Starting phenix.real_space_refine on Sat Dec 9 23:54:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8j_9782/12_2023/6j8j_9782_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8j_9782/12_2023/6j8j_9782.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8j_9782/12_2023/6j8j_9782_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8j_9782/12_2023/6j8j_9782_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8j_9782/12_2023/6j8j_9782_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8j_9782/12_2023/6j8j_9782.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8j_9782/12_2023/6j8j_9782.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8j_9782/12_2023/6j8j_9782_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8j_9782/12_2023/6j8j_9782_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 966 atoms to isotropic. 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 97 5.16 5 C 7725 2.51 5 N 1857 2.21 5 O 2085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 31": "OE1" <-> "OE2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "C ARG 135": "NH1" <-> "NH2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 771": "OE1" <-> "OE2" Residue "A GLU 802": "OE1" <-> "OE2" Residue "A ARG 838": "NH1" <-> "NH2" Residue "A ASP 902": "OD1" <-> "OD2" Residue "A ARG 922": "NH1" <-> "NH2" Residue "A GLU 930": "OE1" <-> "OE2" Residue "A ARG 1182": "NH1" <-> "NH2" Residue "A ARG 1218": "NH1" <-> "NH2" Residue "A GLU 1227": "OE1" <-> "OE2" Residue "A ARG 1293": "NH1" <-> "NH2" Residue "A ARG 1308": "NH1" <-> "NH2" Residue "A TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1477": "OE1" <-> "OE2" Residue "A ARG 1499": "NH1" <-> "NH2" Residue "A ARG 1610": "NH1" <-> "NH2" Residue "A ARG 1613": "NH1" <-> "NH2" Residue "A ARG 1619": "NH1" <-> "NH2" Residue "A ARG 1622": "NH1" <-> "NH2" Residue "A GLU 1672": "OE1" <-> "OE2" Residue "A GLU 1768": "OE1" <-> "OE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 152": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11764 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 980 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 113} Chain: "A" Number of atoms: 9192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 9192 Classifications: {'peptide': 1140} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 1108} Chain breaks: 3 Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "D" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 50 Unusual residues: {'9SR': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.28, per 1000 atoms: 0.53 Number of scatterers: 11764 At special positions: 0 Unit cell: (134.193, 139.648, 114.555, 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 97 16.00 O 2085 8.00 N 1857 7.00 C 7725 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.57 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS A 895 " distance=2.24 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.04 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 315 " distance=1.98 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.02 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=1.91 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=1.98 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.12 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 43 " distance=2.00 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.00 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A2005 " - " ASN A1375 " " NAG A2006 " - " ASN A 283 " " NAG B 301 " - " ASN B 93 " " NAG B 302 " - " ASN B 110 " " NAG B 303 " - " ASN B 114 " " NAG B 304 " - " ASN B 135 " " NAG C 301 " - " ASN C 66 " " NAG D 1 " - " ASN A1352 " " NAG E 1 " - " ASN A1366 " Time building additional restraints: 4.83 Conformation dependent library (CDL) restraints added in 2.2 seconds 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2714 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 8 sheets defined 63.2% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 105 through 107 No H-bonds generated for 'chain 'C' and resid 105 through 107' Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 126 through 145 removed outlier: 3.666A pdb=" N MET A 130 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 144 " --> pdb=" O CYS A 140 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N MET A 145 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 175 removed outlier: 3.570A pdb=" N VAL A 169 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 172 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA A 173 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG A 174 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY A 175 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 Processing helix chain 'A' and resid 188 through 203 removed outlier: 3.659A pdb=" N ASP A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 199 " --> pdb=" O VAL A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 227 removed outlier: 3.838A pdb=" N THR A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ARG A 220 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ALA A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 267 removed outlier: 3.770A pdb=" N LYS A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASP A 247 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 286 through 292 removed outlier: 3.937A pdb=" N ASN A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 302 removed outlier: 3.886A pdb=" N TYR A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 358 Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 376 through 389 removed outlier: 3.701A pdb=" N ILE A 380 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 386 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 387 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 388 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY A 389 " --> pdb=" O ILE A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 416 removed outlier: 3.533A pdb=" N GLU A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 740 removed outlier: 3.515A pdb=" N PHE A 733 " --> pdb=" O TYR A 729 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 734 " --> pdb=" O TRP A 730 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N CYS A 736 " --> pdb=" O LYS A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 762 Processing helix chain 'A' and resid 770 through 805 removed outlier: 3.624A pdb=" N LEU A 795 " --> pdb=" O MET A 791 " (cutoff:3.500A) Proline residue: A 800 - end of helix Processing helix chain 'A' and resid 807 through 821 removed outlier: 3.700A pdb=" N LEU A 814 " --> pdb=" O ILE A 810 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 815 " --> pdb=" O PHE A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 846 removed outlier: 4.176A pdb=" N PHE A 837 " --> pdb=" O VAL A 833 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG A 838 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU A 839 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU A 840 " --> pdb=" O SER A 836 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ARG A 841 " --> pdb=" O PHE A 837 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N VAL A 842 " --> pdb=" O ARG A 838 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N PHE A 843 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LYS A 844 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LEU A 845 " --> pdb=" O ARG A 841 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ALA A 846 " --> pdb=" O VAL A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 863 removed outlier: 3.595A pdb=" N SER A 862 " --> pdb=" O ILE A 858 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 899 removed outlier: 4.404A pdb=" N ASN A 868 " --> pdb=" O ALA A 865 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 880 " --> pdb=" O VAL A 877 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 884 " --> pdb=" O ALA A 881 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 888 " --> pdb=" O MET A 885 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY A 889 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LYS A 890 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR A 892 " --> pdb=" O GLY A 889 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N CYS A 895 " --> pdb=" O TYR A 892 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL A 896 " --> pdb=" O LYS A 893 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N CYS A 897 " --> pdb=" O GLU A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 924 Processing helix chain 'A' and resid 928 through 939 removed outlier: 4.119A pdb=" N ASP A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 971 Processing helix chain 'A' and resid 1177 through 1190 Processing helix chain 'A' and resid 1192 through 1210 removed outlier: 3.984A pdb=" N LEU A1209 " --> pdb=" O SER A1205 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA A1210 " --> pdb=" O SER A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1217 removed outlier: 4.200A pdb=" N GLU A1217 " --> pdb=" O ILE A1214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1214 through 1217' Processing helix chain 'A' and resid 1220 through 1254 removed outlier: 3.894A pdb=" N LYS A1231 " --> pdb=" O GLU A1227 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A1232 " --> pdb=" O TYR A1228 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N TYR A1250 " --> pdb=" O ILE A1246 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N LYS A1251 " --> pdb=" O ALA A1247 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR A1252 " --> pdb=" O TYR A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1278 Processing helix chain 'A' and resid 1284 through 1303 Proline residue: A1297 - end of helix Processing helix chain 'A' and resid 1305 through 1343 removed outlier: 3.520A pdb=" N VAL A1310 " --> pdb=" O GLY A1306 " (cutoff:3.500A) Proline residue: A1319 - end of helix removed outlier: 3.537A pdb=" N ASN A1323 " --> pdb=" O PRO A1319 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A1324 " --> pdb=" O SER A1320 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1376 removed outlier: 3.640A pdb=" N ALA A1372 " --> pdb=" O SER A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1404 Processing helix chain 'A' and resid 1408 through 1417 removed outlier: 3.537A pdb=" N ALA A1414 " --> pdb=" O ILE A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1444 removed outlier: 3.532A pdb=" N VAL A1439 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY A1444 " --> pdb=" O ILE A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1466 Processing helix chain 'A' and resid 1476 through 1489 removed outlier: 3.764A pdb=" N LEU A1488 " --> pdb=" O ALA A1484 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY A1489 " --> pdb=" O MET A1485 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1513 removed outlier: 3.538A pdb=" N VAL A1512 " --> pdb=" O ILE A1508 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1534 removed outlier: 3.541A pdb=" N MET A1532 " --> pdb=" O ASN A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1575 removed outlier: 7.399A pdb=" N HIS A1571 " --> pdb=" O ILE A1567 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N TYR A1572 " --> pdb=" O SER A1568 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR A1573 " --> pdb=" O LEU A1569 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE A1574 " --> pdb=" O ARG A1570 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A1575 " --> pdb=" O HIS A1571 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1602 Processing helix chain 'A' and resid 1606 through 1626 removed outlier: 3.555A pdb=" N VAL A1611 " --> pdb=" O THR A1607 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA A1615 " --> pdb=" O VAL A1611 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ARG A1616 " --> pdb=" O ILE A1612 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE A1617 " --> pdb=" O ARG A1613 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLY A1618 " --> pdb=" O LEU A1614 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ARG A1619 " --> pdb=" O ALA A1615 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A1621 " --> pdb=" O ILE A1617 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG A1622 " --> pdb=" O GLY A1618 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU A1623 " --> pdb=" O ARG A1619 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL A1624 " --> pdb=" O ILE A1620 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS A1625 " --> pdb=" O LEU A1621 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY A1626 " --> pdb=" O ARG A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1628 through 1666 removed outlier: 3.539A pdb=" N LEU A1633 " --> pdb=" O GLY A1629 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A1637 " --> pdb=" O LEU A1633 " (cutoff:3.500A) Proline residue: A1642 - end of helix Processing helix chain 'A' and resid 1684 through 1695 Processing helix chain 'A' and resid 1700 through 1708 Proline residue: A1706 - end of helix Processing helix chain 'A' and resid 1733 through 1767 removed outlier: 3.500A pdb=" N ASN A1753 " --> pdb=" O LEU A1749 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 191 removed outlier: 3.504A pdb=" N TYR B 164 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 31 through 34 removed outlier: 4.114A pdb=" N GLU C 31 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 37 through 40 removed outlier: 7.686A pdb=" N LEU C 38 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N HIS C 143 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL C 40 " --> pdb=" O HIS C 143 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLN C 145 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 81 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR C 69 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N MET C 79 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 46 through 48 Processing sheet with id= D, first strand: chain 'A' and resid 273 through 277 Processing sheet with id= E, first strand: chain 'A' and resid 1349 through 1352 Processing sheet with id= F, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.740A pdb=" N GLU B 145 " --> pdb=" O ALA B 30 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 36 through 41 Processing sheet with id= H, first strand: chain 'B' and resid 133 through 144 removed outlier: 3.503A pdb=" N VAL B 138 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ASN B 50 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 71 " --> pdb=" O TRP B 57 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N PHE B 59 " --> pdb=" O LYS B 69 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N LYS B 69 " --> pdb=" O PHE B 59 " (cutoff:3.500A) 659 hydrogen bonds defined for protein. 1752 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: 4.00 Time building geometry restraints manager: 5.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.36: 3621 1.36 - 1.52: 6832 1.52 - 1.69: 1431 1.69 - 1.85: 155 1.85 - 2.01: 1 Bond restraints: 12040 Sorted by residual: bond pdb=" C07 9SR A2007 " pdb=" O01 9SR A2007 " ideal model delta sigma weight residual 1.625 1.466 0.159 2.00e-02 2.50e+03 6.30e+01 bond pdb=" C15 9SR A2007 " pdb=" C17 9SR A2007 " ideal model delta sigma weight residual 1.624 1.491 0.133 2.00e-02 2.50e+03 4.39e+01 bond pdb=" CB CYS C 127 " pdb=" SG CYS C 127 " ideal model delta sigma weight residual 1.808 2.008 -0.200 3.30e-02 9.18e+02 3.66e+01 bond pdb=" C19 9SR A2007 " pdb=" O20 9SR A2007 " ideal model delta sigma weight residual 1.467 1.349 0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" C CYS A 324 " pdb=" N PRO A 325 " ideal model delta sigma weight residual 1.332 1.404 -0.073 1.26e-02 6.30e+03 3.31e+01 ... (remaining 12035 not shown) Histogram of bond angle deviations from ideal: 94.30 - 103.23: 128 103.23 - 112.16: 5766 112.16 - 121.09: 7276 121.09 - 130.01: 3054 130.01 - 138.94: 93 Bond angle restraints: 16317 Sorted by residual: angle pdb=" N CYS A 925 " pdb=" CA CYS A 925 " pdb=" C CYS A 925 " ideal model delta sigma weight residual 110.55 94.30 16.25 1.35e+00 5.49e-01 1.45e+02 angle pdb=" N GLN A1378 " pdb=" CA GLN A1378 " pdb=" C GLN A1378 " ideal model delta sigma weight residual 111.36 124.11 -12.75 1.09e+00 8.42e-01 1.37e+02 angle pdb=" N TRP A 928 " pdb=" CA TRP A 928 " pdb=" C TRP A 928 " ideal model delta sigma weight residual 111.28 122.43 -11.15 1.09e+00 8.42e-01 1.05e+02 angle pdb=" N LEU B 101 " pdb=" CA LEU B 101 " pdb=" C LEU B 101 " ideal model delta sigma weight residual 111.07 121.97 -10.90 1.07e+00 8.73e-01 1.04e+02 angle pdb=" N TYR A 304 " pdb=" CA TYR A 304 " pdb=" C TYR A 304 " ideal model delta sigma weight residual 111.07 120.56 -9.49 1.07e+00 8.73e-01 7.86e+01 ... (remaining 16312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 5817 17.79 - 35.57: 807 35.57 - 53.36: 437 53.36 - 71.15: 169 71.15 - 88.94: 17 Dihedral angle restraints: 7247 sinusoidal: 3045 harmonic: 4202 Sorted by residual: dihedral pdb=" CB CYS B 21 " pdb=" SG CYS B 21 " pdb=" SG CYS B 43 " pdb=" CB CYS B 43 " ideal model delta sinusoidal sigma weight residual 93.00 -179.52 -87.48 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS A 935 " pdb=" SG CYS A 935 " pdb=" SG CYS A 944 " pdb=" CB CYS A 944 " ideal model delta sinusoidal sigma weight residual 93.00 179.51 -86.51 1 1.00e+01 1.00e-02 9.01e+01 dihedral pdb=" CB CYS A1350 " pdb=" SG CYS A1350 " pdb=" SG CYS A1370 " pdb=" CB CYS A1370 " ideal model delta sinusoidal sigma weight residual -86.00 -150.21 64.21 1 1.00e+01 1.00e-02 5.42e+01 ... (remaining 7244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.064: 1906 1.064 - 2.127: 0 2.127 - 3.191: 0 3.191 - 4.255: 0 4.255 - 5.318: 1 Chirality restraints: 1907 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-02 2.50e+03 1.44e+03 chirality pdb=" C03 9SR A2007 " pdb=" C02 9SR A2007 " pdb=" C05 9SR A2007 " pdb=" C21 9SR A2007 " both_signs ideal model delta sigma weight residual False 2.67 -2.65 5.32 2.00e-01 2.50e+01 7.07e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.91e+01 ... (remaining 1904 not shown) Planarity restraints: 1993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 110 " 0.212 2.00e-02 2.50e+03 2.52e-01 7.92e+02 pdb=" CG ASN B 110 " -0.083 2.00e-02 2.50e+03 pdb=" OD1 ASN B 110 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 110 " -0.418 2.00e-02 2.50e+03 pdb=" C1 NAG B 302 " 0.300 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 283 " 0.085 2.00e-02 2.50e+03 1.95e-01 4.75e+02 pdb=" CG ASN A 283 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN A 283 " 0.105 2.00e-02 2.50e+03 pdb=" ND2 ASN A 283 " -0.350 2.00e-02 2.50e+03 pdb=" C1 NAG A2006 " 0.216 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 135 " -0.116 2.00e-02 2.50e+03 1.71e-01 3.64e+02 pdb=" CG ASN B 135 " 0.055 2.00e-02 2.50e+03 pdb=" OD1 ASN B 135 " -0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN B 135 " 0.300 2.00e-02 2.50e+03 pdb=" C1 NAG B 304 " -0.192 2.00e-02 2.50e+03 ... (remaining 1990 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 149 2.44 - 3.06: 8929 3.06 - 3.67: 17041 3.67 - 4.29: 25954 4.29 - 4.90: 42313 Nonbonded interactions: 94386 Sorted by model distance: nonbonded pdb=" O ASP A1677 " pdb=" OD1 ASP A1677 " model vdw 1.829 3.040 nonbonded pdb=" O ILE A 899 " pdb=" ND2 ASN A 900 " model vdw 1.878 2.520 nonbonded pdb=" N GLN A1541 " pdb=" OE1 GLN A1541 " model vdw 1.886 2.520 nonbonded pdb=" O3 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 1.980 2.440 nonbonded pdb=" OE1 GLU B 87 " pdb=" N GLY B 88 " model vdw 2.013 2.520 ... (remaining 94381 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' } 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=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 3.440 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 33.820 Find NCS groups from input model: 0.320 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 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 0.200 12040 Z= 0.661 Angle : 1.512 23.043 16317 Z= 1.048 Chirality : 0.159 5.318 1907 Planarity : 0.009 0.185 1984 Dihedral : 21.905 88.937 4503 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 71.00 Ramachandran Plot: Outliers : 1.34 % Allowed : 2.46 % Favored : 96.20 % Rotamer: Outliers : 28.80 % Allowed : 19.25 % Favored : 51.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.21), residues: 1421 helix: 3.02 (0.16), residues: 797 sheet: 1.66 (0.45), residues: 126 loop : -0.11 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 92 HIS 0.013 0.002 HIS A 766 PHE 0.022 0.002 PHE B 54 TYR 0.022 0.002 TYR A 367 ARG 0.004 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 371 poor density : 319 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 371 outliers final: 145 residues processed: 577 average time/residue: 0.2640 time to fit residues: 209.3888 Evaluate side-chains 368 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 223 time to evaluate : 1.400 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 145 outliers final: 1 residues processed: 145 average time/residue: 0.1559 time to fit residues: 38.8765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 118 GLN A 154 ASN A 278 ASN A 282 ASN A 360 GLN A 365 ASN A 766 HIS A 774 ASN A 900 ASN A 909 HIS A 941 GLN A1191 HIS A1462 GLN A1514 ASN A1528 ASN ** A1721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1732 ASN A1762 ASN B 75 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 12040 Z= 0.259 Angle : 0.852 26.686 16317 Z= 0.422 Chirality : 0.069 2.132 1907 Planarity : 0.005 0.081 1984 Dihedral : 7.175 59.221 1783 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.67 % Favored : 97.04 % Rotamer: Outliers : 5.67 % Allowed : 23.29 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.21), residues: 1421 helix: 2.06 (0.17), residues: 824 sheet: 1.19 (0.47), residues: 117 loop : -0.46 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 363 HIS 0.009 0.001 HIS A 766 PHE 0.041 0.002 PHE A 843 TYR 0.022 0.002 TYR A 305 ARG 0.008 0.001 ARG C 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 269 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 32 residues processed: 318 average time/residue: 0.2397 time to fit residues: 109.9915 Evaluate side-chains 251 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 219 time to evaluate : 1.393 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.1307 time to fit residues: 9.3086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 126 ASN ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 ASN A1341 ASN A1378 GLN A1462 GLN A1483 ASN B 115 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12040 Z= 0.280 Angle : 0.771 26.684 16317 Z= 0.378 Chirality : 0.067 2.140 1907 Planarity : 0.005 0.063 1984 Dihedral : 6.797 58.893 1783 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.38 % Favored : 96.41 % Rotamer: Outliers : 4.58 % Allowed : 24.92 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.22), residues: 1421 helix: 1.57 (0.17), residues: 830 sheet: 0.80 (0.46), residues: 124 loop : -0.66 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1382 HIS 0.005 0.001 HIS A 766 PHE 0.045 0.002 PHE A 843 TYR 0.023 0.002 TYR A 362 ARG 0.005 0.001 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 230 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 23 residues processed: 268 average time/residue: 0.2379 time to fit residues: 92.4203 Evaluate side-chains 237 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 214 time to evaluate : 1.426 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 2 residues processed: 23 average time/residue: 0.1176 time to fit residues: 7.0071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 130 optimal weight: 0.0010 chunk 138 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 HIS A 139 ASN ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12040 Z= 0.172 Angle : 0.701 28.338 16317 Z= 0.333 Chirality : 0.063 2.062 1907 Planarity : 0.004 0.050 1984 Dihedral : 6.598 58.895 1783 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.59 % Favored : 96.20 % Rotamer: Outliers : 3.26 % Allowed : 25.62 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.22), residues: 1421 helix: 1.61 (0.17), residues: 832 sheet: 0.84 (0.46), residues: 122 loop : -0.67 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1382 HIS 0.004 0.001 HIS A1721 PHE 0.022 0.001 PHE B 54 TYR 0.017 0.001 TYR A1739 ARG 0.003 0.000 ARG C 115 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 230 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 21 residues processed: 257 average time/residue: 0.2370 time to fit residues: 89.6556 Evaluate side-chains 238 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 217 time to evaluate : 1.222 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 21 outliers final: 1 residues processed: 21 average time/residue: 0.1162 time to fit residues: 6.1610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 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 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN B 143 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12040 Z= 0.185 Angle : 0.710 27.737 16317 Z= 0.335 Chirality : 0.064 2.088 1907 Planarity : 0.004 0.042 1984 Dihedral : 6.562 59.859 1783 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.45 % Favored : 96.41 % Rotamer: Outliers : 2.56 % Allowed : 26.24 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.22), residues: 1421 helix: 1.58 (0.18), residues: 834 sheet: 0.79 (0.46), residues: 122 loop : -0.78 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1382 HIS 0.004 0.001 HIS A 766 PHE 0.047 0.001 PHE A 843 TYR 0.022 0.001 TYR A 362 ARG 0.005 0.000 ARG C 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 227 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 14 residues processed: 247 average time/residue: 0.2315 time to fit residues: 83.2508 Evaluate side-chains 225 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 211 time to evaluate : 1.422 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 14 average time/residue: 0.1144 time to fit residues: 4.8652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 12040 Z= 0.354 Angle : 0.772 26.621 16317 Z= 0.372 Chirality : 0.067 2.125 1907 Planarity : 0.005 0.038 1984 Dihedral : 6.744 58.611 1783 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.08 % Favored : 95.71 % Rotamer: Outliers : 3.57 % Allowed : 26.16 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.22), residues: 1421 helix: 1.19 (0.18), residues: 845 sheet: 0.30 (0.45), residues: 124 loop : -0.96 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 190 HIS 0.006 0.001 HIS A 766 PHE 0.021 0.002 PHE B 54 TYR 0.033 0.002 TYR A 362 ARG 0.006 0.001 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 206 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 23 residues processed: 234 average time/residue: 0.2269 time to fit residues: 77.9781 Evaluate side-chains 220 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 197 time to evaluate : 1.219 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 2 residues processed: 23 average time/residue: 0.1104 time to fit residues: 6.4902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1505 GLN B 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12040 Z= 0.175 Angle : 0.709 28.088 16317 Z= 0.333 Chirality : 0.063 2.075 1907 Planarity : 0.004 0.038 1984 Dihedral : 6.561 59.513 1783 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.66 % Favored : 96.20 % Rotamer: Outliers : 1.94 % Allowed : 27.25 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.22), residues: 1421 helix: 1.44 (0.18), residues: 839 sheet: 0.39 (0.45), residues: 125 loop : -0.99 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1382 HIS 0.002 0.001 HIS A1721 PHE 0.055 0.001 PHE A 843 TYR 0.017 0.001 TYR A1739 ARG 0.006 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 216 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 231 average time/residue: 0.2425 time to fit residues: 81.6282 Evaluate side-chains 216 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 205 time to evaluate : 1.446 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 11 average time/residue: 0.1257 time to fit residues: 4.4037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 125 optimal weight: 8.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12040 Z= 0.246 Angle : 0.726 27.227 16317 Z= 0.343 Chirality : 0.065 2.106 1907 Planarity : 0.004 0.039 1984 Dihedral : 6.521 59.730 1783 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.87 % Favored : 95.99 % Rotamer: Outliers : 1.63 % Allowed : 27.56 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.22), residues: 1421 helix: 1.29 (0.18), residues: 850 sheet: 0.25 (0.45), residues: 124 loop : -1.06 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 190 HIS 0.004 0.001 HIS A 766 PHE 0.056 0.002 PHE A 843 TYR 0.019 0.002 TYR A1743 ARG 0.004 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 210 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 218 average time/residue: 0.2342 time to fit residues: 74.4780 Evaluate side-chains 215 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 202 time to evaluate : 1.316 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.1145 time to fit residues: 4.3863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12040 Z= 0.260 Angle : 0.735 27.336 16317 Z= 0.347 Chirality : 0.065 2.097 1907 Planarity : 0.004 0.036 1984 Dihedral : 6.575 58.223 1783 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.01 % Favored : 95.85 % Rotamer: Outliers : 0.93 % Allowed : 27.95 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.22), residues: 1421 helix: 1.22 (0.18), residues: 850 sheet: 0.23 (0.44), residues: 124 loop : -1.14 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 190 HIS 0.004 0.001 HIS A 766 PHE 0.058 0.002 PHE A 843 TYR 0.018 0.002 TYR A1755 ARG 0.005 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 207 time to evaluate : 1.256 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 210 average time/residue: 0.2282 time to fit residues: 70.1235 Evaluate side-chains 214 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 205 time to evaluate : 1.338 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.1166 time to fit residues: 3.8359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 131 optimal weight: 0.3980 chunk 113 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 12040 Z= 0.193 Angle : 0.732 28.058 16317 Z= 0.341 Chirality : 0.064 2.073 1907 Planarity : 0.004 0.042 1984 Dihedral : 6.393 59.887 1783 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.80 % Favored : 96.06 % Rotamer: Outliers : 0.47 % Allowed : 28.65 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.22), residues: 1421 helix: 1.37 (0.18), residues: 846 sheet: 0.33 (0.45), residues: 124 loop : -1.05 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 190 HIS 0.002 0.001 HIS A 766 PHE 0.054 0.001 PHE A 843 TYR 0.016 0.001 TYR A1739 ARG 0.006 0.000 ARG A 217 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 216 time to evaluate : 1.407 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 218 average time/residue: 0.2383 time to fit residues: 76.5166 Evaluate side-chains 215 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 210 time to evaluate : 1.329 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1298 time to fit residues: 3.0058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.155985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.118429 restraints weight = 17226.731| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.35 r_work: 0.3245 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12040 Z= 0.233 Angle : 0.736 27.480 16317 Z= 0.344 Chirality : 0.064 2.095 1907 Planarity : 0.004 0.037 1984 Dihedral : 6.383 59.829 1783 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.15 % Favored : 95.71 % Rotamer: Outliers : 0.78 % Allowed : 28.57 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.22), residues: 1421 helix: 1.31 (0.18), residues: 845 sheet: 0.21 (0.44), residues: 124 loop : -1.09 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 190 HIS 0.004 0.001 HIS A 766 PHE 0.053 0.001 PHE A 843 TYR 0.018 0.002 TYR B 180 ARG 0.006 0.000 ARG A 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3008.36 seconds wall clock time: 54 minutes 59.03 seconds (3299.03 seconds total)