Starting phenix.real_space_refine on Mon Apr 8 11:10:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmo_38484/04_2024/8xmo_38484_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmo_38484/04_2024/8xmo_38484.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmo_38484/04_2024/8xmo_38484_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmo_38484/04_2024/8xmo_38484_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmo_38484/04_2024/8xmo_38484_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmo_38484/04_2024/8xmo_38484.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmo_38484/04_2024/8xmo_38484.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmo_38484/04_2024/8xmo_38484_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmo_38484/04_2024/8xmo_38484_updated.pdb" } resolution = 3.39 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= 0.010 sd= 0.063 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 12 5.49 5 S 99 5.16 5 C 8773 2.51 5 N 2063 2.21 5 O 2376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 31": "OE1" <-> "OE2" Residue "C ASP 45": "OD1" <-> "OD2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 134": "OD1" <-> "OD2" Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 24": "OE1" <-> "OE2" Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 34": "OE1" <-> "OE2" Residue "A ASP 52": "OD1" <-> "OD2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 65": "OD1" <-> "OD2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A ASP 79": "OD1" <-> "OD2" Residue "A TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 84": "OD1" <-> "OD2" Residue "A PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 181": "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 TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 203": "OE1" <-> "OE2" Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A ASP 320": "OD1" <-> "OD2" Residue "A GLU 326": "OE1" <-> "OE2" Residue "A TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 361": "OD1" <-> "OD2" Residue "A PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 407": "OE1" <-> "OE2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 743": "OD1" <-> "OD2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A GLU 770": "OE1" <-> "OE2" Residue "A PHE 783": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 790": "OE1" <-> "OE2" Residue "A TYR 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 812": "OD1" <-> "OD2" Residue "A PHE 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 835": "NH1" <-> "NH2" Residue "A PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 880": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "A ASP 902": "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 ASP 974": "OD1" <-> "OD2" Residue "A TYR 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1182": "NH1" <-> "NH2" Residue "A TYR 1186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1195": "OE1" <-> "OE2" Residue "A PHE 1197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1217": "OE1" <-> "OE2" Residue "A ARG 1218": "NH1" <-> "NH2" Residue "A PHE 1233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1240": "OE1" <-> "OE2" Residue "A TYR 1248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1267": "OD1" <-> "OD2" Residue "A ARG 1293": "NH1" <-> "NH2" Residue "A GLU 1305": "OE1" <-> "OE2" Residue "A ARG 1308": "NH1" <-> "NH2" Residue "A PHE 1343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1369": "OE1" <-> "OE2" Residue "A ASP 1390": "OD1" <-> "OD2" Residue "A TYR 1396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1428": "OE1" <-> "OE2" Residue "A TYR 1429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1458": "OD1" <-> "OD2" Residue "A PHE 1460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1476": "OE1" <-> "OE2" Residue "A TYR 1482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1499": "NH1" <-> "NH2" Residue "A PHE 1509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1510": "OD1" <-> "OD2" Residue "A PHE 1517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1518": "OD1" <-> "OD2" Residue "A GLU 1537": "OE1" <-> "OE2" Residue "A PHE 1558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1581": "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 1609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1610": "NH1" <-> "NH2" Residue "A ARG 1613": "NH1" <-> "NH2" Residue "A ARG 1619": "NH1" <-> "NH2" Residue "A TYR 1658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1701": "OD1" <-> "OD2" Residue "A ASP 1714": "OD1" <-> "OD2" Residue "A GLU 1727": "OE1" <-> "OE2" Residue "A PHE 1738": "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 "A GLU 1768": "OE1" <-> "OE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B ASP 103": "OD1" <-> "OD2" Residue "B PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 148": "OD1" <-> "OD2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 190": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13323 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 980 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 119, 971 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 119, 971 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 981 Chain: "A" Number of atoms: 10387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1286, 10387 Classifications: {'peptide': 1286} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 1243} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 428 Unusual residues: {'LPE': 7, 'NAG': 2, 'PCW': 5} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 6 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: 7.48, per 1000 atoms: 0.56 Number of scatterers: 13323 At special positions: 0 Unit cell: (120.769, 133.944, 137.238, 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 99 16.00 P 12 15.00 O 2376 8.00 N 2063 7.00 C 8773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS A 895 " distance=2.02 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 324 " distance=2.02 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.02 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=1.96 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 A2001 " - " ASN A1375 " " NAG A2002 " - " ASN A 283 " " NAG B 301 " - " ASN B 93 " " NAG B 302 " - " ASN B 135 " " NAG B 303 " - " ASN B 110 " " NAG B 304 " - " ASN B 114 " " NAG D 1 " - " ASN A1352 " " NAG E 1 " - " ASN A1366 " Time building additional restraints: 5.42 Conformation dependent library (CDL) restraints added in 2.4 seconds 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3004 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 11 sheets defined 59.3% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.54 Creating SS restraints... Processing helix chain 'C' and resid 105 through 107 No H-bonds generated for 'chain 'C' and resid 105 through 107' Processing helix chain 'A' and resid 17 through 32 removed outlier: 4.002A pdb=" N GLN A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A 31 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) 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 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' 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 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 114 through 124 Processing helix chain 'A' and resid 126 through 143 Processing helix chain 'A' and resid 150 through 174 removed outlier: 4.057A pdb=" N ASN A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 173 " --> pdb=" O VAL A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 205 removed outlier: 4.149A pdb=" N LEU A 191 " --> pdb=" O PRO A 187 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 227 removed outlier: 3.936A pdb=" N LEU A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG A 220 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 243 through 267 removed outlier: 3.873A pdb=" N SER A 246 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASP A 247 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 248 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 263 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A 267 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.621A pdb=" N ASN A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 302 removed outlier: 3.728A 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 358 Processing helix chain 'A' and resid 363 through 373 Processing helix chain 'A' and resid 376 through 388 removed outlier: 3.751A pdb=" N MET A 379 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE A 380 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 385 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 386 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE A 387 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 430 Processing helix chain 'A' and resid 729 through 741 Processing helix chain 'A' and resid 743 through 763 removed outlier: 3.667A pdb=" N ASP A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LEU A 748 " --> pdb=" O PRO A 744 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET A 763 " --> pdb=" O LEU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 797 Processing helix chain 'A' and resid 800 through 803 No H-bonds generated for 'chain 'A' and resid 800 through 803' Processing helix chain 'A' and resid 807 through 824 Processing helix chain 'A' and resid 833 through 847 removed outlier: 3.688A pdb=" N ARG A 838 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 839 " --> pdb=" O SER A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 863 removed outlier: 3.621A pdb=" N SER A 862 " --> pdb=" O ILE A 858 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 888 Processing helix chain 'A' and resid 891 through 894 No H-bonds generated for 'chain 'A' and resid 891 through 894' Processing helix chain 'A' and resid 913 through 925 Processing helix chain 'A' and resid 930 through 939 Processing helix chain 'A' and resid 941 through 971 Processing helix chain 'A' and resid 987 through 1013 removed outlier: 3.679A pdb=" N VAL A 992 " --> pdb=" O LEU A 988 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY A 998 " --> pdb=" O ARG A 994 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A1001 " --> pdb=" O LYS A 997 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A1006 " --> pdb=" O VAL A1002 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG A1007 " --> pdb=" O LYS A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1189 Processing helix chain 'A' and resid 1192 through 1210 Processing helix chain 'A' and resid 1214 through 1217 removed outlier: 4.232A pdb=" N GLU A1217 " --> pdb=" O ILE A1214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1214 through 1217' Processing helix chain 'A' and resid 1220 through 1254 removed outlier: 3.765A pdb=" N LYS A1231 " --> pdb=" O GLU A1227 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N TYR A1250 " --> pdb=" O ILE A1246 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N LYS A1251 " --> pdb=" O ALA A1247 " (cutoff:3.500A) removed outlier: 3.835A 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 1280 through 1282 No H-bonds generated for 'chain 'A' and resid 1280 through 1282' Processing helix chain 'A' and resid 1284 through 1302 removed outlier: 3.669A pdb=" N THR A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU A1292 " --> pdb=" O SER A1288 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A1293 " --> pdb=" O LEU A1289 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA A1294 " --> pdb=" O ARG A1290 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU A1295 " --> pdb=" O THR A1291 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ARG A1296 " --> pdb=" O LEU A1292 " (cutoff:3.500A) Proline residue: A1297 - end of helix removed outlier: 4.836A pdb=" N ALA A1300 " --> pdb=" O ARG A1296 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU A1301 " --> pdb=" O PRO A1297 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N SER A1302 " --> pdb=" O LEU A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1316 Processing helix chain 'A' and resid 1318 through 1343 Processing helix chain 'A' and resid 1367 through 1376 Processing helix chain 'A' and resid 1392 through 1403 Processing helix chain 'A' and resid 1408 through 1415 Processing helix chain 'A' and resid 1431 through 1444 removed outlier: 4.199A pdb=" N GLY A1444 " --> pdb=" O ILE A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1467 Processing helix chain 'A' and resid 1476 through 1490 removed outlier: 4.302A pdb=" N GLY A1489 " --> pdb=" O MET A1485 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER A1490 " --> pdb=" O LYS A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1512 Processing helix chain 'A' and resid 1517 through 1533 Processing helix chain 'A' and resid 1541 through 1568 removed outlier: 3.684A pdb=" N GLU A1545 " --> pdb=" O GLN A1541 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER A1568 " --> pdb=" O LEU A1564 " (cutoff:3.500A) Processing helix chain 'A' and resid 1573 through 1575 No H-bonds generated for 'chain 'A' and resid 1573 through 1575' Processing helix chain 'A' and resid 1577 through 1601 Processing helix chain 'A' and resid 1606 through 1626 removed outlier: 4.154A pdb=" N ALA A1615 " --> pdb=" O VAL A1611 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ARG A1616 " --> pdb=" O ILE A1612 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE A1617 " --> pdb=" O ARG A1613 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLY A1618 " --> pdb=" O LEU A1614 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ARG A1619 " --> pdb=" O ALA A1615 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG A1622 " --> pdb=" O GLY A1618 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU A1623 " --> pdb=" O ARG A1619 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL A1624 " --> pdb=" O ILE A1620 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LYS A1625 " --> pdb=" O LEU A1621 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY A1626 " --> pdb=" O ARG A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1665 Proline residue: A1642 - end of helix Processing helix chain 'A' and resid 1684 through 1696 removed outlier: 3.981A 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 1766 Processing helix chain 'B' and resid 154 through 191 Processing sheet with id= A, first strand: chain 'C' and resid 31 through 33 removed outlier: 4.403A pdb=" N GLU C 31 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR C 51 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 37 through 41 removed outlier: 7.941A pdb=" N LEU C 38 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N HIS C 143 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL C 40 " --> pdb=" O HIS C 143 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLN C 145 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TYR C 69 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N MET C 79 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 88 " --> pdb=" O GLN C 82 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 46 through 48 removed outlier: 3.818A pdb=" N MET C 113 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU C 100 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 88 through 90 Processing sheet with id= E, first strand: chain 'A' and resid 274 through 277 removed outlier: 3.563A pdb=" N VAL A 331 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1349 through 1352 Processing sheet with id= G, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.068A pdb=" N GLU B 145 " --> pdb=" O ALA B 30 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 36 through 38 Processing sheet with id= I, first strand: chain 'B' and resid 55 through 61 Processing sheet with id= J, first strand: chain 'B' and resid 71 through 74 Processing sheet with id= K, first strand: chain 'B' and resid 126 through 128 removed outlier: 3.935A pdb=" N LEU B 127 " --> pdb=" O HIS B 134 " (cutoff:3.500A) 691 hydrogen bonds defined for protein. 1872 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.24 Time building geometry restraints manager: 5.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2038 1.30 - 1.43: 3726 1.43 - 1.56: 7664 1.56 - 1.69: 25 1.69 - 1.82: 160 Bond restraints: 13613 Sorted by residual: bond pdb=" CA TYR A 304 " pdb=" C TYR A 304 " ideal model delta sigma weight residual 1.524 1.424 0.100 1.23e-02 6.61e+03 6.64e+01 bond pdb=" CA TYR A 305 " pdb=" C TYR A 305 " ideal model delta sigma weight residual 1.522 1.429 0.093 1.20e-02 6.94e+03 5.99e+01 bond pdb=" CA ARG A1367 " pdb=" C ARG A1367 " ideal model delta sigma weight residual 1.523 1.424 0.100 1.30e-02 5.92e+03 5.89e+01 bond pdb=" CA LEU A 793 " pdb=" C LEU A 793 " ideal model delta sigma weight residual 1.524 1.427 0.097 1.27e-02 6.20e+03 5.84e+01 bond pdb=" CA ASP A 912 " pdb=" C ASP A 912 " ideal model delta sigma weight residual 1.524 1.432 0.092 1.23e-02 6.61e+03 5.59e+01 ... (remaining 13608 not shown) Histogram of bond angle deviations from ideal: 97.92 - 105.21: 315 105.21 - 112.50: 6941 112.50 - 119.78: 5120 119.78 - 127.07: 5869 127.07 - 134.36: 130 Bond angle restraints: 18375 Sorted by residual: angle pdb=" N LEU A 793 " pdb=" CA LEU A 793 " pdb=" C LEU A 793 " ideal model delta sigma weight residual 111.07 99.79 11.28 1.07e+00 8.73e-01 1.11e+02 angle pdb=" N PHE A 176 " pdb=" CA PHE A 176 " pdb=" C PHE A 176 " ideal model delta sigma weight residual 114.12 99.68 14.44 1.39e+00 5.18e-01 1.08e+02 angle pdb=" N SER B 47 " pdb=" CA SER B 47 " pdb=" C SER B 47 " ideal model delta sigma weight residual 111.28 121.87 -10.59 1.09e+00 8.42e-01 9.45e+01 angle pdb=" N CYS B 21 " pdb=" CA CYS B 21 " pdb=" C CYS B 21 " ideal model delta sigma weight residual 110.23 124.00 -13.77 1.45e+00 4.76e-01 9.02e+01 angle pdb=" C LYS A1711 " pdb=" N PRO A1712 " pdb=" CA PRO A1712 " ideal model delta sigma weight residual 119.66 112.80 6.86 7.30e-01 1.88e+00 8.83e+01 ... (remaining 18370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 7903 35.95 - 71.90: 340 71.90 - 107.86: 25 107.86 - 143.81: 3 143.81 - 179.76: 1 Dihedral angle restraints: 8272 sinusoidal: 3626 harmonic: 4646 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 10.41 82.59 1 1.00e+01 1.00e-02 8.36e+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 93.00 166.05 -73.05 1 1.00e+01 1.00e-02 6.80e+01 dihedral pdb=" CB CYS C 72 " pdb=" SG CYS C 72 " pdb=" SG CYS C 75 " pdb=" CB CYS C 75 " ideal model delta sinusoidal sigma weight residual 93.00 161.59 -68.59 1 1.00e+01 1.00e-02 6.10e+01 ... (remaining 8269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1814 0.116 - 0.232: 202 0.232 - 0.348: 49 0.348 - 0.465: 19 0.465 - 0.581: 2 Chirality restraints: 2086 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.90e+01 chirality pdb=" CA ASP A1677 " pdb=" N ASP A1677 " pdb=" C ASP A1677 " pdb=" CB ASP A1677 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.43e+00 chirality pdb=" CA GLU A 294 " pdb=" N GLU A 294 " pdb=" C GLU A 294 " pdb=" CB GLU A 294 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.92e+00 ... (remaining 2083 not shown) Planarity restraints: 2222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " 0.307 2.00e-02 2.50e+03 2.69e-01 9.04e+02 pdb=" C7 NAG E 1 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " 0.126 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " -0.483 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 302 " 0.166 2.00e-02 2.50e+03 1.37e-01 2.34e+02 pdb=" C7 NAG B 302 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG B 302 " 0.123 2.00e-02 2.50e+03 pdb=" N2 NAG B 302 " -0.220 2.00e-02 2.50e+03 pdb=" O7 NAG B 302 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 301 " -0.156 2.00e-02 2.50e+03 1.27e-01 2.03e+02 pdb=" C7 NAG B 301 " 0.044 2.00e-02 2.50e+03 pdb=" C8 NAG B 301 " -0.116 2.00e-02 2.50e+03 pdb=" N2 NAG B 301 " 0.201 2.00e-02 2.50e+03 pdb=" O7 NAG B 301 " 0.028 2.00e-02 2.50e+03 ... (remaining 2219 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 264 2.61 - 3.18: 13117 3.18 - 3.76: 20556 3.76 - 4.33: 28494 4.33 - 4.90: 45779 Nonbonded interactions: 108210 Sorted by model distance: nonbonded pdb=" N GLN A1494 " pdb=" OE1 GLN A1494 " model vdw 2.039 2.520 nonbonded pdb=" O SER A1430 " pdb=" OG SER A1430 " model vdw 2.151 2.440 nonbonded pdb=" OD1 ASP C 45 " pdb=" NE ARG C 115 " model vdw 2.202 2.520 nonbonded pdb=" OG1 THR C 68 " pdb=" ND2 ASN C 126 " model vdw 2.214 2.520 nonbonded pdb=" N GLU A 771 " pdb=" OE1 GLU A 771 " model vdw 2.216 2.520 ... (remaining 108205 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.14 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.190 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 38.730 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 : 0.015 0.130 13613 Z= 1.013 Angle : 1.574 14.747 18375 Z= 0.953 Chirality : 0.091 0.581 2086 Planarity : 0.010 0.269 2214 Dihedral : 18.704 179.759 5235 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.87 % Favored : 95.01 % Rotamer: Outliers : 2.81 % Allowed : 5.35 % Favored : 91.84 % Cbeta Deviations : 0.87 % Peptide Plane: Cis-proline : 4.35 % 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: -0.94 (0.20), residues: 1565 helix: -0.13 (0.16), residues: 889 sheet: -0.39 (0.43), residues: 150 loop : -1.34 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.004 TRP A 908 HIS 0.012 0.002 HIS A 765 PHE 0.043 0.004 PHE B 54 TYR 0.040 0.004 TYR B 132 ARG 0.018 0.002 ARG A1308 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 231 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ARG cc_start: 0.7671 (mmm-85) cc_final: 0.7391 (mmm-85) REVERT: A 379 MET cc_start: 0.7914 (ttp) cc_final: 0.7616 (ttt) REVERT: A 794 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7144 (tppp) REVERT: A 854 MET cc_start: 0.6997 (tpp) cc_final: 0.6357 (tpp) REVERT: A 1182 ARG cc_start: 0.6711 (ttt-90) cc_final: 0.6471 (ttt-90) REVERT: A 1359 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8463 (m-10) REVERT: A 1537 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7042 (tt0) REVERT: B 166 LEU cc_start: 0.9578 (mp) cc_final: 0.9339 (mp) REVERT: B 183 LYS cc_start: 0.8829 (mttt) cc_final: 0.8436 (mttm) outliers start: 40 outliers final: 15 residues processed: 262 average time/residue: 0.2728 time to fit residues: 102.7445 Evaluate side-chains 197 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 179 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1359 PHE Chi-restraints excluded: chain A residue 1454 CYS Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 189 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 122 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 0.0370 chunk 141 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 273 HIS ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN A 774 ASN A 809 ASN A1483 ASN ** A1505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13613 Z= 0.210 Angle : 0.697 9.387 18375 Z= 0.363 Chirality : 0.044 0.373 2086 Planarity : 0.005 0.046 2214 Dihedral : 15.089 162.912 2227 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.53 % Allowed : 14.78 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 (0.21), residues: 1565 helix: 0.35 (0.17), residues: 917 sheet: -0.62 (0.41), residues: 146 loop : -1.29 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 908 HIS 0.008 0.001 HIS C 136 PHE 0.030 0.002 PHE A1233 TYR 0.019 0.002 TYR B 119 ARG 0.006 0.001 ARG A 26 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 215 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 113 MET cc_start: 0.5188 (OUTLIER) cc_final: 0.4335 (mmm) REVERT: A 130 MET cc_start: 0.8391 (tmm) cc_final: 0.7735 (tpp) REVERT: A 296 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6495 (mm-30) REVERT: A 841 ARG cc_start: 0.7013 (ttm110) cc_final: 0.6802 (mtt90) REVERT: A 854 MET cc_start: 0.6870 (tpp) cc_final: 0.6163 (tpp) REVERT: A 1485 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7413 (tmm) REVERT: B 162 MET cc_start: 0.7433 (mmm) cc_final: 0.7037 (mmt) REVERT: B 177 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7991 (mm-30) REVERT: B 180 TYR cc_start: 0.8508 (t80) cc_final: 0.8043 (t80) REVERT: B 183 LYS cc_start: 0.8501 (mttt) cc_final: 0.8198 (mtmt) REVERT: B 184 LYS cc_start: 0.8869 (mtmm) cc_final: 0.8605 (mtmt) outliers start: 36 outliers final: 15 residues processed: 233 average time/residue: 0.2466 time to fit residues: 85.4945 Evaluate side-chains 211 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 193 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 1181 ILE Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1454 CYS Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1485 MET Chi-restraints excluded: chain A residue 1526 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 170 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 30.0000 chunk 43 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN A 360 GLN A1420 ASN ** A1505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1762 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 13613 Z= 0.391 Angle : 0.711 8.614 18375 Z= 0.368 Chirality : 0.046 0.430 2086 Planarity : 0.005 0.040 2214 Dihedral : 13.736 159.804 2200 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.74 % Allowed : 18.86 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.47 (0.21), residues: 1565 helix: 0.32 (0.17), residues: 908 sheet: -0.76 (0.41), residues: 146 loop : -1.16 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 908 HIS 0.008 0.002 HIS A 765 PHE 0.031 0.002 PHE A1603 TYR 0.026 0.002 TYR B 132 ARG 0.007 0.001 ARG C 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 195 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: C 113 MET cc_start: 0.5579 (OUTLIER) cc_final: 0.4842 (mmm) REVERT: A 296 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6705 (mm-30) REVERT: A 854 MET cc_start: 0.6949 (tpp) cc_final: 0.6568 (tpp) REVERT: A 945 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8911 (tt) REVERT: B 162 MET cc_start: 0.7503 (mmm) cc_final: 0.7125 (mmt) REVERT: B 183 LYS cc_start: 0.8508 (mttt) cc_final: 0.8232 (mmtp) outliers start: 39 outliers final: 25 residues processed: 216 average time/residue: 0.2420 time to fit residues: 78.7966 Evaluate side-chains 211 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 183 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 1181 ILE Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1420 ASN Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1526 CYS Chi-restraints excluded: chain A residue 1562 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 166 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 142 optimal weight: 0.9980 chunk 150 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 134 optimal weight: 6.9990 chunk 40 optimal weight: 0.0020 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN A 270 ASN A 360 GLN ** A1505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13613 Z= 0.157 Angle : 0.593 9.507 18375 Z= 0.304 Chirality : 0.041 0.362 2086 Planarity : 0.004 0.038 2214 Dihedral : 12.534 154.221 2197 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.67 % Allowed : 21.11 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.10 (0.21), residues: 1565 helix: 0.67 (0.17), residues: 909 sheet: -0.77 (0.41), residues: 146 loop : -1.05 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 908 HIS 0.006 0.001 HIS C 136 PHE 0.022 0.001 PHE A1603 TYR 0.016 0.001 TYR B 119 ARG 0.006 0.000 ARG C 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 207 time to evaluate : 1.537 Fit side-chains revert: symmetry clash REVERT: C 113 MET cc_start: 0.5603 (OUTLIER) cc_final: 0.4945 (mmm) REVERT: A 130 MET cc_start: 0.8423 (tmm) cc_final: 0.7799 (tpp) REVERT: A 296 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6583 (mm-30) REVERT: A 854 MET cc_start: 0.6778 (tpp) cc_final: 0.6219 (tpp) REVERT: B 72 ARG cc_start: 0.7996 (ttt90) cc_final: 0.7773 (ttt90) REVERT: B 162 MET cc_start: 0.7539 (mmm) cc_final: 0.7301 (mmt) REVERT: B 183 LYS cc_start: 0.8494 (mttt) cc_final: 0.8212 (mmtp) outliers start: 38 outliers final: 21 residues processed: 230 average time/residue: 0.2536 time to fit residues: 86.6829 Evaluate side-chains 211 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 188 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1420 ASN Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1526 CYS Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 128 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 0.4980 chunk 135 optimal weight: 0.0770 chunk 38 optimal weight: 6.9990 overall best weight: 1.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7800 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13613 Z= 0.236 Angle : 0.599 9.211 18375 Z= 0.307 Chirality : 0.042 0.385 2086 Planarity : 0.004 0.037 2214 Dihedral : 12.127 153.498 2196 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.46 % Allowed : 21.67 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 (0.21), residues: 1565 helix: 0.65 (0.17), residues: 911 sheet: -0.74 (0.41), residues: 146 loop : -1.08 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 908 HIS 0.009 0.001 HIS C 136 PHE 0.024 0.001 PHE A1554 TYR 0.029 0.002 TYR A 157 ARG 0.007 0.001 ARG A 838 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 200 time to evaluate : 1.503 Fit side-chains revert: symmetry clash REVERT: C 113 MET cc_start: 0.5580 (OUTLIER) cc_final: 0.4955 (mmm) REVERT: A 130 MET cc_start: 0.8375 (tmm) cc_final: 0.7698 (tpp) REVERT: A 296 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6631 (mm-30) REVERT: A 854 MET cc_start: 0.6835 (tpp) cc_final: 0.6350 (tpp) REVERT: B 162 MET cc_start: 0.7472 (mmm) cc_final: 0.7265 (mmt) REVERT: B 179 ILE cc_start: 0.9196 (tp) cc_final: 0.8894 (tp) REVERT: B 180 TYR cc_start: 0.8727 (t80) cc_final: 0.8176 (t80) REVERT: B 183 LYS cc_start: 0.8525 (mttt) cc_final: 0.8122 (mmtp) REVERT: B 184 LYS cc_start: 0.8994 (mmtm) cc_final: 0.8569 (mtmt) outliers start: 35 outliers final: 22 residues processed: 224 average time/residue: 0.2398 time to fit residues: 81.0683 Evaluate side-chains 212 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 188 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1526 CYS Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 125 optimal weight: 0.0970 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN ** A1505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13613 Z= 0.241 Angle : 0.594 9.653 18375 Z= 0.304 Chirality : 0.042 0.399 2086 Planarity : 0.004 0.036 2214 Dihedral : 11.737 151.302 2194 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.89 % Allowed : 21.67 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.14 (0.21), residues: 1565 helix: 0.62 (0.17), residues: 912 sheet: -0.79 (0.41), residues: 146 loop : -1.04 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 908 HIS 0.007 0.001 HIS C 136 PHE 0.024 0.001 PHE A1554 TYR 0.015 0.002 TYR B 132 ARG 0.006 0.001 ARG C 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 199 time to evaluate : 1.707 Fit side-chains revert: symmetry clash REVERT: C 113 MET cc_start: 0.5584 (OUTLIER) cc_final: 0.4930 (mmm) REVERT: A 123 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8532 (tp) REVERT: A 130 MET cc_start: 0.8394 (tmm) cc_final: 0.7722 (tpp) REVERT: A 214 ARG cc_start: 0.7088 (mmm-85) cc_final: 0.6631 (mmm-85) REVERT: A 217 ARG cc_start: 0.7827 (mmt180) cc_final: 0.7611 (mpt180) REVERT: A 296 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6640 (mm-30) REVERT: A 854 MET cc_start: 0.6802 (tpp) cc_final: 0.6346 (tpp) REVERT: B 170 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8725 (tt) REVERT: B 179 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8909 (tp) REVERT: B 180 TYR cc_start: 0.8691 (t80) cc_final: 0.8119 (t80) REVERT: B 183 LYS cc_start: 0.8535 (mttt) cc_final: 0.8135 (mmtp) REVERT: B 184 LYS cc_start: 0.8986 (mmtm) cc_final: 0.8553 (mtmt) outliers start: 41 outliers final: 28 residues processed: 223 average time/residue: 0.2431 time to fit residues: 81.4424 Evaluate side-chains 219 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 186 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 1222 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1488 LEU Chi-restraints excluded: chain A residue 1518 ASP Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1526 CYS Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN A 360 GLN A 861 ASN A1461 ASN ** A1505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13613 Z= 0.166 Angle : 0.571 9.377 18375 Z= 0.290 Chirality : 0.041 0.361 2086 Planarity : 0.004 0.036 2214 Dihedral : 11.271 149.163 2194 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.89 % Allowed : 22.24 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.03 (0.21), residues: 1565 helix: 0.78 (0.17), residues: 911 sheet: -0.80 (0.41), residues: 147 loop : -1.00 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 67 HIS 0.007 0.001 HIS C 136 PHE 0.029 0.001 PHE A1509 TYR 0.028 0.001 TYR A 157 ARG 0.012 0.001 ARG C 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 200 time to evaluate : 1.665 Fit side-chains revert: symmetry clash REVERT: C 113 MET cc_start: 0.5552 (OUTLIER) cc_final: 0.4887 (mmm) REVERT: A 214 ARG cc_start: 0.6899 (mmm-85) cc_final: 0.6461 (mmm-85) REVERT: A 296 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6582 (mm-30) REVERT: A 426 MET cc_start: 0.6596 (mmm) cc_final: 0.5452 (ttp) REVERT: A 854 MET cc_start: 0.6701 (tpp) cc_final: 0.6123 (tpp) REVERT: B 45 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8075 (ttp-170) REVERT: B 72 ARG cc_start: 0.7978 (ttt90) cc_final: 0.7685 (ttt90) REVERT: B 170 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8741 (tt) REVERT: B 177 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8207 (mt-10) REVERT: B 179 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8930 (tp) REVERT: B 180 TYR cc_start: 0.8655 (t80) cc_final: 0.8037 (t80) REVERT: B 183 LYS cc_start: 0.8526 (mttt) cc_final: 0.8126 (mmtp) REVERT: B 184 LYS cc_start: 0.8980 (mmtm) cc_final: 0.8537 (mtmt) outliers start: 41 outliers final: 30 residues processed: 226 average time/residue: 0.2483 time to fit residues: 84.3806 Evaluate side-chains 223 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 188 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 1222 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1488 LEU Chi-restraints excluded: chain A residue 1518 ASP Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1526 CYS Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 14 optimal weight: 0.0970 chunk 118 optimal weight: 5.9990 chunk 136 optimal weight: 0.6980 chunk 144 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN A 861 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13613 Z= 0.197 Angle : 0.573 8.944 18375 Z= 0.291 Chirality : 0.041 0.372 2086 Planarity : 0.004 0.036 2214 Dihedral : 11.085 149.169 2194 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.10 % Allowed : 22.45 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.06 (0.21), residues: 1565 helix: 0.79 (0.17), residues: 913 sheet: -0.79 (0.40), residues: 149 loop : -0.95 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 67 HIS 0.006 0.001 HIS C 136 PHE 0.026 0.001 PHE A1509 TYR 0.024 0.001 TYR A 157 ARG 0.010 0.000 ARG C 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 195 time to evaluate : 1.512 Fit side-chains revert: symmetry clash REVERT: C 113 MET cc_start: 0.5545 (OUTLIER) cc_final: 0.4876 (mmm) REVERT: A 123 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8520 (tp) REVERT: A 130 MET cc_start: 0.8403 (tmm) cc_final: 0.7753 (tpp) REVERT: A 217 ARG cc_start: 0.7490 (mpt180) cc_final: 0.7075 (mmt-90) REVERT: A 296 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6606 (mm-30) REVERT: A 426 MET cc_start: 0.6448 (mmm) cc_final: 0.5130 (ttp) REVERT: A 854 MET cc_start: 0.6707 (tpp) cc_final: 0.6146 (tpp) REVERT: A 1569 LEU cc_start: 0.8854 (mp) cc_final: 0.8473 (mp) REVERT: B 45 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8067 (ttp-170) REVERT: B 170 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8726 (tt) REVERT: B 177 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8206 (mt-10) REVERT: B 179 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8957 (tp) REVERT: B 180 TYR cc_start: 0.8569 (t80) cc_final: 0.7894 (t80) REVERT: B 183 LYS cc_start: 0.8548 (mttt) cc_final: 0.8143 (mmtp) REVERT: B 184 LYS cc_start: 0.8989 (mmtm) cc_final: 0.8558 (mtmt) outliers start: 44 outliers final: 31 residues processed: 224 average time/residue: 0.2288 time to fit residues: 78.1328 Evaluate side-chains 228 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 191 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 861 ASN Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 1222 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1518 ASP Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1526 CYS Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 139 optimal weight: 0.0370 chunk 92 optimal weight: 0.7980 overall best weight: 1.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN A 861 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13613 Z= 0.216 Angle : 0.584 9.125 18375 Z= 0.296 Chirality : 0.042 0.380 2086 Planarity : 0.004 0.035 2214 Dihedral : 10.994 149.115 2194 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.89 % Allowed : 22.73 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1565 helix: 0.77 (0.17), residues: 913 sheet: -0.80 (0.40), residues: 149 loop : -0.94 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 908 HIS 0.006 0.001 HIS C 136 PHE 0.029 0.001 PHE A1554 TYR 0.014 0.001 TYR A 392 ARG 0.007 0.000 ARG C 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 194 time to evaluate : 1.475 Fit side-chains revert: symmetry clash REVERT: C 113 MET cc_start: 0.5542 (OUTLIER) cc_final: 0.4848 (mmm) REVERT: C 135 ARG cc_start: 0.7805 (mmp80) cc_final: 0.7488 (mmp80) REVERT: A 123 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8503 (tp) REVERT: A 130 MET cc_start: 0.8455 (tmm) cc_final: 0.7836 (tpp) REVERT: A 214 ARG cc_start: 0.7030 (mmm-85) cc_final: 0.6434 (mmm-85) REVERT: A 296 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6589 (mm-30) REVERT: A 426 MET cc_start: 0.6399 (mmm) cc_final: 0.5098 (ttp) REVERT: A 854 MET cc_start: 0.6710 (tpp) cc_final: 0.6188 (tpp) REVERT: A 1569 LEU cc_start: 0.8819 (mp) cc_final: 0.8444 (mp) REVERT: B 45 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8067 (ttp-170) REVERT: B 170 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8712 (tt) REVERT: B 177 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8195 (mt-10) REVERT: B 179 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8968 (tp) REVERT: B 183 LYS cc_start: 0.8552 (mttt) cc_final: 0.8163 (mmtp) REVERT: B 184 LYS cc_start: 0.8996 (mmtm) cc_final: 0.8604 (mtmm) outliers start: 41 outliers final: 34 residues processed: 220 average time/residue: 0.2331 time to fit residues: 78.1289 Evaluate side-chains 232 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 192 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 861 ASN Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 1222 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1488 LEU Chi-restraints excluded: chain A residue 1518 ASP Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1526 CYS Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1632 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 155 optimal weight: 8.9990 chunk 143 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 75 optimal weight: 0.2980 chunk 98 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13613 Z= 0.163 Angle : 0.579 9.579 18375 Z= 0.293 Chirality : 0.041 0.355 2086 Planarity : 0.004 0.035 2214 Dihedral : 10.802 148.379 2194 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.74 % Allowed : 23.22 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.14 (0.21), residues: 1565 helix: 0.84 (0.17), residues: 913 sheet: -0.76 (0.40), residues: 149 loop : -0.88 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 67 HIS 0.006 0.001 HIS C 136 PHE 0.032 0.001 PHE A1554 TYR 0.026 0.001 TYR B 180 ARG 0.006 0.000 ARG C 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 202 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 113 MET cc_start: 0.5473 (OUTLIER) cc_final: 0.4765 (mmm) REVERT: C 118 GLN cc_start: 0.5099 (pm20) cc_final: 0.4567 (pm20) REVERT: C 135 ARG cc_start: 0.7792 (mmp80) cc_final: 0.7499 (mmp80) REVERT: A 130 MET cc_start: 0.8474 (tmm) cc_final: 0.7856 (tpp) REVERT: A 214 ARG cc_start: 0.6984 (mmm-85) cc_final: 0.6412 (mmm160) REVERT: A 296 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6622 (mm-30) REVERT: A 426 MET cc_start: 0.6206 (mmm) cc_final: 0.5018 (ttp) REVERT: A 854 MET cc_start: 0.6738 (tpp) cc_final: 0.5889 (tpp) REVERT: A 1569 LEU cc_start: 0.8862 (mp) cc_final: 0.8493 (mp) REVERT: B 45 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.8049 (ttp-170) REVERT: B 72 ARG cc_start: 0.7931 (ttt90) cc_final: 0.7662 (ttt90) REVERT: B 154 MET cc_start: 0.6730 (tpp) cc_final: 0.6436 (tmm) REVERT: B 170 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8704 (tt) REVERT: B 177 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8188 (mt-10) REVERT: B 179 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8967 (tp) REVERT: B 183 LYS cc_start: 0.8531 (mttt) cc_final: 0.8139 (mmtp) outliers start: 39 outliers final: 32 residues processed: 227 average time/residue: 0.2440 time to fit residues: 83.1081 Evaluate side-chains 235 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 198 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 861 ASN Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1222 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1488 LEU Chi-restraints excluded: chain A residue 1518 ASP Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1526 CYS Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1632 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 123 optimal weight: 0.5980 chunk 51 optimal weight: 20.0000 chunk 127 optimal weight: 0.1980 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.144546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.102364 restraints weight = 38600.692| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.33 r_work: 0.3188 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13613 Z= 0.162 Angle : 0.583 11.650 18375 Z= 0.294 Chirality : 0.041 0.341 2086 Planarity : 0.004 0.035 2214 Dihedral : 10.621 148.489 2194 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.53 % Allowed : 23.50 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.17 (0.21), residues: 1565 helix: 0.86 (0.17), residues: 911 sheet: -0.72 (0.40), residues: 149 loop : -0.86 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1549 HIS 0.006 0.001 HIS C 136 PHE 0.039 0.001 PHE A1554 TYR 0.026 0.001 TYR A 157 ARG 0.006 0.000 ARG C 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2901.36 seconds wall clock time: 53 minutes 58.16 seconds (3238.16 seconds total)