Starting phenix.real_space_refine (version: dev) on Tue Feb 21 00:21:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xm9_33292/02_2023/7xm9_33292_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xm9_33292/02_2023/7xm9_33292.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xm9_33292/02_2023/7xm9_33292_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xm9_33292/02_2023/7xm9_33292_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xm9_33292/02_2023/7xm9_33292_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xm9_33292/02_2023/7xm9_33292.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xm9_33292/02_2023/7xm9_33292.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xm9_33292/02_2023/7xm9_33292_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xm9_33292/02_2023/7xm9_33292_neut_updated.pdb" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.099 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 963 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 24": "OE1" <-> "OE2" Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 407": "OE1" <-> "OE2" Residue "A TYR 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 743": "OD1" <-> "OD2" Residue "A PHE 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A GLU 770": "OE1" <-> "OE2" Residue "A GLU 771": "OE1" <-> "OE2" Residue "A ASP 799": "OD1" <-> "OD2" Residue "A GLU 802": "OE1" <-> "OE2" Residue "A TYR 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 835": "NH1" <-> "NH2" Residue "A PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 922": "NH1" <-> "NH2" Residue "A GLU 927": "OE1" <-> "OE2" Residue "A PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1182": "NH1" <-> "NH2" Residue "A TYR 1186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1212": "OE1" <-> "OE2" Residue "A ARG 1218": "NH1" <-> "NH2" Residue "A ASP 1230": "OD1" <-> "OD2" Residue "A PHE 1254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1293": "NH1" <-> "NH2" Residue "A ARG 1308": "NH1" <-> "NH2" Residue "A GLU 1369": "OE1" <-> "OE2" Residue "A ASP 1422": "OD1" <-> "OD2" Residue "A TYR 1436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1499": "NH1" <-> "NH2" Residue "A ASP 1510": "OD1" <-> "OD2" Residue "A GLU 1535": "OE1" <-> "OE2" Residue "A GLU 1545": "OE1" <-> "OE2" Residue "A PHE 1574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1597": "OD1" <-> "OD2" Residue "A GLU 1600": "OE1" <-> "OE2" Residue "A ARG 1613": "NH1" <-> "NH2" Residue "A ARG 1619": "NH1" <-> "NH2" Residue "A ARG 1622": "NH1" <-> "NH2" Residue "A ARG 1631": "NH1" <-> "NH2" Residue "A PHE 1645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1729": "OD1" <-> "OD2" Residue "A TYR 1739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1761": "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 76": "OE1" <-> "OE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "C ARG 135": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 12490 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1230, 9896 Classifications: {'peptide': 1230} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 1189} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: "C" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 977 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 113} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 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 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 chiralities: 2 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {'6OU': 1, 'G2E': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 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 chiralities: 4 Time building chain proxies: 7.26, per 1000 atoms: 0.58 Number of scatterers: 12490 At special positions: 0 Unit cell: (126.88, 138.32, 123.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 97 16.00 P 1 15.00 O 2212 8.00 N 1965 7.00 C 8215 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 324 " distance=1.65 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=2.75 Simple disulfide: pdb=" SG CYS A 895 " - pdb=" SG CYS C 55 " distance=1.81 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=2.03 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.03 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 43 " distance=2.61 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.58 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.04 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 A2301 " - " ASN A1375 " " NAG B 501 " - " ASN B 93 " " NAG B 502 " - " ASN B 110 " " NAG B 503 " - " ASN B 114 " " NAG B 504 " - " ASN B 135 " " NAG D 1 " - " ASN A1352 " " NAG E 1 " - " ASN A1366 " Time building additional restraints: 5.48 Conformation dependent library (CDL) restraints added in 1.8 seconds 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2884 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 9 sheets defined 59.0% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 17 through 29 Processing helix chain 'A' and resid 51 through 53 No H-bonds generated for 'chain 'A' and resid 51 through 53' Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 80 through 83 No H-bonds generated for 'chain 'A' and resid 80 through 83' Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 126 through 145 removed outlier: 4.099A pdb=" N THR A 144 " --> pdb=" O CYS A 140 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N MET A 145 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 174 removed outlier: 3.563A pdb=" N LYS A 153 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 203 removed outlier: 4.097A pdb=" N LEU A 191 " --> pdb=" O TRP A 188 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 195 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 227 removed outlier: 4.257A pdb=" N PHE A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LEU A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ARG A 220 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ALA A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 267 removed outlier: 3.557A pdb=" N GLY A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASP A 247 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 4.692A 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 286 through 290 Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' 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 416 removed outlier: 3.663A pdb=" N MET A 379 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 386 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 387 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 388 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 389 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N SER A 390 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE A 391 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR A 392 " --> pdb=" O GLY A 389 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 393 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 415 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 740 Processing helix chain 'A' and resid 743 through 761 removed outlier: 3.671A pdb=" N ASP A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU A 748 " --> pdb=" O PRO A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 803 Proline residue: A 800 - end of helix Processing helix chain 'A' and resid 807 through 822 removed outlier: 4.679A pdb=" N GLU A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 847 removed outlier: 4.258A pdb=" N ARG A 838 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU A 839 " --> pdb=" O SER A 836 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS A 847 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 862 Processing helix chain 'A' and resid 867 through 894 removed outlier: 5.328A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N SER A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 898 No H-bonds generated for 'chain 'A' and resid 896 through 898' Processing helix chain 'A' and resid 913 through 924 Processing helix chain 'A' and resid 929 through 939 removed outlier: 4.114A pdb=" N ASP A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 971 removed outlier: 3.548A pdb=" N PHE A 971 " --> pdb=" O LEU A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1190 Processing helix chain 'A' and resid 1192 through 1209 removed outlier: 4.137A pdb=" N LEU A1209 " --> pdb=" O SER A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1216 No H-bonds generated for 'chain 'A' and resid 1214 through 1216' Processing helix chain 'A' and resid 1220 through 1254 removed outlier: 4.072A pdb=" N LYS A1231 " --> pdb=" O GLU A1227 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N TYR A1250 " --> pdb=" O ILE A1246 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N LYS A1251 " --> pdb=" O ALA A1247 " (cutoff:3.500A) removed outlier: 3.970A 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 1285 through 1300 removed outlier: 4.059A pdb=" N THR A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU A1292 " --> pdb=" O SER A1288 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG A1293 " --> pdb=" O LEU A1289 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ALA A1294 " --> pdb=" O ARG A1290 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LEU A1295 " --> pdb=" O THR A1291 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG A1296 " --> pdb=" O LEU A1292 " (cutoff:3.500A) Proline residue: A1297 - end of helix removed outlier: 4.911A pdb=" N ALA A1300 " --> pdb=" O ARG A1296 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1343 removed outlier: 4.037A pdb=" N VAL A1310 " --> pdb=" O GLY A1306 " (cutoff:3.500A) Proline residue: A1319 - end of helix Processing helix chain 'A' and resid 1367 through 1376 removed outlier: 3.560A 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 1409 through 1417 removed outlier: 3.807A pdb=" N ALA A1414 " --> pdb=" O ILE A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1466 removed outlier: 3.817A pdb=" N PHE A1446 " --> pdb=" O ILE A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1489 removed outlier: 4.142A pdb=" N LEU A1488 " --> pdb=" O ALA A1484 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY A1489 " --> pdb=" O MET A1485 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1513 Processing helix chain 'A' and resid 1515 through 1533 Processing helix chain 'A' and resid 1541 through 1569 Processing helix chain 'A' and resid 1577 through 1602 Processing helix chain 'A' and resid 1606 through 1625 removed outlier: 4.386A pdb=" N ALA A1615 " --> pdb=" O VAL A1611 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ARG A1616 " --> pdb=" O ILE A1612 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ILE A1617 " --> pdb=" O ARG A1613 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLY A1618 " --> pdb=" O LEU A1614 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ARG A1619 " --> pdb=" O ALA A1615 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU A1623 " --> pdb=" O ARG A1619 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N VAL A1624 " --> pdb=" O ILE A1620 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LYS A1625 " --> pdb=" O LEU A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1628 through 1665 removed outlier: 3.931A pdb=" N LEU A1633 " --> pdb=" O GLY A1629 " (cutoff:3.500A) Proline residue: A1642 - end of helix Processing helix chain 'A' and resid 1684 through 1696 removed outlier: 3.879A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1700 through 1708 Proline residue: A1706 - end of helix Processing helix chain 'A' and resid 1733 through 1751 Processing helix chain 'A' and resid 1755 through 1768 Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 154 through 190 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 sheet with id= A, first strand: chain 'A' and resid 87 through 91 Processing sheet with id= B, first strand: chain 'A' and resid 273 through 277 Processing sheet with id= C, first strand: chain 'A' and resid 1349 through 1352 Processing sheet with id= D, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.001A pdb=" N GLU B 145 " --> pdb=" O ALA B 30 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 36 through 38 Processing sheet with id= F, first strand: chain 'B' and resid 135 through 144 removed outlier: 3.675A pdb=" N LEU B 71 " --> pdb=" O TRP B 57 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE B 59 " --> pdb=" O LYS B 69 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LYS B 69 " --> pdb=" O PHE B 59 " (cutoff:3.500A) Processing sheet with id= G, 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= H, 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: 7.440A pdb=" N VAL C 40 " --> pdb=" O HIS C 143 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLN C 145 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 3.527A 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: 5.435A pdb=" N MET C 79 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 46 through 48 681 hydrogen bonds defined for protein. 1815 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: 3.67 Time building geometry restraints manager: 5.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.34: 3765 1.34 - 1.51: 3834 1.51 - 1.67: 5032 1.67 - 1.84: 154 1.84 - 2.01: 2 Bond restraints: 12787 Sorted by residual: bond pdb=" C06 G2E A2302 " pdb=" C07 G2E A2302 " ideal model delta sigma weight residual 0.845 1.492 -0.647 2.00e-02 2.50e+03 1.04e+03 bond pdb=" C06 G2E A2302 " pdb=" C08 G2E A2302 " ideal model delta sigma weight residual 0.923 1.508 -0.585 2.00e-02 2.50e+03 8.56e+02 bond pdb=" C12 G2E A2302 " pdb=" O01 G2E A2302 " ideal model delta sigma weight residual 1.049 1.574 -0.525 2.00e-02 2.50e+03 6.90e+02 bond pdb=" C10 G2E A2302 " pdb=" N05 G2E A2302 " ideal model delta sigma weight residual 1.082 1.494 -0.412 2.00e-02 2.50e+03 4.25e+02 bond pdb=" C11 G2E A2302 " pdb=" N05 G2E A2302 " ideal model delta sigma weight residual 1.219 1.501 -0.282 2.00e-02 2.50e+03 1.99e+02 ... (remaining 12782 not shown) Histogram of bond angle deviations from ideal: 92.20 - 101.50: 62 101.50 - 110.80: 4346 110.80 - 120.10: 7512 120.10 - 129.40: 5313 129.40 - 138.70: 84 Bond angle restraints: 17317 Sorted by residual: angle pdb=" N TYR A 801 " pdb=" CA TYR A 801 " pdb=" C TYR A 801 " ideal model delta sigma weight residual 111.40 125.24 -13.84 1.22e+00 6.72e-01 1.29e+02 angle pdb=" N MET A 379 " pdb=" CA MET A 379 " pdb=" C MET A 379 " ideal model delta sigma weight residual 111.82 102.70 9.12 1.16e+00 7.43e-01 6.19e+01 angle pdb=" C ASN C 131 " pdb=" N PRO C 132 " pdb=" CA PRO C 132 " ideal model delta sigma weight residual 119.66 114.10 5.56 7.20e-01 1.93e+00 5.97e+01 angle pdb=" N GLU A 802 " pdb=" CA GLU A 802 " pdb=" C GLU A 802 " ideal model delta sigma weight residual 112.89 103.88 9.01 1.24e+00 6.50e-01 5.28e+01 angle pdb=" N ASP A 320 " pdb=" CA ASP A 320 " pdb=" C ASP A 320 " ideal model delta sigma weight residual 111.36 118.41 -7.05 1.09e+00 8.42e-01 4.19e+01 ... (remaining 17312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.08: 6912 24.08 - 48.17: 535 48.17 - 72.25: 70 72.25 - 96.33: 19 96.33 - 120.41: 2 Dihedral angle restraints: 7538 sinusoidal: 3073 harmonic: 4465 Sorted by residual: dihedral pdb=" CA GLY A 322 " pdb=" C GLY A 322 " pdb=" N GLN A 323 " pdb=" CA GLN A 323 " ideal model delta harmonic sigma weight residual -180.00 -59.59 -120.41 0 5.00e+00 4.00e-02 5.80e+02 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 -161.56 75.56 1 1.00e+01 1.00e-02 7.21e+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 -86.00 -161.51 75.51 1 1.00e+01 1.00e-02 7.20e+01 ... (remaining 7535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.307: 1991 0.307 - 0.614: 5 0.614 - 0.920: 0 0.920 - 1.227: 0 1.227 - 1.534: 1 Chirality restraints: 1997 Sorted by residual: chirality pdb=" C06 G2E A2302 " pdb=" C07 G2E A2302 " pdb=" C08 G2E A2302 " pdb=" C09 G2E A2302 " both_signs ideal model delta sigma weight residual False -0.75 -2.28 1.53 2.00e-01 2.50e+01 5.88e+01 chirality pdb=" CA PHE A1679 " pdb=" N PHE A1679 " pdb=" C PHE A1679 " pdb=" CB PHE A1679 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.75e+00 chirality pdb=" CA CYS A 897 " pdb=" N CYS A 897 " pdb=" C CYS A 897 " pdb=" CB CYS A 897 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.74e+00 ... (remaining 1994 not shown) Planarity restraints: 2123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 104 " 0.061 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO C 105 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO C 105 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 105 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 378 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C TYR A 378 " 0.056 2.00e-02 2.50e+03 pdb=" O TYR A 378 " -0.021 2.00e-02 2.50e+03 pdb=" N MET A 379 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 132 " -0.053 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO C 133 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 133 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 133 " -0.043 5.00e-02 4.00e+02 ... (remaining 2120 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 83 2.53 - 3.12: 10064 3.12 - 3.71: 19338 3.71 - 4.31: 27298 4.31 - 4.90: 45075 Nonbonded interactions: 101858 Sorted by model distance: nonbonded pdb=" OD1 ASP A 361 " pdb=" O GLY A 926 " model vdw 1.933 3.040 nonbonded pdb=" CD2 TYR C 128 " pdb=" NH2 ARG C 137 " model vdw 2.087 3.420 nonbonded pdb=" O GLN C 62 " pdb=" CD PRO C 132 " model vdw 2.107 3.440 nonbonded pdb=" CE2 PHE C 101 " pdb=" O GLY C 103 " model vdw 2.108 3.340 nonbonded pdb=" O GLY A1444 " pdb=" OG1 THR A1448 " model vdw 2.163 2.440 ... (remaining 101853 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 97 5.16 5 C 8215 2.51 5 N 1965 2.21 5 O 2212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.210 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: 4.860 Check model and map are aligned: 0.210 Process input model: 34.510 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.120 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 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 : 0.012 0.647 12787 Z= 0.839 Angle : 0.834 16.816 17317 Z= 0.481 Chirality : 0.063 1.534 1997 Planarity : 0.005 0.093 2116 Dihedral : 16.669 120.415 4621 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.71 % Favored : 95.03 % Rotamer Outliers : 3.45 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.91 (0.20), residues: 1509 helix: -0.81 (0.15), residues: 850 sheet: -0.98 (0.43), residues: 136 loop : -1.91 (0.27), residues: 523 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 325 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 22 residues processed: 361 average time/residue: 0.2446 time to fit residues: 127.4789 Evaluate side-chains 286 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 264 time to evaluate : 1.366 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1416 time to fit residues: 7.4622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 138 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN A 139 ASN ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN A 360 GLN A 395 ASN A 412 ASN A 757 ASN A 774 ASN A 809 ASN A 909 HIS A 911 ASN A1384 ASN A1424 GLN A1459 ASN A1502 ASN A1505 GLN A1579 ASN A1709 ASN A1753 ASN A1762 ASN B 50 ASN B 102 GLN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 12787 Z= 0.251 Angle : 0.667 11.462 17317 Z= 0.343 Chirality : 0.044 0.308 1997 Planarity : 0.005 0.054 2116 Dihedral : 8.207 100.998 1731 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 3.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.66 (0.21), residues: 1509 helix: 0.39 (0.17), residues: 851 sheet: -1.29 (0.41), residues: 141 loop : -1.47 (0.26), residues: 517 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 262 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 27 residues processed: 293 average time/residue: 0.2265 time to fit residues: 98.7679 Evaluate side-chains 266 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 239 time to evaluate : 1.436 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1269 time to fit residues: 8.2791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 138 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 chunk 123 optimal weight: 0.0870 chunk 137 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 110 optimal weight: 0.6980 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 265 GLN A 408 GLN A 765 HIS A 774 ASN A1378 GLN A1528 ASN A1709 ASN A1753 ASN B 102 GLN B 115 HIS B 134 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 12787 Z= 0.265 Angle : 0.606 9.879 17317 Z= 0.318 Chirality : 0.042 0.326 1997 Planarity : 0.005 0.043 2116 Dihedral : 7.869 101.406 1731 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer Outliers : 2.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % 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: -0.28 (0.21), residues: 1509 helix: 0.71 (0.17), residues: 848 sheet: -1.03 (0.42), residues: 139 loop : -1.35 (0.27), residues: 522 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 243 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 18 residues processed: 266 average time/residue: 0.2107 time to fit residues: 85.6388 Evaluate side-chains 256 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 238 time to evaluate : 1.475 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1563 time to fit residues: 6.9106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 15 optimal weight: 0.1980 chunk 65 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 138 optimal weight: 8.9990 chunk 146 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN A1753 ASN C 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 12787 Z= 0.239 Angle : 0.589 9.680 17317 Z= 0.306 Chirality : 0.042 0.306 1997 Planarity : 0.004 0.039 2116 Dihedral : 7.519 100.857 1731 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % 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: -0.04 (0.21), residues: 1509 helix: 0.92 (0.18), residues: 841 sheet: -0.75 (0.43), residues: 134 loop : -1.31 (0.27), residues: 534 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 248 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 20 residues processed: 267 average time/residue: 0.2202 time to fit residues: 88.9363 Evaluate side-chains 253 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 233 time to evaluate : 1.409 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1148 time to fit residues: 6.2837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 ASN ** A1379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1505 GLN A1753 ASN B 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 12787 Z= 0.192 Angle : 0.569 9.051 17317 Z= 0.294 Chirality : 0.041 0.280 1997 Planarity : 0.004 0.037 2116 Dihedral : 7.337 100.799 1731 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % 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: 0.11 (0.22), residues: 1509 helix: 1.07 (0.18), residues: 842 sheet: -0.68 (0.43), residues: 138 loop : -1.30 (0.27), residues: 529 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 232 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 246 average time/residue: 0.2122 time to fit residues: 79.6742 Evaluate side-chains 238 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 227 time to evaluate : 1.519 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1206 time to fit residues: 4.6053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 147 optimal weight: 20.0000 chunk 122 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN A1505 GLN A1579 ASN A1753 ASN B 102 GLN C 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 12787 Z= 0.199 Angle : 0.568 9.148 17317 Z= 0.294 Chirality : 0.041 0.282 1997 Planarity : 0.004 0.039 2116 Dihedral : 7.135 100.635 1731 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % 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: 0.28 (0.22), residues: 1509 helix: 1.23 (0.18), residues: 835 sheet: -0.56 (0.43), residues: 139 loop : -1.27 (0.27), residues: 535 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 233 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 245 average time/residue: 0.2171 time to fit residues: 81.3994 Evaluate side-chains 238 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 225 time to evaluate : 1.567 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1212 time to fit residues: 5.1162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 40.0000 chunk 16 optimal weight: 0.0870 chunk 83 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 chunk 91 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 ASN ** A1379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1505 GLN A1753 ASN B 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 12787 Z= 0.166 Angle : 0.557 9.175 17317 Z= 0.288 Chirality : 0.041 0.284 1997 Planarity : 0.004 0.036 2116 Dihedral : 6.979 100.588 1731 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % 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: 0.39 (0.22), residues: 1509 helix: 1.33 (0.18), residues: 832 sheet: -0.55 (0.43), residues: 138 loop : -1.19 (0.27), residues: 539 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 235 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 246 average time/residue: 0.2133 time to fit residues: 80.3533 Evaluate side-chains 233 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 225 time to evaluate : 1.476 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1173 time to fit residues: 3.7354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 0.0770 chunk 44 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1505 GLN A1579 ASN B 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 12787 Z= 0.238 Angle : 0.589 10.734 17317 Z= 0.304 Chirality : 0.042 0.282 1997 Planarity : 0.004 0.034 2116 Dihedral : 6.984 100.358 1731 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % 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: 0.41 (0.22), residues: 1509 helix: 1.31 (0.18), residues: 834 sheet: -0.37 (0.44), residues: 134 loop : -1.17 (0.27), residues: 541 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 228 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 232 average time/residue: 0.2201 time to fit residues: 77.4657 Evaluate side-chains 228 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 223 time to evaluate : 1.435 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1213 time to fit residues: 3.1604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 123 optimal weight: 0.0000 chunk 129 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 144 optimal weight: 0.0060 overall best weight: 0.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN ** A1379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1732 ASN B 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 12787 Z= 0.164 Angle : 0.569 10.723 17317 Z= 0.292 Chirality : 0.041 0.316 1997 Planarity : 0.004 0.034 2116 Dihedral : 6.869 100.373 1731 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % 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: 0.54 (0.22), residues: 1509 helix: 1.47 (0.18), residues: 827 sheet: -0.32 (0.43), residues: 138 loop : -1.18 (0.27), residues: 544 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 226 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 234 average time/residue: 0.2224 time to fit residues: 79.8771 Evaluate side-chains 223 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 219 time to evaluate : 1.467 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1252 time to fit residues: 2.9725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 151 optimal weight: 20.0000 chunk 139 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN ** A1505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 12787 Z= 0.211 Angle : 0.593 10.987 17317 Z= 0.303 Chirality : 0.042 0.282 1997 Planarity : 0.004 0.040 2116 Dihedral : 6.868 99.995 1731 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % 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: 0.48 (0.22), residues: 1509 helix: 1.36 (0.18), residues: 835 sheet: -0.30 (0.43), residues: 138 loop : -1.15 (0.27), residues: 536 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3018 Ramachandran restraints generated. 1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 227 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 228 average time/residue: 0.2183 time to fit residues: 76.1279 Evaluate side-chains 223 residues out of total 1367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 222 time to evaluate : 1.597 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1132 time to fit residues: 2.2508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.0770 chunk 111 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 120 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN A 408 GLN A1462 GLN ** A1505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.191551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.123103 restraints weight = 14509.987| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.08 r_work: 0.3218 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4142 r_free = 0.4142 target_work(ls_wunit_k1) = 0.192 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4142 r_free = 0.4142 target_work(ls_wunit_k1) = 0.192 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 12787 Z= 0.206 Angle : 0.590 10.380 17317 Z= 0.301 Chirality : 0.042 0.283 1997 Planarity : 0.004 0.045 2116 Dihedral : 6.873 100.077 1731 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % 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: 0.51 (0.22), residues: 1509 helix: 1.40 (0.18), residues: 831 sheet: -0.29 (0.43), residues: 138 loop : -1.14 (0.27), residues: 540 =============================================================================== Job complete usr+sys time: 2994.71 seconds wall clock time: 54 minutes 34.84 seconds (3274.84 seconds total)