Starting phenix.real_space_refine on Thu Jun 27 00:52:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmm_38482/06_2024/8xmm_38482_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmm_38482/06_2024/8xmm_38482.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmm_38482/06_2024/8xmm_38482_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmm_38482/06_2024/8xmm_38482_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmm_38482/06_2024/8xmm_38482_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmm_38482/06_2024/8xmm_38482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmm_38482/06_2024/8xmm_38482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmm_38482/06_2024/8xmm_38482_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmm_38482/06_2024/8xmm_38482_updated.pdb" } resolution = 2.89 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= 0.009 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 17 5.49 5 S 87 5.16 5 C 7567 2.51 5 N 1700 2.21 5 O 2018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 116": "NH1" <-> "NH2" Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A ASP 186": "OD1" <-> "OD2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 320": "OD1" <-> "OD2" Residue "A TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 345": "OD1" <-> "OD2" Residue "A PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A TYR 738": "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 GLU 790": "OE1" <-> "OE2" Residue "A TYR 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 812": "OD1" <-> "OD2" Residue "A GLU 822": "OE1" <-> "OE2" Residue "A ASP 827": "OD1" <-> "OD2" Residue "A ARG 841": "NH1" <-> "NH2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "A ASP 901": "OD1" <-> "OD2" Residue "A ASP 912": "OD1" <-> "OD2" Residue "A PHE 914": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 922": "NH1" <-> "NH2" Residue "A GLU 927": "OE1" <-> "OE2" Residue "A ASP 934": "OD1" <-> "OD2" Residue "A PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1182": "NH1" <-> "NH2" Residue "A GLU 1190": "OE1" <-> "OE2" Residue "A PHE 1194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1212": "OE1" <-> "OE2" Residue "A ARG 1218": "NH1" <-> "NH2" Residue "A GLU 1227": "OE1" <-> "OE2" Residue "A PHE 1233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1240": "OE1" <-> "OE2" Residue "A TYR 1248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1293": "NH1" <-> "NH2" Residue "A GLU 1305": "OE1" <-> "OE2" Residue "A ARG 1308": "NH1" <-> "NH2" Residue "A PHE 1347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1369": "OE1" <-> "OE2" Residue "A PHE 1371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1390": "OD1" <-> "OD2" Residue "A TYR 1396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1422": "OD1" <-> "OD2" Residue "A TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1428": "OE1" <-> "OE2" Residue "A PHE 1437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1471": "OD1" <-> "OD2" Residue "A TYR 1481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1499": "NH1" <-> "NH2" Residue "A PHE 1517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1545": "OE1" <-> "OE2" Residue "A TYR 1548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1561": "OE1" <-> "OE2" Residue "A TYR 1573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1582": "OD1" <-> "OD2" Residue "A PHE 1594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1597": "OD1" <-> "OD2" Residue "A PHE 1603": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 1652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1682": "OE1" <-> "OE2" Residue "A ASP 1701": "OD1" <-> "OD2" Residue "A GLU 1727": "OE1" <-> "OE2" Residue "A TYR 1739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1761": "OE1" <-> "OE2" Residue "A PHE 1763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B ASP 103": "OD1" <-> "OD2" Residue "B TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 120": "OE1" <-> "OE2" Residue "B PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 11389 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1145, 9253 Classifications: {'peptide': 1145} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 1114} Chain breaks: 2 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: 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: "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: "A" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 608 Unusual residues: {'1PW': 1, 'CLR': 1, 'LPE': 9, 'NAG': 2, 'PCW': 6} Classifications: {'peptide': 1, 'undetermined': 19} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'1PW:plan-1': 1, 'PCW:plan-4': 4} Unresolved non-hydrogen planarities: 12 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: 8.20, per 1000 atoms: 0.72 Number of scatterers: 11389 At special positions: 0 Unit cell: (133.944, 126.259, 114.182, 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 87 16.00 P 17 15.00 O 2018 8.00 N 1700 7.00 C 7567 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 324 " distance=2.01 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 324 " distance=2.97 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=2.01 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=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A2001 " - " ASN A1375 " " NAG A2002 " - " 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 1 " - " ASN A1352 " " NAG D 1 " - " ASN A1366 " Time building additional restraints: 6.50 Conformation dependent library (CDL) restraints added in 1.9 seconds 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2496 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 5 sheets defined 66.3% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 126 through 144 removed outlier: 3.645A pdb=" N MET A 130 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR A 144 " --> pdb=" O CYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 174 removed outlier: 3.665A pdb=" N ARG A 174 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 204 Processing helix chain 'A' and resid 210 through 227 removed outlier: 3.775A pdb=" N PHE A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ARG A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LEU A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ARG A 220 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N THR A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N SER A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A 227 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 266 removed outlier: 4.060A pdb=" N THR A 233 " --> pdb=" O PRO A 229 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ASP A 247 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 5.023A 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 292 Processing helix chain 'A' and resid 296 through 302 removed outlier: 3.912A pdb=" N LYS A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) 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 359 Processing helix chain 'A' and resid 363 through 373 Processing helix chain 'A' and resid 376 through 416 removed outlier: 3.786A pdb=" N MET A 379 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A 380 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 388 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY A 389 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER A 390 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N PHE A 391 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR A 392 " --> pdb=" O GLY A 389 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 395 " --> pdb=" O TYR A 392 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 416 " --> pdb=" O ILE A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 741 Processing helix chain 'A' and resid 744 through 763 removed outlier: 3.645A pdb=" N MET A 763 " --> pdb=" O LEU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 796 Processing helix chain 'A' and resid 800 through 805 removed outlier: 3.840A pdb=" N GLN A 805 " --> pdb=" O TYR A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 824 removed outlier: 3.596A pdb=" N PHE A 811 " --> pdb=" O GLY A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 847 removed outlier: 3.692A pdb=" N ARG A 838 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LEU A 839 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LEU A 840 " --> pdb=" O SER A 836 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ARG A 841 " --> pdb=" O PHE A 837 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL A 842 " --> pdb=" O ARG A 838 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N PHE A 843 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LYS A 844 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU A 845 " --> pdb=" O ARG A 841 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ALA A 846 " --> pdb=" O VAL A 842 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LYS A 847 " --> pdb=" O PHE A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 861 Processing helix chain 'A' and resid 863 through 894 removed outlier: 5.175A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N SER A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS A 893 " --> pdb=" O GLY A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 899 No H-bonds generated for 'chain 'A' and resid 896 through 899' Processing helix chain 'A' and resid 913 through 924 Processing helix chain 'A' and resid 930 through 939 Processing helix chain 'A' and resid 941 through 955 Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.835A pdb=" N LEU A 964 " --> pdb=" O LEU A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1190 Processing helix chain 'A' and resid 1192 through 1210 Processing helix chain 'A' and resid 1220 through 1248 removed outlier: 3.979A pdb=" N LYS A1231 " --> pdb=" O GLU A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1254 Processing helix chain 'A' and resid 1257 through 1277 Processing helix chain 'A' and resid 1284 through 1289 removed outlier: 3.758A pdb=" N SER A1288 " --> pdb=" O GLY A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1300 Proline residue: A1297 - end of helix Processing helix chain 'A' and resid 1305 through 1343 removed outlier: 3.974A pdb=" N ALA A1317 " --> pdb=" O ALA A1313 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A1318 " --> pdb=" O LEU A1314 " (cutoff:3.500A) Proline residue: A1319 - end of helix removed outlier: 3.669A pdb=" N ASN A1323 " --> pdb=" O PRO A1319 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1376 Processing helix chain 'A' and resid 1392 through 1404 removed outlier: 3.602A pdb=" N LEU A1397 " --> pdb=" O GLY A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1416 Processing helix chain 'A' and resid 1431 through 1466 removed outlier: 3.628A pdb=" N ILE A1435 " --> pdb=" O TYR A1432 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A1443 " --> pdb=" O PHE A1440 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A1444 " --> pdb=" O ILE A1441 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N SER A1445 " --> pdb=" O ILE A1442 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A1446 " --> pdb=" O PHE A1443 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A1447 " --> pdb=" O GLY A1444 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A1448 " --> pdb=" O SER A1445 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A1449 " --> pdb=" O PHE A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1489 Processing helix chain 'A' and resid 1505 through 1513 Processing helix chain 'A' and resid 1515 through 1534 Processing helix chain 'A' and resid 1541 through 1569 Processing helix chain 'A' and resid 1577 through 1601 Processing helix chain 'A' and resid 1606 through 1626 removed outlier: 4.577A pdb=" N ALA A1615 " --> pdb=" O VAL A1611 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ARG A1616 " --> pdb=" O ILE A1612 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ILE A1617 " --> pdb=" O ARG A1613 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLY A1618 " --> pdb=" O LEU A1614 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG A1619 " --> pdb=" O ALA A1615 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A1622 " --> pdb=" O GLY A1618 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU A1623 " --> pdb=" O ARG A1619 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL A1624 " --> pdb=" O ILE A1620 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LYS A1625 " --> pdb=" O LEU A1621 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLY A1626 " --> pdb=" O ARG A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1628 through 1665 Proline residue: A1642 - end of helix Processing helix chain 'A' and resid 1684 through 1696 removed outlier: 4.087A 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 1767 removed outlier: 4.037A pdb=" N ASN A1753 " --> pdb=" O LEU A1749 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 191 removed outlier: 3.988A pdb=" N GLU B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 273 through 276 Processing sheet with id= B, first strand: chain 'A' and resid 1349 through 1352 Processing sheet with id= C, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.261A pdb=" N GLU B 145 " --> pdb=" O ALA B 30 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 36 through 38 Processing sheet with id= E, first strand: chain 'B' and resid 133 through 144 removed outlier: 4.567A pdb=" N ASN B 50 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 71 " --> pdb=" O TRP B 57 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE B 59 " --> pdb=" O LYS B 69 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LYS B 69 " --> pdb=" O PHE B 59 " (cutoff:3.500A) 639 hydrogen bonds defined for protein. 1662 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: 3.41 Time building geometry restraints manager: 6.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.30: 1680 1.30 - 1.44: 3226 1.44 - 1.58: 6554 1.58 - 1.72: 33 1.72 - 1.86: 140 Bond restraints: 11633 Sorted by residual: bond pdb=" CA LYS A1187 " pdb=" C LYS A1187 " ideal model delta sigma weight residual 1.524 1.417 0.106 1.29e-02 6.01e+03 6.78e+01 bond pdb=" C PHE A 381 " pdb=" O PHE A 381 " ideal model delta sigma weight residual 1.236 1.154 0.083 1.15e-02 7.56e+03 5.18e+01 bond pdb=" CA TYR A1573 " pdb=" C TYR A1573 " ideal model delta sigma weight residual 1.524 1.435 0.090 1.29e-02 6.01e+03 4.82e+01 bond pdb=" C31 PCW A2012 " pdb=" O2 PCW A2012 " ideal model delta sigma weight residual 1.333 1.470 -0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" CA PHE A 381 " pdb=" C PHE A 381 " ideal model delta sigma weight residual 1.524 1.439 0.085 1.27e-02 6.20e+03 4.49e+01 ... (remaining 11628 not shown) Histogram of bond angle deviations from ideal: 96.69 - 104.92: 170 104.92 - 113.14: 6526 113.14 - 121.37: 6703 121.37 - 129.59: 2215 129.59 - 137.82: 69 Bond angle restraints: 15683 Sorted by residual: angle pdb=" N TYR A1573 " pdb=" CA TYR A1573 " pdb=" C TYR A1573 " ideal model delta sigma weight residual 111.40 100.48 10.92 1.22e+00 6.72e-01 8.01e+01 angle pdb=" N SER A1568 " pdb=" CA SER A1568 " pdb=" C SER A1568 " ideal model delta sigma weight residual 111.36 119.79 -8.43 1.09e+00 8.42e-01 5.99e+01 angle pdb=" N PCW A2010 " pdb=" C5 PCW A2010 " pdb=" C4 PCW A2010 " ideal model delta sigma weight residual 116.95 96.69 20.26 3.00e+00 1.11e-01 4.56e+01 angle pdb=" N CYS A 897 " pdb=" CA CYS A 897 " pdb=" C CYS A 897 " ideal model delta sigma weight residual 111.36 118.21 -6.85 1.09e+00 8.42e-01 3.95e+01 angle pdb=" C HIS A 766 " pdb=" N PRO A 767 " pdb=" CA PRO A 767 " ideal model delta sigma weight residual 119.84 112.21 7.63 1.25e+00 6.40e-01 3.73e+01 ... (remaining 15678 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.96: 6646 33.96 - 67.91: 386 67.91 - 101.87: 49 101.87 - 135.82: 14 135.82 - 169.78: 4 Dihedral angle restraints: 7099 sinusoidal: 3233 harmonic: 3866 Sorted by residual: dihedral pdb=" CB CYS A1715 " pdb=" SG CYS A1715 " pdb=" SG CYS A1730 " pdb=" CB CYS A1730 " ideal model delta sinusoidal sigma weight residual 93.00 15.13 77.87 1 1.00e+01 1.00e-02 7.58e+01 dihedral pdb=" CB CYS A 315 " pdb=" SG CYS A 315 " pdb=" SG CYS A 330 " pdb=" CB CYS A 330 " ideal model delta sinusoidal sigma weight residual 93.00 145.16 -52.16 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" CA PHE B 54 " pdb=" C PHE B 54 " pdb=" N THR B 55 " pdb=" CA THR B 55 " ideal model delta harmonic sigma weight residual -180.00 -155.63 -24.37 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 7096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 1717 0.119 - 0.238: 45 0.238 - 0.357: 10 0.357 - 0.477: 2 0.477 - 0.596: 2 Chirality restraints: 1776 Sorted by residual: chirality pdb=" C1 NAG B 304 " pdb=" ND2 ASN B 135 " pdb=" C2 NAG B 304 " pdb=" O5 NAG B 304 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.87e+00 chirality pdb=" CA PHE A 391 " pdb=" N PHE A 391 " pdb=" C PHE A 391 " pdb=" CB PHE A 391 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.56e+00 chirality pdb=" C2 PCW A2011 " pdb=" C1 PCW A2011 " pdb=" C3 PCW A2011 " pdb=" O2 PCW A2011 " both_signs ideal model delta sigma weight residual False -2.32 -2.69 0.36 2.00e-01 2.50e+01 3.32e+00 ... (remaining 1773 not shown) Planarity restraints: 1850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 390 " -0.021 2.00e-02 2.50e+03 4.08e-02 1.67e+01 pdb=" C SER A 390 " 0.071 2.00e-02 2.50e+03 pdb=" O SER A 390 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE A 391 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 896 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.96e+00 pdb=" C VAL A 896 " 0.049 2.00e-02 2.50e+03 pdb=" O VAL A 896 " -0.018 2.00e-02 2.50e+03 pdb=" N CYS A 897 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1437 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.35e+00 pdb=" C PHE A1437 " -0.044 2.00e-02 2.50e+03 pdb=" O PHE A1437 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE A1438 " 0.015 2.00e-02 2.50e+03 ... (remaining 1847 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 150 2.64 - 3.21: 10657 3.21 - 3.77: 16840 3.77 - 4.34: 24078 4.34 - 4.90: 39892 Nonbonded interactions: 91617 Sorted by model distance: nonbonded pdb=" C4 PCW A2010 " pdb=" C7 PCW A2010 " model vdw 2.077 3.088 nonbonded pdb=" OE1 GLU B 23 " pdb=" NZ LYS B 140 " model vdw 2.295 2.520 nonbonded pdb=" N GLU B 82 " pdb=" OE1 GLU B 82 " model vdw 2.300 2.520 nonbonded pdb=" C31 LPE A2008 " pdb=" C3N LPE A2008 " model vdw 2.301 3.088 nonbonded pdb=" OD1 ASP A 192 " pdb=" NZ LYS A 223 " model vdw 2.306 2.520 ... (remaining 91612 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 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.940 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 37.990 Find NCS groups from input model: 0.290 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: 0.000 Load rotamer database and sin/cos tables:13.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 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 0.137 11633 Z= 0.619 Angle : 1.159 20.258 15683 Z= 0.581 Chirality : 0.059 0.596 1776 Planarity : 0.005 0.059 1842 Dihedral : 21.128 169.778 4576 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.34 % Allowed : 1.53 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.13 (0.23), residues: 1310 helix: 0.75 (0.17), residues: 862 sheet: -0.71 (0.64), residues: 67 loop : -1.13 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A1408 HIS 0.006 0.002 HIS B 115 PHE 0.022 0.002 PHE A1263 TYR 0.022 0.002 TYR A 392 ARG 0.015 0.001 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 158 time to evaluate : 1.266 Fit side-chains revert: symmetry clash REVERT: A 133 MET cc_start: 0.6523 (mmp) cc_final: 0.6283 (mmm) REVERT: A 184 LEU cc_start: 0.7629 (mm) cc_final: 0.6825 (tm) REVERT: A 278 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8632 (t0) REVERT: A 742 MET cc_start: 0.7232 (mmm) cc_final: 0.6816 (tpp) REVERT: A 858 ILE cc_start: 0.8743 (mm) cc_final: 0.8147 (mp) REVERT: A 861 ASN cc_start: 0.7549 (m-40) cc_final: 0.7344 (p0) REVERT: A 1322 MET cc_start: 0.8281 (mmp) cc_final: 0.8036 (mmp) outliers start: 4 outliers final: 1 residues processed: 162 average time/residue: 1.0227 time to fit residues: 181.8246 Evaluate side-chains 132 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 324 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN A 282 ASN A 360 GLN A 410 GLN A 774 ASN A 809 ASN A 941 GLN A1276 ASN A1463 GLN ** A1721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 11633 Z= 0.194 Angle : 0.593 9.222 15683 Z= 0.310 Chirality : 0.042 0.408 1776 Planarity : 0.005 0.058 1842 Dihedral : 19.124 177.226 2095 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.86 % Allowed : 11.19 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.78 (0.23), residues: 1310 helix: 1.29 (0.17), residues: 851 sheet: -0.47 (0.61), residues: 68 loop : -0.96 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 730 HIS 0.003 0.001 HIS B 115 PHE 0.018 0.001 PHE A1263 TYR 0.015 0.001 TYR A 405 ARG 0.005 0.001 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 1.341 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.7818 (mmt) cc_final: 0.7425 (mmp) REVERT: A 742 MET cc_start: 0.7494 (mmm) cc_final: 0.7047 (tpp) REVERT: A 760 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8089 (t80) REVERT: A 861 ASN cc_start: 0.7628 (m-40) cc_final: 0.7362 (m-40) REVERT: A 1639 MET cc_start: 0.7984 (mmm) cc_final: 0.7670 (mmm) outliers start: 22 outliers final: 3 residues processed: 152 average time/residue: 1.0644 time to fit residues: 177.1686 Evaluate side-chains 137 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 133 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 760 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 118 optimal weight: 0.0170 chunk 40 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN A 368 GLN A 774 ASN A 809 ASN A1276 ASN ** A1721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11633 Z= 0.205 Angle : 0.544 9.572 15683 Z= 0.284 Chirality : 0.041 0.395 1776 Planarity : 0.005 0.055 1842 Dihedral : 17.086 178.608 2092 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.12 % Allowed : 13.81 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.95 (0.24), residues: 1310 helix: 1.38 (0.18), residues: 853 sheet: -0.14 (0.63), residues: 67 loop : -0.83 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 730 HIS 0.003 0.001 HIS A 765 PHE 0.018 0.001 PHE A1263 TYR 0.020 0.001 TYR B 180 ARG 0.003 0.000 ARG A1303 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: A 742 MET cc_start: 0.7354 (mmm) cc_final: 0.6888 (tpp) REVERT: A 760 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.7925 (t80) REVERT: A 861 ASN cc_start: 0.7780 (m-40) cc_final: 0.7351 (m-40) REVERT: A 1187 LYS cc_start: 0.8300 (mtpp) cc_final: 0.7959 (tmtt) REVERT: A 1639 MET cc_start: 0.8042 (mmm) cc_final: 0.7832 (mmm) outliers start: 25 outliers final: 11 residues processed: 150 average time/residue: 1.0792 time to fit residues: 176.8507 Evaluate side-chains 144 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 172 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 119 optimal weight: 0.0470 chunk 126 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN A 774 ASN A 809 ASN A1276 ASN A1721 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11633 Z= 0.166 Angle : 0.506 9.690 15683 Z= 0.264 Chirality : 0.040 0.361 1776 Planarity : 0.004 0.053 1842 Dihedral : 16.226 175.601 2092 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.20 % Allowed : 14.92 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.09 (0.24), residues: 1310 helix: 1.51 (0.18), residues: 851 sheet: 0.00 (0.62), residues: 67 loop : -0.82 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 730 HIS 0.003 0.001 HIS A 765 PHE 0.017 0.001 PHE A 843 TYR 0.012 0.001 TYR A 803 ARG 0.002 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 1.248 Fit side-chains revert: symmetry clash REVERT: A 760 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.7983 (t80) REVERT: A 861 ASN cc_start: 0.7720 (m-40) cc_final: 0.7269 (m-40) REVERT: A 1187 LYS cc_start: 0.8306 (mtpp) cc_final: 0.7978 (tmtt) REVERT: A 1639 MET cc_start: 0.8111 (mmm) cc_final: 0.7826 (mmm) outliers start: 26 outliers final: 9 residues processed: 156 average time/residue: 1.0255 time to fit residues: 175.9274 Evaluate side-chains 145 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1715 CYS Chi-restraints excluded: chain B residue 49 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 108 optimal weight: 0.0020 chunk 87 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11633 Z= 0.188 Angle : 0.515 10.499 15683 Z= 0.268 Chirality : 0.040 0.365 1776 Planarity : 0.004 0.052 1842 Dihedral : 15.730 177.209 2092 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.63 % Allowed : 16.10 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.10 (0.24), residues: 1310 helix: 1.48 (0.18), residues: 859 sheet: 0.19 (0.62), residues: 66 loop : -0.81 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 730 HIS 0.003 0.001 HIS A 765 PHE 0.018 0.001 PHE A 843 TYR 0.020 0.001 TYR B 180 ARG 0.003 0.000 ARG A 835 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 1.009 Fit side-chains REVERT: A 742 MET cc_start: 0.7074 (mmm) cc_final: 0.6596 (tpp) REVERT: A 760 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.7973 (t80) REVERT: A 861 ASN cc_start: 0.7651 (m-40) cc_final: 0.7208 (m-40) REVERT: A 1187 LYS cc_start: 0.8315 (mtpp) cc_final: 0.7993 (tmtt) REVERT: A 1639 MET cc_start: 0.8088 (mmm) cc_final: 0.7842 (mmm) REVERT: A 1755 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.8273 (t80) outliers start: 31 outliers final: 15 residues processed: 159 average time/residue: 1.0039 time to fit residues: 175.5334 Evaluate side-chains 152 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1715 CYS Chi-restraints excluded: chain A residue 1755 TYR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 172 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN A 774 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 11633 Z= 0.189 Angle : 0.523 10.559 15683 Z= 0.269 Chirality : 0.040 0.354 1776 Planarity : 0.004 0.050 1842 Dihedral : 15.435 178.833 2092 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.29 % Allowed : 17.71 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.11 (0.24), residues: 1310 helix: 1.50 (0.18), residues: 859 sheet: 0.48 (0.63), residues: 62 loop : -0.91 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 730 HIS 0.002 0.001 HIS A 765 PHE 0.018 0.001 PHE A 843 TYR 0.011 0.001 TYR A1482 ARG 0.002 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.355 Fit side-chains revert: symmetry clash REVERT: A 413 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7968 (mp) REVERT: A 742 MET cc_start: 0.7212 (mmm) cc_final: 0.6757 (tpp) REVERT: A 760 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.7985 (t80) REVERT: A 791 MET cc_start: 0.7979 (tmm) cc_final: 0.7311 (tpp) REVERT: A 861 ASN cc_start: 0.7637 (m-40) cc_final: 0.7180 (m-40) REVERT: A 1187 LYS cc_start: 0.8309 (mtpp) cc_final: 0.7990 (tmtt) REVERT: A 1639 MET cc_start: 0.8076 (mmm) cc_final: 0.7757 (mmm) REVERT: A 1755 TYR cc_start: 0.8571 (OUTLIER) cc_final: 0.8286 (t80) outliers start: 27 outliers final: 15 residues processed: 157 average time/residue: 1.0323 time to fit residues: 178.1191 Evaluate side-chains 156 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1715 CYS Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1755 TYR Chi-restraints excluded: chain B residue 49 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11633 Z= 0.178 Angle : 0.514 10.783 15683 Z= 0.265 Chirality : 0.040 0.346 1776 Planarity : 0.004 0.050 1842 Dihedral : 15.018 179.415 2092 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.29 % Allowed : 18.22 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.13 (0.24), residues: 1310 helix: 1.54 (0.18), residues: 855 sheet: 0.39 (0.62), residues: 63 loop : -0.92 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 730 HIS 0.003 0.001 HIS A 765 PHE 0.016 0.001 PHE A 843 TYR 0.023 0.001 TYR B 180 ARG 0.002 0.000 ARG A1303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.309 Fit side-chains revert: symmetry clash REVERT: A 413 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7924 (mp) REVERT: A 742 MET cc_start: 0.7009 (mmm) cc_final: 0.6485 (tpp) REVERT: A 760 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8029 (t80) REVERT: A 861 ASN cc_start: 0.7644 (m-40) cc_final: 0.7160 (m-40) REVERT: A 1187 LYS cc_start: 0.8302 (mtpp) cc_final: 0.7994 (tmtt) REVERT: A 1639 MET cc_start: 0.8089 (mmm) cc_final: 0.7820 (mmm) REVERT: A 1755 TYR cc_start: 0.8583 (OUTLIER) cc_final: 0.8243 (t80) outliers start: 27 outliers final: 15 residues processed: 156 average time/residue: 1.0557 time to fit residues: 181.4805 Evaluate side-chains 152 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1715 CYS Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1755 TYR Chi-restraints excluded: chain B residue 49 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 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 240 GLN A 774 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11633 Z= 0.167 Angle : 0.516 11.549 15683 Z= 0.264 Chirality : 0.040 0.332 1776 Planarity : 0.004 0.049 1842 Dihedral : 14.522 177.654 2092 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.61 % Allowed : 19.66 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.05 (0.24), residues: 1310 helix: 1.47 (0.18), residues: 867 sheet: 0.43 (0.62), residues: 63 loop : -1.02 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 730 HIS 0.002 0.000 HIS A 765 PHE 0.014 0.001 PHE A 843 TYR 0.010 0.001 TYR A1739 ARG 0.002 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: A 133 MET cc_start: 0.6039 (mmm) cc_final: 0.5722 (mtt) REVERT: A 413 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7938 (mp) REVERT: A 742 MET cc_start: 0.6785 (mmm) cc_final: 0.6275 (tpp) REVERT: A 760 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.8036 (t80) REVERT: A 791 MET cc_start: 0.7964 (tmm) cc_final: 0.7214 (tpp) REVERT: A 835 ARG cc_start: 0.7362 (mmt180) cc_final: 0.7041 (mpt90) REVERT: A 861 ASN cc_start: 0.7642 (m-40) cc_final: 0.7142 (m-40) REVERT: A 1187 LYS cc_start: 0.8294 (mtpp) cc_final: 0.7991 (tmtt) REVERT: A 1639 MET cc_start: 0.8012 (mmm) cc_final: 0.7734 (mmm) REVERT: A 1755 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.8242 (t80) REVERT: B 154 MET cc_start: 0.7132 (tpp) cc_final: 0.6903 (tpp) REVERT: B 163 MET cc_start: 0.8358 (ttt) cc_final: 0.8095 (ttt) outliers start: 19 outliers final: 13 residues processed: 148 average time/residue: 1.0822 time to fit residues: 175.4041 Evaluate side-chains 149 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1715 CYS Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1755 TYR Chi-restraints excluded: chain B residue 49 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 0.2980 chunk 110 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11633 Z= 0.158 Angle : 0.504 9.979 15683 Z= 0.258 Chirality : 0.039 0.318 1776 Planarity : 0.004 0.049 1842 Dihedral : 14.056 177.950 2092 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.78 % Allowed : 19.41 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.24 (0.24), residues: 1310 helix: 1.61 (0.18), residues: 856 sheet: 0.57 (0.62), residues: 63 loop : -0.87 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 730 HIS 0.002 0.000 HIS A 915 PHE 0.017 0.001 PHE A1447 TYR 0.025 0.001 TYR B 180 ARG 0.002 0.000 ARG A1303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 1.278 Fit side-chains revert: symmetry clash REVERT: A 742 MET cc_start: 0.6701 (mmm) cc_final: 0.6273 (tpp) REVERT: A 760 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8028 (t80) REVERT: A 791 MET cc_start: 0.7996 (tmm) cc_final: 0.7257 (tpp) REVERT: A 835 ARG cc_start: 0.7369 (mmt180) cc_final: 0.7139 (mpt90) REVERT: A 861 ASN cc_start: 0.7630 (m-40) cc_final: 0.7121 (m-40) REVERT: A 1187 LYS cc_start: 0.8293 (mtpp) cc_final: 0.7975 (tmtt) REVERT: A 1639 MET cc_start: 0.8021 (mmm) cc_final: 0.7811 (mmm) REVERT: A 1755 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.8224 (t80) REVERT: B 163 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8268 (ttt) outliers start: 21 outliers final: 13 residues processed: 150 average time/residue: 1.0651 time to fit residues: 175.3883 Evaluate side-chains 150 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 134 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1715 CYS Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1755 TYR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 163 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 86 optimal weight: 0.0040 chunk 130 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN A 853 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11633 Z= 0.193 Angle : 0.529 10.454 15683 Z= 0.268 Chirality : 0.040 0.340 1776 Planarity : 0.004 0.049 1842 Dihedral : 13.914 178.528 2092 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.53 % Allowed : 20.08 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.21 (0.24), residues: 1310 helix: 1.57 (0.18), residues: 856 sheet: 0.58 (0.62), residues: 63 loop : -0.84 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 730 HIS 0.002 0.001 HIS A 765 PHE 0.017 0.001 PHE A 963 TYR 0.011 0.001 TYR A1482 ARG 0.002 0.000 ARG A 117 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 1.261 Fit side-chains revert: symmetry clash REVERT: A 742 MET cc_start: 0.6696 (mmm) cc_final: 0.6266 (tpp) REVERT: A 760 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.8006 (t80) REVERT: A 791 MET cc_start: 0.8028 (tmm) cc_final: 0.7317 (tpp) REVERT: A 835 ARG cc_start: 0.7413 (mmt180) cc_final: 0.7197 (mpt90) REVERT: A 861 ASN cc_start: 0.7637 (m-40) cc_final: 0.7114 (m-40) REVERT: A 1187 LYS cc_start: 0.8329 (mtpp) cc_final: 0.8028 (tttm) REVERT: A 1639 MET cc_start: 0.8014 (mmm) cc_final: 0.7722 (mmm) REVERT: A 1751 VAL cc_start: 0.8398 (OUTLIER) cc_final: 0.8156 (t) REVERT: A 1755 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.8324 (t80) REVERT: B 154 MET cc_start: 0.7074 (tpp) cc_final: 0.6802 (tpt) outliers start: 18 outliers final: 13 residues processed: 149 average time/residue: 1.0444 time to fit residues: 170.2996 Evaluate side-chains 150 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 134 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1715 CYS Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1755 TYR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 151 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1502 ASN A1505 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.131859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.092151 restraints weight = 16558.179| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.07 r_work: 0.2979 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11633 Z= 0.316 Angle : 0.587 10.775 15683 Z= 0.299 Chirality : 0.043 0.406 1776 Planarity : 0.004 0.049 1842 Dihedral : 14.053 173.113 2092 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.69 % Allowed : 19.92 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.03 (0.24), residues: 1310 helix: 1.43 (0.18), residues: 856 sheet: 0.47 (0.63), residues: 62 loop : -0.88 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 730 HIS 0.004 0.001 HIS A 765 PHE 0.020 0.002 PHE B 54 TYR 0.023 0.002 TYR B 180 ARG 0.002 0.000 ARG A 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3701.42 seconds wall clock time: 65 minutes 40.44 seconds (3940.44 seconds total)