Starting phenix.real_space_refine on Fri Mar 15 20:41:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8i_9782/03_2024/6j8i_9782_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8i_9782/03_2024/6j8i_9782.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8i_9782/03_2024/6j8i_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/6j8i_9782/03_2024/6j8i_9782_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8i_9782/03_2024/6j8i_9782_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8i_9782/03_2024/6j8i_9782.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8i_9782/03_2024/6j8i_9782.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8i_9782/03_2024/6j8i_9782_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j8i_9782/03_2024/6j8i_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-dev-5265/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: 6.79, per 1000 atoms: 0.58 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=2.04 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=1.85 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.00 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=2.01 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: 4.82 Conformation dependent library (CDL) restraints added in 2.1 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: 4.05 Time building geometry restraints manager: 5.27 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: 3619 1.36 - 1.52: 6837 1.52 - 1.69: 1428 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=" C ASN A1753 " pdb=" N MET A1754 " ideal model delta sigma weight residual 1.335 1.434 -0.099 1.31e-02 5.83e+03 5.76e+01 bond pdb=" C TYR A1755 " pdb=" N ILE A1756 " ideal model delta sigma weight residual 1.334 1.426 -0.092 1.26e-02 6.30e+03 5.31e+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 ... (remaining 12035 not shown) Histogram of bond angle deviations from ideal: 94.30 - 103.23: 128 103.23 - 112.16: 5767 112.16 - 121.09: 7278 121.09 - 130.01: 3051 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: 5818 17.79 - 35.57: 807 35.57 - 53.36: 437 53.36 - 71.15: 168 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 -179.56 -87.44 1 1.00e+01 1.00e-02 9.17e+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 93.00 179.93 -86.93 1 1.00e+01 1.00e-02 9.09e+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 -150.40 64.40 1 1.00e+01 1.00e-02 5.45e+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: 150 2.44 - 3.06: 8932 3.06 - 3.67: 17047 3.67 - 4.29: 25962 4.29 - 4.90: 42307 Nonbonded interactions: 94398 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 94393 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 3.640 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 35.290 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 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= 0.668 Angle : 1.511 23.043 16317 Z= 1.048 Chirality : 0.159 5.318 1907 Planarity : 0.009 0.185 1984 Dihedral : 21.891 88.937 4503 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 71.34 Ramachandran Plot: Outliers : 1.34 % Allowed : 2.46 % Favored : 96.20 % Rotamer: Outliers : 28.73 % Allowed : 19.33 % 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: 2.78 (0.21), residues: 1421 helix: 3.01 (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 689 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 370 poor density : 319 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7414 (mp) REVERT: A 122 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7643 (mt) REVERT: A 166 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6480 (pt0) REVERT: A 206 ASN cc_start: 0.5207 (OUTLIER) cc_final: 0.4998 (p0) REVERT: A 220 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6952 (mtt90) REVERT: A 231 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7443 (mp) REVERT: A 243 LYS cc_start: 0.8054 (mtpp) cc_final: 0.7727 (mptt) REVERT: A 255 CYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7407 (m) REVERT: A 293 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7417 (pt) REVERT: A 296 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6911 (tp30) REVERT: A 300 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7406 (mtt90) REVERT: A 356 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8091 (ttt180) REVERT: A 371 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8705 (mp) REVERT: A 379 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7781 (ttt) REVERT: A 415 GLU cc_start: 0.5797 (OUTLIER) cc_final: 0.4283 (mm-30) REVERT: A 761 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.7172 (mtm) REVERT: A 765 HIS cc_start: 0.8412 (OUTLIER) cc_final: 0.7887 (m-70) REVERT: A 766 HIS cc_start: 0.6852 (OUTLIER) cc_final: 0.6110 (t-170) REVERT: A 839 LEU cc_start: 0.8633 (mm) cc_final: 0.8408 (mm) REVERT: A 857 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.7070 (tttt) REVERT: A 1209 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8995 (mt) REVERT: A 1223 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8425 (ttpt) REVERT: A 1246 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7949 (mm) REVERT: A 1267 ASP cc_start: 0.8089 (m-30) cc_final: 0.7880 (m-30) REVERT: A 1278 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7318 (tp) REVERT: A 1322 MET cc_start: 0.8846 (mmm) cc_final: 0.8558 (mmt) REVERT: A 1358 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.5969 (mtm-85) REVERT: A 1423 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7629 (mmtp) REVERT: A 1449 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7998 (tp) REVERT: A 1504 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7529 (pt) REVERT: A 1537 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7712 (tm-30) REVERT: A 1602 TYR cc_start: 0.7055 (m-10) cc_final: 0.6033 (t80) REVERT: A 1603 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.7149 (m-80) REVERT: A 1670 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7805 (ttpp) REVERT: A 1711 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.7208 (pttt) REVERT: A 1749 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8609 (mm) REVERT: B 81 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6780 (tp30) REVERT: B 131 ASN cc_start: 0.6969 (OUTLIER) cc_final: 0.6707 (t0) REVERT: B 141 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8300 (mtpp) REVERT: B 190 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6590 (tp30) REVERT: B 191 THR cc_start: 0.4611 (OUTLIER) cc_final: 0.4113 (m) outliers start: 370 outliers final: 144 residues processed: 577 average time/residue: 0.2668 time to fit residues: 211.5308 Evaluate side-chains 405 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 225 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 PHE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 349 TRP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 835 ARG Chi-restraints excluded: chain A residue 837 PHE Chi-restraints excluded: chain A residue 841 ARG Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 898 LYS Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain A residue 1217 GLU Chi-restraints excluded: chain A residue 1223 LYS Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1290 ARG Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1293 ARG Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1307 MET Chi-restraints excluded: chain A residue 1309 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1358 ARG Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1409 THR Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1422 ASP Chi-restraints excluded: chain A residue 1423 LYS Chi-restraints excluded: chain A residue 1426 LYS Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1499 ARG Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1505 GLN Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1512 VAL Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1532 MET Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1546 VAL Chi-restraints excluded: chain A residue 1550 ILE Chi-restraints excluded: chain A residue 1566 LEU Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1598 LEU Chi-restraints excluded: chain A residue 1600 GLU Chi-restraints excluded: chain A residue 1601 THR Chi-restraints excluded: chain A residue 1603 PHE Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1605 SER Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1670 LYS Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1711 LYS Chi-restraints excluded: chain A residue 1718 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 32 TYR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 191 THR 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: 0.6980 chunk 37 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 68 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 146 ASN A 154 ASN A 278 ASN A 282 ASN A 291 ASN A 360 GLN A 365 ASN A 410 GLN A 774 ASN A 909 HIS A 941 GLN A1191 HIS A1378 GLN A1462 GLN A1505 GLN A1514 ASN ** A1528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1732 ASN A1762 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 12040 Z= 0.273 Angle : 0.860 26.448 16317 Z= 0.424 Chirality : 0.069 2.134 1907 Planarity : 0.006 0.081 1984 Dihedral : 15.296 93.869 2174 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.67 % Favored : 97.04 % Rotamer: Outliers : 12.97 % Allowed : 22.13 % Favored : 64.91 % 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: 1.60 (0.21), residues: 1421 helix: 1.91 (0.17), residues: 828 sheet: 1.17 (0.47), residues: 117 loop : -0.47 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 363 HIS 0.006 0.001 HIS A 765 PHE 0.045 0.002 PHE A 843 TYR 0.020 0.002 TYR A 305 ARG 0.010 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 421 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 254 time to evaluate : 1.625 Fit side-chains revert: symmetry clash REVERT: C 70 GLN cc_start: 0.4587 (mt0) cc_final: 0.4237 (tt0) REVERT: C 148 MET cc_start: 0.3436 (mmm) cc_final: 0.2135 (tmm) REVERT: A 231 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7703 (mp) REVERT: A 243 LYS cc_start: 0.7941 (mtpp) cc_final: 0.7703 (mptt) REVERT: A 290 MET cc_start: 0.7426 (mmp) cc_final: 0.7013 (mmp) REVERT: A 299 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7611 (t80) REVERT: A 300 ARG cc_start: 0.7502 (ttm-80) cc_final: 0.7243 (ttm-80) REVERT: A 735 LYS cc_start: 0.5325 (OUTLIER) cc_final: 0.4681 (tmmt) REVERT: A 766 HIS cc_start: 0.6814 (OUTLIER) cc_final: 0.6469 (t-170) REVERT: A 791 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7151 (tmm) REVERT: A 805 GLN cc_start: 0.6740 (tm130) cc_final: 0.5959 (mt0) REVERT: A 857 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.6903 (tttt) REVERT: A 900 ASN cc_start: 0.7429 (OUTLIER) cc_final: 0.7113 (m-40) REVERT: A 916 SER cc_start: 0.8472 (OUTLIER) cc_final: 0.8207 (p) REVERT: A 1177 ILE cc_start: 0.8075 (mm) cc_final: 0.7820 (tp) REVERT: A 1182 ARG cc_start: 0.8143 (mtp85) cc_final: 0.5993 (tmt170) REVERT: A 1209 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8945 (mt) REVERT: A 1449 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8016 (tp) REVERT: A 1522 MET cc_start: 0.7678 (tpp) cc_final: 0.7415 (tpp) REVERT: A 1602 TYR cc_start: 0.6875 (m-10) cc_final: 0.6110 (t80) REVERT: A 1603 PHE cc_start: 0.7837 (m-80) cc_final: 0.7546 (m-80) REVERT: A 1749 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8531 (mt) REVERT: B 96 ARG cc_start: 0.7519 (ttm110) cc_final: 0.7287 (mmm-85) REVERT: B 190 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6342 (tp30) REVERT: B 191 THR cc_start: 0.5541 (OUTLIER) cc_final: 0.4954 (m) outliers start: 167 outliers final: 86 residues processed: 376 average time/residue: 0.2314 time to fit residues: 125.3673 Evaluate side-chains 318 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 219 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 875 ILE Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1422 ASP Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1562 CYS Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1637 LEU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1694 ILE Chi-restraints excluded: chain A residue 1718 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1749 LEU Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 191 THR 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: 0.9980 chunk 108 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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** A1341 ASN A1462 GLN A1483 ASN A1528 ASN ** A1721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS B 131 ASN B 143 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12040 Z= 0.237 Angle : 0.754 27.318 16317 Z= 0.365 Chirality : 0.066 2.115 1907 Planarity : 0.005 0.068 1984 Dihedral : 11.274 59.982 1925 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.45 % Favored : 96.34 % Rotamer: Outliers : 9.86 % Allowed : 23.52 % Favored : 66.61 % 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: 1.14 (0.22), residues: 1421 helix: 1.58 (0.17), residues: 828 sheet: 0.91 (0.47), residues: 124 loop : -0.75 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 928 HIS 0.005 0.001 HIS B 143 PHE 0.022 0.002 PHE B 54 TYR 0.020 0.002 TYR A1739 ARG 0.007 0.001 ARG B 85 *********************** 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 356 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 229 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 148 MET cc_start: 0.3356 (mmm) cc_final: 0.1830 (tmm) REVERT: A 145 MET cc_start: 0.7734 (tpp) cc_final: 0.7396 (mpp) REVERT: A 192 ASP cc_start: 0.8273 (t0) cc_final: 0.7881 (m-30) REVERT: A 231 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7943 (mp) REVERT: A 243 LYS cc_start: 0.7950 (mtpp) cc_final: 0.7727 (mptt) REVERT: A 293 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7571 (pt) REVERT: A 299 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7597 (t80) REVERT: A 300 ARG cc_start: 0.7509 (ttm-80) cc_final: 0.7297 (ttm-80) REVERT: A 354 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8465 (mm) REVERT: A 742 MET cc_start: 0.4953 (mtt) cc_final: 0.4637 (ttm) REVERT: A 766 HIS cc_start: 0.7002 (OUTLIER) cc_final: 0.6746 (t-170) REVERT: A 791 MET cc_start: 0.7776 (ttp) cc_final: 0.7252 (tmm) REVERT: A 900 ASN cc_start: 0.7558 (OUTLIER) cc_final: 0.7222 (m-40) REVERT: A 1177 ILE cc_start: 0.8100 (mm) cc_final: 0.7777 (tp) REVERT: A 1182 ARG cc_start: 0.8286 (mtp85) cc_final: 0.6026 (tmt170) REVERT: A 1183 LYS cc_start: 0.8016 (ptpt) cc_final: 0.7635 (ptpt) REVERT: A 1209 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9139 (mt) REVERT: A 1522 MET cc_start: 0.7813 (tpp) cc_final: 0.7420 (mmp) REVERT: A 1543 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7568 (tpt) REVERT: A 1602 TYR cc_start: 0.6890 (m-10) cc_final: 0.6115 (t80) REVERT: A 1603 PHE cc_start: 0.7917 (m-80) cc_final: 0.7337 (t80) REVERT: A 1676 ASN cc_start: 0.8703 (OUTLIER) cc_final: 0.8451 (p0) REVERT: B 190 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6217 (tp30) REVERT: B 191 THR cc_start: 0.5361 (OUTLIER) cc_final: 0.4820 (m) outliers start: 127 outliers final: 71 residues processed: 314 average time/residue: 0.2204 time to fit residues: 101.0673 Evaluate side-chains 289 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 207 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 766 HIS Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1379 ASN Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1718 LYS Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 75 ASN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 191 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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** A1462 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12040 Z= 0.270 Angle : 0.737 27.177 16317 Z= 0.352 Chirality : 0.066 2.109 1907 Planarity : 0.004 0.053 1984 Dihedral : 10.111 58.179 1874 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.80 % Favored : 95.99 % Rotamer: Outliers : 9.16 % Allowed : 23.52 % Favored : 67.31 % 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: 0.90 (0.22), residues: 1421 helix: 1.41 (0.17), residues: 832 sheet: 0.40 (0.47), residues: 124 loop : -0.77 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1382 HIS 0.005 0.001 HIS A 765 PHE 0.023 0.002 PHE B 54 TYR 0.019 0.002 TYR A 157 ARG 0.004 0.001 ARG C 47 *********************** 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 342 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 224 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 109 ASP cc_start: 0.5517 (t0) cc_final: 0.5300 (t0) REVERT: C 148 MET cc_start: 0.3250 (mmm) cc_final: 0.1741 (tmm) REVERT: A 145 MET cc_start: 0.7915 (tpp) cc_final: 0.7605 (mpp) REVERT: A 231 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8034 (mp) REVERT: A 243 LYS cc_start: 0.7989 (mtpp) cc_final: 0.7758 (mptt) REVERT: A 299 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7575 (t80) REVERT: A 300 ARG cc_start: 0.7590 (ttm-80) cc_final: 0.7367 (ttm-80) REVERT: A 354 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8572 (mm) REVERT: A 358 MET cc_start: 0.8426 (tmm) cc_final: 0.7759 (ttt) REVERT: A 742 MET cc_start: 0.4912 (mtt) cc_final: 0.4560 (ttm) REVERT: A 791 MET cc_start: 0.7707 (ttp) cc_final: 0.7214 (tmm) REVERT: A 900 ASN cc_start: 0.7602 (OUTLIER) cc_final: 0.7266 (m-40) REVERT: A 1177 ILE cc_start: 0.8026 (mm) cc_final: 0.7724 (tp) REVERT: A 1183 LYS cc_start: 0.8062 (ptpt) cc_final: 0.7791 (ptmt) REVERT: A 1522 MET cc_start: 0.7859 (tpp) cc_final: 0.7496 (mmp) REVERT: A 1543 MET cc_start: 0.7967 (mmt) cc_final: 0.7552 (tpt) REVERT: A 1602 TYR cc_start: 0.6773 (m-10) cc_final: 0.6098 (t80) REVERT: A 1603 PHE cc_start: 0.7807 (m-80) cc_final: 0.7315 (t80) REVERT: A 1628 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7347 (tmmt) REVERT: A 1634 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8924 (mt) REVERT: B 190 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6259 (tp30) outliers start: 118 outliers final: 76 residues processed: 308 average time/residue: 0.2257 time to fit residues: 100.5766 Evaluate side-chains 291 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 208 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 778 ILE Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1315 ILE Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1379 ASN Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1507 CYS Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1718 LYS Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain B residue 21 CYS Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 190 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 766 HIS A1505 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12040 Z= 0.174 Angle : 0.700 28.097 16317 Z= 0.328 Chirality : 0.063 2.074 1907 Planarity : 0.004 0.043 1984 Dihedral : 9.314 59.651 1856 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.38 % Favored : 96.41 % Rotamer: Outliers : 7.30 % Allowed : 25.31 % Favored : 67.39 % 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: 0.99 (0.22), residues: 1421 helix: 1.52 (0.18), residues: 832 sheet: 0.33 (0.46), residues: 124 loop : -0.80 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 190 HIS 0.003 0.001 HIS A 765 PHE 0.034 0.001 PHE A1509 TYR 0.018 0.001 TYR A1739 ARG 0.007 0.000 ARG B 96 *********************** 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 316 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 222 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 THR cc_start: -0.0630 (OUTLIER) cc_final: -0.0835 (p) REVERT: C 148 MET cc_start: 0.3177 (mmm) cc_final: 0.1678 (tmm) REVERT: A 145 MET cc_start: 0.7807 (tpp) cc_final: 0.7469 (mpp) REVERT: A 243 LYS cc_start: 0.7975 (mtpp) cc_final: 0.7680 (mptt) REVERT: A 354 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8498 (mm) REVERT: A 358 MET cc_start: 0.8407 (tmm) cc_final: 0.7737 (ttt) REVERT: A 742 MET cc_start: 0.4622 (mtt) cc_final: 0.4373 (ttm) REVERT: A 791 MET cc_start: 0.7620 (ttp) cc_final: 0.7116 (tmm) REVERT: A 900 ASN cc_start: 0.7579 (OUTLIER) cc_final: 0.7270 (m-40) REVERT: A 1177 ILE cc_start: 0.8026 (mm) cc_final: 0.7786 (tp) REVERT: A 1183 LYS cc_start: 0.8090 (ptpt) cc_final: 0.7887 (ptmt) REVERT: A 1290 ARG cc_start: 0.8272 (ttt-90) cc_final: 0.7904 (ttm-80) REVERT: A 1522 MET cc_start: 0.7823 (tpp) cc_final: 0.7509 (mmp) REVERT: A 1543 MET cc_start: 0.7999 (mmt) cc_final: 0.7507 (tpt) REVERT: A 1602 TYR cc_start: 0.6702 (m-10) cc_final: 0.6035 (t80) REVERT: A 1603 PHE cc_start: 0.7775 (m-80) cc_final: 0.7410 (t80) REVERT: A 1628 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7389 (tmmt) REVERT: A 1676 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8333 (p0) REVERT: B 183 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7306 (mtpp) REVERT: B 190 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6291 (tp30) outliers start: 94 outliers final: 65 residues processed: 285 average time/residue: 0.2338 time to fit residues: 97.9375 Evaluate side-chains 282 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 210 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1379 ASN Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1663 MET Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1718 LYS Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 190 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 11 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7576 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12040 Z= 0.221 Angle : 0.696 27.495 16317 Z= 0.326 Chirality : 0.064 2.095 1907 Planarity : 0.004 0.036 1984 Dihedral : 8.806 59.048 1841 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.73 % Favored : 96.06 % Rotamer: Outliers : 7.84 % Allowed : 25.70 % Favored : 66.46 % 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: 0.88 (0.22), residues: 1421 helix: 1.43 (0.18), residues: 838 sheet: 0.33 (0.47), residues: 124 loop : -0.89 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1382 HIS 0.004 0.001 HIS A 765 PHE 0.022 0.001 PHE B 54 TYR 0.016 0.002 TYR A 157 ARG 0.008 0.000 ARG B 96 *********************** 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 320 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 219 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 79 MET cc_start: 0.2576 (mtp) cc_final: 0.0896 (mmm) REVERT: C 148 MET cc_start: 0.3051 (mmm) cc_final: 0.1598 (tmm) REVERT: A 145 MET cc_start: 0.7837 (tpp) cc_final: 0.7446 (mpp) REVERT: A 222 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8701 (tt) REVERT: A 243 LYS cc_start: 0.7982 (mtpp) cc_final: 0.7703 (mptt) REVERT: A 354 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8627 (mm) REVERT: A 357 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8411 (mt) REVERT: A 358 MET cc_start: 0.8418 (tmm) cc_final: 0.7772 (ttt) REVERT: A 742 MET cc_start: 0.4466 (mtt) cc_final: 0.4083 (ttm) REVERT: A 791 MET cc_start: 0.7752 (ttp) cc_final: 0.7039 (ttt) REVERT: A 900 ASN cc_start: 0.7572 (OUTLIER) cc_final: 0.7250 (m-40) REVERT: A 1177 ILE cc_start: 0.7965 (mm) cc_final: 0.7747 (tp) REVERT: A 1290 ARG cc_start: 0.8301 (ttt-90) cc_final: 0.7966 (ttm-80) REVERT: A 1522 MET cc_start: 0.7855 (tpp) cc_final: 0.7539 (mmp) REVERT: A 1543 MET cc_start: 0.7992 (mmt) cc_final: 0.7569 (tpt) REVERT: A 1602 TYR cc_start: 0.6671 (m-10) cc_final: 0.6068 (t80) REVERT: A 1603 PHE cc_start: 0.7729 (m-80) cc_final: 0.7373 (t80) REVERT: A 1628 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7259 (tmmt) REVERT: A 1676 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.8388 (p0) REVERT: B 183 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7295 (mtpp) REVERT: B 190 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6116 (tp30) outliers start: 101 outliers final: 65 residues processed: 289 average time/residue: 0.2194 time to fit residues: 93.5750 Evaluate side-chains 281 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 208 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1315 ILE Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1379 ASN Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1589 SER Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 190 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 4.9990 chunk 15 optimal weight: 0.0670 chunk 78 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12040 Z= 0.173 Angle : 0.687 28.134 16317 Z= 0.320 Chirality : 0.063 2.069 1907 Planarity : 0.004 0.036 1984 Dihedral : 8.359 59.175 1833 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.73 % Favored : 96.06 % Rotamer: Outliers : 6.68 % Allowed : 26.24 % Favored : 67.08 % 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: 0.94 (0.22), residues: 1421 helix: 1.50 (0.18), residues: 838 sheet: 0.27 (0.46), residues: 125 loop : -0.87 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1382 HIS 0.003 0.001 HIS A 765 PHE 0.041 0.001 PHE A 843 TYR 0.017 0.001 TYR A1739 ARG 0.007 0.000 ARG B 96 *********************** 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 298 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 212 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 109 ASP cc_start: 0.5476 (t0) cc_final: 0.5253 (t0) REVERT: C 148 MET cc_start: 0.3166 (mmm) cc_final: 0.2029 (tmm) REVERT: A 222 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8601 (tt) REVERT: A 243 LYS cc_start: 0.7950 (mtpp) cc_final: 0.7660 (mptt) REVERT: A 354 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8531 (mm) REVERT: A 357 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8351 (mt) REVERT: A 358 MET cc_start: 0.8367 (tmm) cc_final: 0.7741 (ttt) REVERT: A 760 PHE cc_start: 0.8533 (t80) cc_final: 0.8219 (t80) REVERT: A 791 MET cc_start: 0.7737 (ttp) cc_final: 0.7028 (ttt) REVERT: A 900 ASN cc_start: 0.7530 (OUTLIER) cc_final: 0.7231 (m-40) REVERT: A 1177 ILE cc_start: 0.7955 (mm) cc_final: 0.7741 (tp) REVERT: A 1290 ARG cc_start: 0.8268 (ttt-90) cc_final: 0.7944 (ttm-80) REVERT: A 1322 MET cc_start: 0.7707 (mmm) cc_final: 0.6479 (mmm) REVERT: A 1522 MET cc_start: 0.7819 (tpp) cc_final: 0.7512 (mmp) REVERT: A 1543 MET cc_start: 0.7925 (mmt) cc_final: 0.7532 (tpt) REVERT: A 1602 TYR cc_start: 0.6641 (m-10) cc_final: 0.6062 (t80) REVERT: A 1603 PHE cc_start: 0.7615 (m-80) cc_final: 0.7287 (t80) REVERT: A 1628 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.7185 (tmmt) REVERT: A 1676 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8327 (p0) REVERT: A 1719 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7554 (tttm) REVERT: B 190 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.6125 (tp30) outliers start: 86 outliers final: 59 residues processed: 270 average time/residue: 0.2205 time to fit residues: 88.2089 Evaluate side-chains 272 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 205 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1379 ASN Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1676 ASN Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 190 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 87 optimal weight: 0.0060 chunk 93 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 HIS ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12040 Z= 0.231 Angle : 0.699 27.426 16317 Z= 0.325 Chirality : 0.064 2.094 1907 Planarity : 0.004 0.035 1984 Dihedral : 8.079 59.656 1827 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.94 % Favored : 95.85 % Rotamer: Outliers : 5.67 % Allowed : 26.86 % Favored : 67.47 % 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: 0.80 (0.22), residues: 1421 helix: 1.39 (0.18), residues: 849 sheet: 0.13 (0.46), residues: 124 loop : -0.97 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1382 HIS 0.004 0.001 HIS B 122 PHE 0.037 0.001 PHE A 843 TYR 0.016 0.001 TYR A 367 ARG 0.008 0.000 ARG B 96 *********************** 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 279 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 206 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 148 MET cc_start: 0.3219 (mmm) cc_final: 0.2102 (tmm) REVERT: A 190 TRP cc_start: 0.7361 (m-10) cc_final: 0.6993 (m-10) REVERT: A 222 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8612 (tt) REVERT: A 243 LYS cc_start: 0.7988 (mtpp) cc_final: 0.7711 (mptt) REVERT: A 354 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8656 (mm) REVERT: A 357 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8412 (mt) REVERT: A 358 MET cc_start: 0.8380 (tmm) cc_final: 0.7896 (ttt) REVERT: A 760 PHE cc_start: 0.8515 (t80) cc_final: 0.8211 (t80) REVERT: A 791 MET cc_start: 0.7750 (ttp) cc_final: 0.7054 (ttt) REVERT: A 900 ASN cc_start: 0.7539 (OUTLIER) cc_final: 0.7239 (m-40) REVERT: A 1177 ILE cc_start: 0.8090 (mm) cc_final: 0.7825 (tp) REVERT: A 1290 ARG cc_start: 0.8258 (ttt-90) cc_final: 0.7894 (ttm-80) REVERT: A 1522 MET cc_start: 0.7849 (tpp) cc_final: 0.7537 (mmp) REVERT: A 1543 MET cc_start: 0.7924 (mmt) cc_final: 0.7547 (tpt) REVERT: A 1602 TYR cc_start: 0.6582 (m-10) cc_final: 0.6005 (t80) REVERT: A 1603 PHE cc_start: 0.7668 (m-80) cc_final: 0.7345 (t80) REVERT: A 1628 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7107 (tmmt) REVERT: A 1691 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8646 (mm) REVERT: A 1719 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7606 (tttm) REVERT: B 190 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6173 (tp30) outliers start: 73 outliers final: 58 residues processed: 255 average time/residue: 0.2292 time to fit residues: 86.2449 Evaluate side-chains 268 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 202 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 730 TRP Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1379 ASN Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1430 SER Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 190 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 128 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 116 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.7562 moved from start: 0.5558 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= 0.191 Angle : 0.694 27.938 16317 Z= 0.321 Chirality : 0.063 2.075 1907 Planarity : 0.004 0.036 1984 Dihedral : 7.973 59.810 1827 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.87 % Favored : 95.92 % Rotamer: Outliers : 5.59 % Allowed : 26.86 % Favored : 67.55 % 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: 0.82 (0.22), residues: 1421 helix: 1.43 (0.18), residues: 850 sheet: 0.03 (0.45), residues: 124 loop : -0.97 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1382 HIS 0.003 0.001 HIS A 765 PHE 0.019 0.001 PHE B 54 TYR 0.017 0.001 TYR A1739 ARG 0.009 0.000 ARG B 96 *********************** 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 280 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 208 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 148 MET cc_start: 0.3262 (mmm) cc_final: 0.2210 (tmm) REVERT: A 190 TRP cc_start: 0.7302 (m-10) cc_final: 0.6991 (m-10) REVERT: A 222 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8563 (tt) REVERT: A 243 LYS cc_start: 0.7945 (mtpp) cc_final: 0.7656 (mptt) REVERT: A 354 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8632 (mm) REVERT: A 357 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8406 (mt) REVERT: A 358 MET cc_start: 0.8340 (tmm) cc_final: 0.7871 (ttt) REVERT: A 760 PHE cc_start: 0.8446 (t80) cc_final: 0.8229 (t80) REVERT: A 791 MET cc_start: 0.7743 (ttp) cc_final: 0.7058 (ttt) REVERT: A 900 ASN cc_start: 0.7530 (OUTLIER) cc_final: 0.7252 (m-40) REVERT: A 1177 ILE cc_start: 0.8026 (mm) cc_final: 0.7764 (tp) REVERT: A 1188 ILE cc_start: 0.9254 (mm) cc_final: 0.9013 (mt) REVERT: A 1290 ARG cc_start: 0.8234 (ttt-90) cc_final: 0.7885 (ttm-80) REVERT: A 1522 MET cc_start: 0.7833 (tpp) cc_final: 0.7521 (mmp) REVERT: A 1543 MET cc_start: 0.7913 (mmt) cc_final: 0.7541 (tpt) REVERT: A 1602 TYR cc_start: 0.6590 (m-10) cc_final: 0.5868 (t80) REVERT: A 1603 PHE cc_start: 0.7700 (m-80) cc_final: 0.7371 (t80) REVERT: A 1628 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.6947 (tmmt) REVERT: A 1691 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8672 (mm) REVERT: A 1719 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7596 (tttm) REVERT: B 190 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.6134 (tp30) outliers start: 72 outliers final: 61 residues processed: 258 average time/residue: 0.2137 time to fit residues: 81.0660 Evaluate side-chains 272 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 203 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 730 TRP Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1379 ASN Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1430 SER Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 190 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 87 optimal weight: 0.3980 chunk 69 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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: 0.7568 moved from start: 0.5584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12040 Z= 0.201 Angle : 0.696 27.804 16317 Z= 0.320 Chirality : 0.063 2.080 1907 Planarity : 0.004 0.036 1984 Dihedral : 7.932 59.811 1827 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.08 % Favored : 95.71 % Rotamer: Outliers : 5.82 % Allowed : 26.63 % Favored : 67.55 % 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: 0.78 (0.22), residues: 1421 helix: 1.40 (0.18), residues: 851 sheet: -0.04 (0.45), residues: 124 loop : -0.99 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1382 HIS 0.004 0.001 HIS A 765 PHE 0.020 0.001 PHE B 54 TYR 0.018 0.001 TYR A 405 ARG 0.009 0.000 ARG B 96 ********************** 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 280 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 205 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 109 ASP cc_start: 0.5789 (t0) cc_final: 0.5584 (t0) REVERT: C 148 MET cc_start: 0.3290 (mmm) cc_final: 0.2265 (tmm) REVERT: A 222 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8570 (tt) REVERT: A 357 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8413 (mt) REVERT: A 358 MET cc_start: 0.8352 (tmm) cc_final: 0.7898 (ttt) REVERT: A 791 MET cc_start: 0.7749 (ttp) cc_final: 0.7067 (ttt) REVERT: A 900 ASN cc_start: 0.7507 (OUTLIER) cc_final: 0.7232 (m-40) REVERT: A 1177 ILE cc_start: 0.8074 (mm) cc_final: 0.7800 (tp) REVERT: A 1188 ILE cc_start: 0.9260 (mm) cc_final: 0.9025 (mt) REVERT: A 1290 ARG cc_start: 0.8223 (ttt-90) cc_final: 0.7886 (ttm-80) REVERT: A 1326 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8756 (tm) REVERT: A 1522 MET cc_start: 0.7828 (tpp) cc_final: 0.7517 (mmp) REVERT: A 1543 MET cc_start: 0.7906 (mmt) cc_final: 0.7541 (tpt) REVERT: A 1602 TYR cc_start: 0.6597 (m-10) cc_final: 0.5871 (t80) REVERT: A 1603 PHE cc_start: 0.7595 (m-80) cc_final: 0.7318 (t80) REVERT: A 1628 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.6939 (tmmt) REVERT: A 1691 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8673 (mm) REVERT: A 1719 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7463 (tttm) REVERT: B 190 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.6097 (tp30) outliers start: 75 outliers final: 61 residues processed: 258 average time/residue: 0.2151 time to fit residues: 81.5493 Evaluate side-chains 271 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 202 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 730 TRP Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 847 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain A residue 1264 LEU Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1295 LEU Chi-restraints excluded: chain A residue 1326 LEU Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1379 ASN Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1419 VAL Chi-restraints excluded: chain A residue 1430 SER Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1514 ASN Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1544 THR Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1719 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 190 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.156797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.120555 restraints weight = 17385.748| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.37 r_work: 0.3268 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12040 Z= 0.172 Angle : 0.683 28.087 16317 Z= 0.313 Chirality : 0.063 2.071 1907 Planarity : 0.004 0.035 1984 Dihedral : 7.563 58.483 1825 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.01 % Favored : 95.78 % Rotamer: Outliers : 5.12 % Allowed : 27.10 % Favored : 67.78 % 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: 1.45 (0.18), residues: 848 sheet: 0.02 (0.45), residues: 124 loop : -0.94 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1382 HIS 0.003 0.001 HIS A 765 PHE 0.021 0.001 PHE A 760 TYR 0.017 0.001 TYR A 405 ARG 0.009 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3008.56 seconds wall clock time: 54 minutes 32.94 seconds (3272.94 seconds total)