residues: 978 sheet: -4.82 (0.35), residues: 113 loop : -4.05 (0.19), residues: 778 *********************** 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 264 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 262 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 263 average time/residue: 0.2216 time to fit residues: 89.7520 Evaluate side-chains 206 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 205 time to evaluate : 1.655 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1229 time to fit residues: 2.2927 ------------------------------------------------------------------------------- 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: 6.9990 chunk 104 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 136 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 164 optimal weight: 50.0000 chunk 46 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 ** A1607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 12999 Z= 0.278 Angle : 0.752 9.786 17793 Z= 0.384 Chirality : 0.047 0.442 2180 Planarity : 0.005 0.087 2322 Dihedral : 6.040 44.696 1965 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.04 % Favored : 87.96 % Rotamer Outliers : 0.21 % 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: -2.62 (0.19), residues: 1869 helix: 0.22 (0.17), residues: 989 sheet: -4.96 (0.37), residues: 94 loop : -4.07 (0.19), residues: 786 *********************** 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 260 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 258 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 260 average time/residue: 0.2308 time to fit residues: 90.3526 Evaluate side-chains 212 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 1.582 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1228 time to fit residues: 2.3345 ------------------------------------------------------------------------------- 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: 10.0000 chunk 45 optimal weight: 1.9990 chunk 183 optimal weight: 0.1980 chunk 152 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 15 optimal weight: 30.0000 chunk 60 optimal weight: 5.9990 chunk 96 optimal weight: 0.0570 overall best weight: 1.8504 ------------------------------------------------------------------------------- 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 71 GLN ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 12999 Z= 0.251 Angle : 0.747 12.957 17793 Z= 0.378 Chirality : 0.047 0.423 2180 Planarity : 0.005 0.082 2322 Dihedral : 5.892 42.520 1965 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.77 % Favored : 88.23 % 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: -2.29 (0.20), residues: 1869 helix: 0.50 (0.17), residues: 988 sheet: -4.84 (0.38), residues: 93 loop : -3.94 (0.19), residues: 788 *********************** 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 251 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.2195 time to fit residues: 85.8424 Evaluate side-chains 201 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.563 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0985 ------------------------------------------------------------------------------- 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: 0.0270 chunk 104 optimal weight: 20.0000 chunk 134 optimal weight: 0.9990 chunk 154 optimal weight: 20.0000 chunk 102 optimal weight: 8.9990 chunk 183 optimal weight: 0.7980 chunk 114 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 overall best weight: 1.7442 ------------------------------------------------------------------------------- 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** A1610 ASN ** A1623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7485 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 12999 Z= 0.247 Angle : 0.747 11.460 17793 Z= 0.376 Chirality : 0.047 0.412 2180 Planarity : 0.005 0.083 2322 Dihedral : 5.793 41.199 1965 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.06 % 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: -2.05 (0.20), residues: 1869 helix: 0.71 (0.17), residues: 987 sheet: -4.75 (0.40), residues: 94 loop : -3.83 (0.19), residues: 788 *********************** 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 242 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2272 time to fit residues: 86.5694 Evaluate side-chains 203 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.587 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9134 ------------------------------------------------------------------------------- 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: 7.9990 chunk 109 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 116 optimal weight: 0.4980 chunk 124 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 143 optimal weight: 9.9990 chunk 166 optimal weight: 30.0000 chunk 175 optimal weight: 30.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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** ** A1623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1678 GLN A1774 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 12999 Z= 0.286 Angle : 0.774 17.054 17793 Z= 0.390 Chirality : 0.048 0.411 2180 Planarity : 0.005 0.083 2322 Dihedral : 5.779 41.388 1965 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.52 % Favored : 87.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.20), residues: 1869 helix: 0.71 (0.17), residues: 988 sheet: -4.64 (0.43), residues: 94 loop : -3.81 (0.20), residues: 787 *********************** 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 244 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.2198 time to fit residues: 83.7633 Evaluate side-chains 209 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.530 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0357 ------------------------------------------------------------------------------- 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: 6.9990 chunk 170 optimal weight: 0.0010 chunk 175 optimal weight: 0.0570 chunk 102 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 154 optimal weight: 4.9990 chunk 161 optimal weight: 30.0000 chunk 112 optimal weight: 0.0670 chunk 180 optimal weight: 50.0000 overall best weight: 0.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1607 ASN ** A1623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1678 GLN A1774 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 12999 Z= 0.185 Angle : 0.720 10.819 17793 Z= 0.358 Chirality : 0.046 0.389 2180 Planarity : 0.005 0.074 2322 Dihedral : 5.547 38.282 1965 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.06 % 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: -1.73 (0.20), residues: 1869 helix: 0.98 (0.17), residues: 989 sheet: -4.47 (0.42), residues: 100 loop : -3.70 (0.20), residues: 780 *********************** 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 251 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.2004 time to fit residues: 78.6689 Evaluate side-chains 213 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.472 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9072 ------------------------------------------------------------------------------- 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: 0.4980 chunk 85 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 chunk 189 optimal weight: 0.8980 chunk 174 optimal weight: 8.9990 chunk 150 optimal weight: 0.0470 chunk 15 optimal weight: 30.0000 chunk 116 optimal weight: 0.0470 chunk 92 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 160 optimal weight: 8.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1774 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 12999 Z= 0.192 Angle : 0.713 11.303 17793 Z= 0.355 Chirality : 0.046 0.413 2180 Planarity : 0.005 0.096 2322 Dihedral : 5.312 35.018 1965 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % 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: -1.51 (0.20), residues: 1869 helix: 1.13 (0.17), residues: 996 sheet: -4.37 (0.42), residues: 99 loop : -3.61 (0.20), residues: 774 ********************** 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 252 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.2187 time to fit residues: 86.5243 Evaluate side-chains 209 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.578 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1102 ------------------------------------------------------------------------------- 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: 0.9990 chunk 138 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN ** A1623 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1774 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.161385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3600 r_free = 0.3600 target = 0.126208 restraints weight = 24070.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.125378 restraints weight = 19036.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.125936 restraints weight = 15862.906| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 12999 Z= 0.222 Angle : 0.721 10.571 17793 Z= 0.360 Chirality : 0.046 0.440 2180 Planarity : 0.005 0.094 2322 Dihedral : 5.337 36.644 1965 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer Outliers : 0.00 % 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: -1.49 (0.20), residues: 1869 helix: 1.14 (0.17), residues: 1005 sheet: -4.41 (0.42), residues: 98 loop : -3.64 (0.20), residues: 766 =============================================================================== Job complete usr+sys time: 2566.33 seconds wall clock time: 47 minutes 13.34 seconds (2833.34 seconds total)