Starting phenix.real_space_refine on Thu Jun 27 15:21:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmn_38483/06_2024/8xmn_38483_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmn_38483/06_2024/8xmn_38483.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmn_38483/06_2024/8xmn_38483_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmn_38483/06_2024/8xmn_38483_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmn_38483/06_2024/8xmn_38483_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmn_38483/06_2024/8xmn_38483.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmn_38483/06_2024/8xmn_38483.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmn_38483/06_2024/8xmn_38483_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xmn_38483/06_2024/8xmn_38483_updated.pdb" } resolution = 3.37 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= 0.015 sd= 0.050 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 8 5.49 5 S 98 5.16 5 C 8627 2.51 5 N 2040 2.21 5 O 2337 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 52": "OD1" <-> "OD2" Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 76": "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 ASP 150": "OD1" <-> "OD2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "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 192": "OD1" <-> "OD2" Residue "A PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 320": "OD1" <-> "OD2" Residue "A ASP 338": "OD1" <-> "OD2" Residue "A ASP 345": "OD1" <-> "OD2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 771": "OE1" <-> "OE2" Residue "A TYR 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 835": "NH1" <-> "NH2" Residue "A PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 843": "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 ASP 901": "OD1" <-> "OD2" Residue "A PHE 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 922": "NH1" <-> "NH2" Residue "A GLU 937": "OE1" <-> "OE2" Residue "A TYR 948": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 974": "OD1" <-> "OD2" Residue "A GLU 980": "OE1" <-> "OE2" Residue "A ASP 982": "OD1" <-> "OD2" Residue "A GLU 1008": "OE1" <-> "OE2" Residue "A PHE 1014": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1182": "NH1" <-> "NH2" Residue "A TYR 1186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1212": "OE1" <-> "OE2" Residue "A ARG 1218": "NH1" <-> "NH2" Residue "A GLU 1227": "OE1" <-> "OE2" Residue "A TYR 1228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1293": "NH1" <-> "NH2" Residue "A PHE 1304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1308": "NH1" <-> "NH2" Residue "A PHE 1343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1367": "NH1" <-> "NH2" Residue "A PHE 1371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1417": "OD1" <-> "OD2" Residue "A ASP 1422": "OD1" <-> "OD2" Residue "A TYR 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1428": "OE1" <-> "OE2" Residue "A TYR 1429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1477": "OE1" <-> "OE2" Residue "A TYR 1481": "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 GLU 1537": "OE1" <-> "OE2" Residue "A PHE 1554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1561": "OE1" <-> "OE2" Residue "A PHE 1574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1597": "OD1" <-> "OD2" Residue "A GLU 1600": "OE1" <-> "OE2" Residue "A TYR 1602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1610": "NH1" <-> "NH2" Residue "A ARG 1613": "NH1" <-> "NH2" Residue "A ARG 1619": "NH1" <-> "NH2" Residue "A PHE 1635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1672": "OE1" <-> "OE2" Residue "A PHE 1681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1714": "OD1" <-> "OD2" Residue "A GLU 1727": "OE1" <-> "OE2" Residue "A ASP 1729": "OD1" <-> "OD2" Residue "A PHE 1738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1740": "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 GLU 23": "OE1" <-> "OE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B ASP 103": "OD1" <-> "OD2" Residue "B PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B ASP 148": "OD1" <-> "OD2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" 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" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 13110 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 10299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1277, 10299 Classifications: {'peptide': 1277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 1234} 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: "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: "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: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 303 Unusual residues: {'LPE': 5, 'NAG': 2, 'PCW': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 8.14, per 1000 atoms: 0.62 Number of scatterers: 13110 At special positions: 0 Unit cell: (113.886, 136.496, 136.496, 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 98 16.00 P 8 15.00 O 2337 8.00 N 2040 7.00 C 8627 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 324 " distance=2.08 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=2.02 Simple disulfide: pdb=" SG CYS A 895 " - pdb=" SG CYS C 55 " distance=2.04 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.05 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.02 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.04 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 43 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.04 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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 110 " " NAG B 303 " - " ASN B 114 " " NAG B 304 " - " ASN B 135 " " NAG D 1 " - " ASN A1366 " " NAG E 1 " - " ASN A1352 " Time building additional restraints: 5.25 Conformation dependent library (CDL) restraints added in 2.5 seconds 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2984 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 10 sheets defined 58.8% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... Processing helix chain 'A' and resid 17 through 31 removed outlier: 4.304A pdb=" N GLU A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLN A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) 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 84 removed outlier: 3.969A pdb=" N ASP A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 80 through 84' 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 123 Processing helix chain 'A' and resid 126 through 143 removed outlier: 3.613A pdb=" N THR A 138 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 174 removed outlier: 3.569A pdb=" N LYS A 153 " --> pdb=" O ASP A 150 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN A 154 " --> pdb=" O TRP A 151 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 169 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU A 172 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG A 174 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 187 through 205 removed outlier: 4.215A pdb=" N ASP A 192 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 202 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL A 205 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 227 removed outlier: 3.637A pdb=" N PHE A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARG A 220 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N THR A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 244 removed outlier: 4.015A pdb=" N LYS A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 267 Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 297 through 300 No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 347 through 358 Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 376 through 421 removed outlier: 4.299A pdb=" N ILE A 380 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 385 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 387 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY A 389 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N SER A 390 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR A 392 " --> pdb=" O GLY A 389 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU A 393 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN A 395 " --> pdb=" O TYR A 392 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 401 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 739 Processing helix chain 'A' and resid 746 through 763 removed outlier: 4.108A 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 805 removed outlier: 4.602A pdb=" N GLN A 805 " --> pdb=" O TYR A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 824 removed outlier: 3.580A pdb=" N PHE A 811 " --> pdb=" O GLY A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 837 removed outlier: 3.656A pdb=" N PHE A 837 " --> pdb=" O LEU A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 848 removed outlier: 3.537A pdb=" N LYS A 847 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 863 removed outlier: 3.832A pdb=" N VAL A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 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 896 through 899 No H-bonds generated for 'chain 'A' and resid 896 through 899' Processing helix chain 'A' and resid 913 through 925 Processing helix chain 'A' and resid 929 through 939 Processing helix chain 'A' and resid 941 through 971 Processing helix chain 'A' and resid 987 through 1013 removed outlier: 3.538A pdb=" N ARG A 994 " --> pdb=" O ILE A 990 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR A1001 " --> pdb=" O LYS A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1190 Processing helix chain 'A' and resid 1192 through 1211 removed outlier: 3.805A pdb=" N ALA A1210 " --> pdb=" O SER A1206 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE A1211 " --> pdb=" O GLY A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1217 removed outlier: 4.459A 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 1248 Processing helix chain 'A' and resid 1250 through 1254 Processing helix chain 'A' and resid 1257 through 1277 Processing helix chain 'A' and resid 1284 through 1302 removed outlier: 3.978A pdb=" N LEU A1289 " --> pdb=" O ILE A1286 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A1290 " --> pdb=" O LYS A1287 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR A1291 " --> pdb=" O SER A1288 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A1294 " --> pdb=" O THR A1291 " (cutoff:3.500A) Proline residue: A1297 - end of helix removed outlier: 4.122A pdb=" N LEU A1301 " --> pdb=" O LEU A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1315 Processing helix chain 'A' and resid 1318 through 1343 removed outlier: 3.684A pdb=" N ASN A1323 " --> pdb=" O PRO A1319 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1374 Processing helix chain 'A' and resid 1392 through 1404 Processing helix chain 'A' and resid 1408 through 1415 Processing helix chain 'A' and resid 1431 through 1465 removed outlier: 3.557A pdb=" N TYR A1434 " --> pdb=" O LEU A1431 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE A1435 " --> pdb=" O TYR A1432 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY A1444 " --> pdb=" O ILE A1441 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A1445 " --> pdb=" O ILE A1442 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N PHE A1447 " --> pdb=" O GLY A1444 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N THR A1448 " --> pdb=" O SER A1445 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU A1449 " --> pdb=" O PHE A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1489 removed outlier: 3.551A pdb=" N LEU A1488 " --> pdb=" O ALA A1484 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY A1489 " --> pdb=" O MET A1485 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1512 Processing helix chain 'A' and resid 1515 through 1533 removed outlier: 3.548A pdb=" N ILE A1519 " --> pdb=" O GLN A1515 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A1531 " --> pdb=" O LEU A1527 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1568 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 1602 Processing helix chain 'A' and resid 1606 through 1626 removed outlier: 4.956A pdb=" N ALA A1615 " --> pdb=" O VAL A1611 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ARG A1616 " --> pdb=" O ILE A1612 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ILE A1617 " --> pdb=" O ARG A1613 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY A1618 " --> pdb=" O LEU A1614 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG A1619 " --> pdb=" O ALA A1615 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A1621 " --> pdb=" O ILE A1617 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG A1622 " --> pdb=" O GLY A1618 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU A1623 " --> pdb=" O ARG A1619 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL A1624 " --> pdb=" O ILE A1620 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS A1625 " --> pdb=" O LEU A1621 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY A1626 " --> pdb=" O ARG A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1631 through 1665 Proline residue: A1642 - end of helix Processing helix chain 'A' and resid 1684 through 1696 removed outlier: 4.047A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1700 through 1705 Processing helix chain 'A' and resid 1733 through 1766 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 191 Processing helix chain 'C' and resid 105 through 107 No H-bonds generated for 'chain 'C' and resid 105 through 107' Processing sheet with id= A, first strand: chain 'A' and resid 88 through 91 Processing sheet with id= B, first strand: chain 'A' and resid 273 through 277 Processing sheet with id= C, first strand: chain 'A' and resid 1349 through 1352 removed outlier: 3.508A pdb=" N ARG A1381 " --> pdb=" O ILE A1351 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.478A pdb=" N GLU B 145 " --> pdb=" O ALA B 30 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 36 through 38 Processing sheet with id= F, first strand: chain 'B' and resid 138 through 144 removed outlier: 4.398A pdb=" N ASN B 50 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 71 " --> pdb=" O TRP B 57 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE B 59 " --> pdb=" O LYS B 69 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N LYS B 69 " --> pdb=" O PHE B 59 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 126 through 128 Processing sheet with id= H, 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: 3.514A pdb=" N THR C 51 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 37 through 41 removed outlier: 7.940A pdb=" N LEU C 38 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N HIS C 143 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 7.320A 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: 3.570A pdb=" N ILE C 88 " --> pdb=" O GLN C 82 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 46 through 48 removed outlier: 3.819A pdb=" N MET C 113 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU C 100 " --> pdb=" O MET C 113 " (cutoff:3.500A) 689 hydrogen bonds defined for protein. 1722 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.84 Time building geometry restraints manager: 5.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2008 1.29 - 1.42: 3563 1.42 - 1.56: 7658 1.56 - 1.70: 16 1.70 - 1.83: 158 Bond restraints: 13403 Sorted by residual: bond pdb=" C ILE A1588 " pdb=" O ILE A1588 " ideal model delta sigma weight residual 1.237 1.151 0.086 1.17e-02 7.31e+03 5.40e+01 bond pdb=" CA PHE A1440 " pdb=" C PHE A1440 " ideal model delta sigma weight residual 1.524 1.437 0.087 1.26e-02 6.30e+03 4.75e+01 bond pdb=" CA TYR A1436 " pdb=" C TYR A1436 " ideal model delta sigma weight residual 1.524 1.438 0.086 1.26e-02 6.30e+03 4.63e+01 bond pdb=" CA ARG A1367 " pdb=" C ARG A1367 " ideal model delta sigma weight residual 1.523 1.436 0.087 1.34e-02 5.57e+03 4.25e+01 bond pdb=" C11 PCW A2008 " pdb=" O3 PCW A2008 " ideal model delta sigma weight residual 1.326 1.451 -0.125 2.00e-02 2.50e+03 3.88e+01 ... (remaining 13398 not shown) Histogram of bond angle deviations from ideal: 96.18 - 103.78: 177 103.78 - 111.39: 5556 111.39 - 118.99: 5431 118.99 - 126.59: 6794 126.59 - 134.20: 152 Bond angle restraints: 18110 Sorted by residual: angle pdb=" N ARG A 217 " pdb=" CA ARG A 217 " pdb=" C ARG A 217 " ideal model delta sigma weight residual 113.23 101.62 11.61 1.24e+00 6.50e-01 8.77e+01 angle pdb=" N ARG A 26 " pdb=" CA ARG A 26 " pdb=" C ARG A 26 " ideal model delta sigma weight residual 111.03 101.02 10.01 1.11e+00 8.12e-01 8.14e+01 angle pdb=" N TYR A1436 " pdb=" CA TYR A1436 " pdb=" C TYR A1436 " ideal model delta sigma weight residual 111.14 101.73 9.41 1.08e+00 8.57e-01 7.59e+01 angle pdb=" N SER C 76 " pdb=" CA SER C 76 " pdb=" C SER C 76 " ideal model delta sigma weight residual 110.50 122.69 -12.19 1.41e+00 5.03e-01 7.48e+01 angle pdb=" N LYS A1628 " pdb=" CA LYS A1628 " pdb=" C LYS A1628 " ideal model delta sigma weight residual 114.62 105.01 9.61 1.14e+00 7.69e-01 7.11e+01 ... (remaining 18105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.12: 7661 31.12 - 62.24: 430 62.24 - 93.36: 29 93.36 - 124.48: 1 124.48 - 155.60: 3 Dihedral angle restraints: 8124 sinusoidal: 3507 harmonic: 4617 Sorted by residual: dihedral pdb=" CB CYS A1350 " pdb=" SG CYS A1350 " pdb=" SG CYS A1370 " pdb=" CB CYS A1370 " ideal model delta sinusoidal sigma weight residual -86.00 -171.40 85.40 1 1.00e+01 1.00e-02 8.83e+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 6.09e+01 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 30.79 62.21 1 1.00e+01 1.00e-02 5.12e+01 ... (remaining 8121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 1936 0.145 - 0.291: 112 0.291 - 0.436: 19 0.436 - 0.582: 2 0.582 - 0.727: 1 Chirality restraints: 2070 Sorted by residual: chirality pdb=" CA CYS A 897 " pdb=" N CYS A 897 " pdb=" C CYS A 897 " pdb=" CB CYS A 897 " both_signs ideal model delta sigma weight residual False 2.51 1.78 0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" CA PHE A 824 " pdb=" N PHE A 824 " pdb=" C PHE A 824 " pdb=" CB PHE A 824 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.35e+00 chirality pdb=" CA PHE A1437 " pdb=" N PHE A1437 " pdb=" C PHE A1437 " pdb=" CB PHE A1437 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.87e+00 ... (remaining 2067 not shown) Planarity restraints: 2202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.288 2.00e-02 2.50e+03 2.42e-01 7.33e+02 pdb=" C7 NAG E 1 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.412 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1443 " 0.025 2.00e-02 2.50e+03 5.01e-02 2.51e+01 pdb=" C PHE A1443 " -0.087 2.00e-02 2.50e+03 pdb=" O PHE A1443 " 0.032 2.00e-02 2.50e+03 pdb=" N GLY A1444 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1408 " 0.033 2.00e-02 2.50e+03 3.00e-02 2.25e+01 pdb=" CG TRP A1408 " -0.081 2.00e-02 2.50e+03 pdb=" CD1 TRP A1408 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP A1408 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A1408 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A1408 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1408 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1408 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1408 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A1408 " 0.003 2.00e-02 2.50e+03 ... (remaining 2199 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2133 2.74 - 3.28: 14165 3.28 - 3.82: 21258 3.82 - 4.36: 25573 4.36 - 4.90: 42277 Nonbonded interactions: 105406 Sorted by model distance: nonbonded pdb=" OD1 ASP C 45 " pdb=" NE ARG C 115 " model vdw 2.202 2.520 nonbonded pdb=" OG SER A 318 " pdb=" OD1 ASP A 320 " model vdw 2.208 2.440 nonbonded pdb=" OG1 THR C 68 " pdb=" ND2 ASN C 126 " model vdw 2.214 2.520 nonbonded pdb=" OE1 GLN B 61 " pdb=" NH1 ARG B 85 " model vdw 2.243 2.520 nonbonded pdb=" O LYS A 244 " pdb=" NZ LYS A 244 " model vdw 2.247 2.520 ... (remaining 105401 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.300 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 38.560 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.125 13403 Z= 0.758 Angle : 1.291 12.194 18110 Z= 0.780 Chirality : 0.081 0.727 2070 Planarity : 0.009 0.242 2194 Dihedral : 17.912 155.602 5107 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.63 % Favored : 93.17 % Rotamer: Outliers : 2.34 % Allowed : 3.26 % Favored : 94.40 % Cbeta Deviations : 0.27 % 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: -1.12 (0.21), residues: 1556 helix: 0.01 (0.17), residues: 899 sheet: -0.43 (0.41), residues: 142 loop : -2.07 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.003 TRP A1408 HIS 0.007 0.002 HIS C 136 PHE 0.030 0.003 PHE B 86 TYR 0.049 0.003 TYR A 362 ARG 0.022 0.002 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 246 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8570 (mmtp) REVERT: A 163 TYR cc_start: 0.7075 (m-80) cc_final: 0.6608 (m-80) REVERT: A 176 PHE cc_start: 0.8031 (t80) cc_final: 0.7524 (t80) REVERT: A 326 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6847 (mp0) REVERT: A 388 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7867 (tt) REVERT: A 742 MET cc_start: 0.8462 (ttt) cc_final: 0.8254 (ttt) REVERT: A 1452 PHE cc_start: 0.8359 (t80) cc_final: 0.7006 (m-10) REVERT: A 1762 ASN cc_start: 0.8817 (t0) cc_final: 0.8546 (t0) REVERT: B 162 MET cc_start: 0.7980 (mmt) cc_final: 0.7188 (mpp) REVERT: B 164 TYR cc_start: 0.8770 (m-80) cc_final: 0.8526 (m-80) REVERT: B 184 LYS cc_start: 0.9143 (tptp) cc_final: 0.8882 (tptp) REVERT: C 39 ASN cc_start: 0.5249 (m-40) cc_final: 0.5028 (p0) REVERT: C 79 MET cc_start: 0.7220 (tmm) cc_final: 0.7017 (tmm) REVERT: C 113 MET cc_start: 0.1885 (mmt) cc_final: 0.1134 (mtt) outliers start: 33 outliers final: 9 residues processed: 271 average time/residue: 0.2225 time to fit residues: 90.3750 Evaluate side-chains 214 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 202 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1466 LYS Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1571 HIS Chi-restraints excluded: chain A residue 1628 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 0.1980 chunk 62 optimal weight: 0.7980 chunk 121 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 140 optimal weight: 0.0040 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN A 765 HIS A 915 HIS A 989 GLN A1505 GLN A1551 ASN A1665 ASN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 ASN C 139 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13403 Z= 0.193 Angle : 0.695 10.425 18110 Z= 0.368 Chirality : 0.045 0.362 2070 Planarity : 0.006 0.059 2194 Dihedral : 12.795 152.349 2129 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.41 % Allowed : 12.12 % Favored : 85.47 % 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: -0.61 (0.21), residues: 1556 helix: 0.42 (0.17), residues: 877 sheet: -0.76 (0.40), residues: 142 loop : -1.61 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1408 HIS 0.008 0.001 HIS C 136 PHE 0.024 0.002 PHE A 165 TYR 0.032 0.002 TYR A 362 ARG 0.015 0.001 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 232 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 PHE cc_start: 0.8158 (t80) cc_final: 0.7627 (t80) REVERT: A 153 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8590 (mmtp) REVERT: A 163 TYR cc_start: 0.6896 (m-80) cc_final: 0.6527 (m-80) REVERT: A 176 PHE cc_start: 0.7739 (t80) cc_final: 0.7387 (t80) REVERT: A 367 TYR cc_start: 0.8340 (t80) cc_final: 0.7300 (t80) REVERT: A 823 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8064 (mm) REVERT: A 943 MET cc_start: 0.7368 (mmm) cc_final: 0.6834 (tpt) REVERT: A 1452 PHE cc_start: 0.7952 (t80) cc_final: 0.7018 (m-10) REVERT: A 1482 TYR cc_start: 0.8286 (t80) cc_final: 0.7946 (t80) REVERT: A 1739 TYR cc_start: 0.8324 (t80) cc_final: 0.8119 (t80) REVERT: B 184 LYS cc_start: 0.9136 (tptp) cc_final: 0.8889 (tptp) REVERT: C 113 MET cc_start: 0.2320 (mmt) cc_final: 0.1560 (ttp) outliers start: 34 outliers final: 20 residues processed: 255 average time/residue: 0.2205 time to fit residues: 85.9277 Evaluate side-chains 227 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 205 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 810 ILE Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1571 HIS Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1673 ASP Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 125 optimal weight: 0.6980 chunk 139 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 HIS A1461 ASN A1462 GLN A1539 GLN A1762 ASN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13403 Z= 0.239 Angle : 0.629 9.463 18110 Z= 0.336 Chirality : 0.044 0.357 2070 Planarity : 0.005 0.042 2194 Dihedral : 12.009 153.640 2115 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.12 % Allowed : 15.59 % Favored : 81.29 % 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: -0.50 (0.21), residues: 1556 helix: 0.51 (0.17), residues: 866 sheet: -0.86 (0.39), residues: 142 loop : -1.45 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1382 HIS 0.009 0.001 HIS A 765 PHE 0.025 0.001 PHE A1509 TYR 0.027 0.002 TYR A 362 ARG 0.007 0.001 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 222 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 PHE cc_start: 0.8112 (t80) cc_final: 0.7620 (t80) REVERT: A 153 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8656 (mttp) REVERT: A 163 TYR cc_start: 0.6984 (m-80) cc_final: 0.6619 (m-80) REVERT: A 358 MET cc_start: 0.8433 (ttt) cc_final: 0.8129 (ttt) REVERT: A 367 TYR cc_start: 0.8416 (t80) cc_final: 0.7213 (t80) REVERT: A 1452 PHE cc_start: 0.8012 (t80) cc_final: 0.6811 (m-10) REVERT: B 76 GLU cc_start: 0.8008 (tp30) cc_final: 0.7452 (tp30) REVERT: B 184 LYS cc_start: 0.9136 (tptp) cc_final: 0.8886 (tptp) REVERT: C 87 ILE cc_start: 0.7388 (mt) cc_final: 0.7187 (mt) REVERT: C 113 MET cc_start: 0.2230 (mmt) cc_final: 0.1615 (ttp) REVERT: C 135 ARG cc_start: 0.7158 (mmm160) cc_final: 0.6291 (mmt180) outliers start: 44 outliers final: 27 residues processed: 250 average time/residue: 0.2089 time to fit residues: 80.0776 Evaluate side-chains 235 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 207 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 810 ILE Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1571 HIS Chi-restraints excluded: chain A residue 1576 VAL Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1673 ASP Chi-restraints excluded: chain A residue 1695 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 141 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 124 optimal weight: 0.0770 overall best weight: 2.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 HIS A1762 ASN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13403 Z= 0.292 Angle : 0.636 13.937 18110 Z= 0.336 Chirality : 0.044 0.357 2070 Planarity : 0.005 0.042 2194 Dihedral : 11.782 153.843 2115 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.34 % Favored : 94.59 % Rotamer: Outliers : 3.40 % Allowed : 18.85 % Favored : 77.75 % 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: -0.49 (0.21), residues: 1556 helix: 0.53 (0.17), residues: 864 sheet: -0.93 (0.39), residues: 144 loop : -1.45 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1382 HIS 0.004 0.001 HIS A 765 PHE 0.028 0.002 PHE A1509 TYR 0.025 0.002 TYR A 362 ARG 0.006 0.001 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 219 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 PHE cc_start: 0.8128 (t80) cc_final: 0.7634 (t80) REVERT: A 163 TYR cc_start: 0.7037 (m-80) cc_final: 0.6663 (m-80) REVERT: A 165 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.7550 (p90) REVERT: A 266 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8179 (mp) REVERT: A 791 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7253 (tpt) REVERT: B 48 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8080 (pm20) REVERT: B 76 GLU cc_start: 0.7961 (tp30) cc_final: 0.7553 (tp30) REVERT: B 184 LYS cc_start: 0.9133 (tptp) cc_final: 0.8890 (tptp) REVERT: C 113 MET cc_start: 0.2490 (mmt) cc_final: 0.1839 (ttp) outliers start: 48 outliers final: 26 residues processed: 248 average time/residue: 0.2139 time to fit residues: 81.2869 Evaluate side-chains 232 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 202 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 810 ILE Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1539 GLN Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1576 VAL Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1673 ASP Chi-restraints excluded: chain A residue 1695 THR Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 7.9990 chunk 2 optimal weight: 0.0050 chunk 111 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 0 optimal weight: 40.0000 chunk 76 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 HIS A1762 ASN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13403 Z= 0.178 Angle : 0.593 11.156 18110 Z= 0.314 Chirality : 0.042 0.350 2070 Planarity : 0.005 0.042 2194 Dihedral : 11.283 155.815 2105 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.76 % Allowed : 20.84 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.22), residues: 1556 helix: 0.68 (0.18), residues: 868 sheet: -0.67 (0.40), residues: 138 loop : -1.36 (0.28), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1382 HIS 0.005 0.001 HIS C 136 PHE 0.030 0.001 PHE A1509 TYR 0.020 0.001 TYR A 362 ARG 0.006 0.001 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 222 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: A 128 PHE cc_start: 0.7963 (t80) cc_final: 0.7486 (t80) REVERT: A 157 TYR cc_start: 0.7948 (m-80) cc_final: 0.7440 (t80) REVERT: A 163 TYR cc_start: 0.7046 (m-80) cc_final: 0.6704 (m-80) REVERT: A 165 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7438 (p90) REVERT: A 790 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7785 (tp30) REVERT: A 791 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7163 (tpt) REVERT: A 798 MET cc_start: 0.7208 (ppp) cc_final: 0.6938 (ppp) REVERT: B 184 LYS cc_start: 0.9125 (tptp) cc_final: 0.8879 (tptp) REVERT: C 113 MET cc_start: 0.2442 (mmt) cc_final: 0.1735 (ttp) REVERT: C 135 ARG cc_start: 0.7022 (mmp80) cc_final: 0.6727 (mpt-90) outliers start: 39 outliers final: 21 residues processed: 247 average time/residue: 0.2077 time to fit residues: 79.5635 Evaluate side-chains 229 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 206 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1539 GLN Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 10.0000 chunk 29 optimal weight: 0.2980 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 69 optimal weight: 0.1980 chunk 12 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 chunk 144 optimal weight: 0.0570 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 HIS ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 13403 Z= 0.153 Angle : 0.600 12.865 18110 Z= 0.308 Chirality : 0.042 0.352 2070 Planarity : 0.004 0.042 2194 Dihedral : 10.812 156.447 2105 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.34 % Allowed : 22.61 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.22), residues: 1556 helix: 0.77 (0.18), residues: 871 sheet: -0.43 (0.40), residues: 136 loop : -1.31 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1578 HIS 0.004 0.001 HIS C 136 PHE 0.024 0.001 PHE A1509 TYR 0.026 0.001 TYR B 32 ARG 0.006 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 233 time to evaluate : 1.445 Fit side-chains revert: symmetry clash REVERT: A 107 TYR cc_start: 0.5774 (t80) cc_final: 0.5547 (t80) REVERT: A 128 PHE cc_start: 0.8144 (t80) cc_final: 0.7610 (t80) REVERT: A 157 TYR cc_start: 0.7902 (m-80) cc_final: 0.7385 (t80) REVERT: A 163 TYR cc_start: 0.6984 (m-80) cc_final: 0.6700 (m-80) REVERT: A 165 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7338 (p90) REVERT: A 176 PHE cc_start: 0.7822 (t80) cc_final: 0.7438 (t80) REVERT: A 362 TYR cc_start: 0.8854 (t80) cc_final: 0.8548 (t80) REVERT: A 790 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7706 (tp30) REVERT: A 791 MET cc_start: 0.8104 (ttm) cc_final: 0.7133 (tpt) REVERT: A 798 MET cc_start: 0.7191 (ppp) cc_final: 0.6863 (ppp) REVERT: A 1333 LEU cc_start: 0.8241 (tt) cc_final: 0.7871 (tt) REVERT: A 1482 TYR cc_start: 0.8020 (t80) cc_final: 0.7578 (t80) REVERT: A 1762 ASN cc_start: 0.8610 (t0) cc_final: 0.8362 (t0) REVERT: B 184 LYS cc_start: 0.9147 (tptp) cc_final: 0.8896 (tptp) REVERT: C 113 MET cc_start: 0.2420 (mmt) cc_final: 0.1660 (tmm) REVERT: C 135 ARG cc_start: 0.6945 (mmp80) cc_final: 0.6650 (mpt-90) outliers start: 33 outliers final: 19 residues processed: 258 average time/residue: 0.2129 time to fit residues: 83.2763 Evaluate side-chains 234 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 214 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1510 ASP Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain C residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 68 optimal weight: 20.0000 chunk 92 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 HIS ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13403 Z= 0.189 Angle : 0.588 8.751 18110 Z= 0.307 Chirality : 0.042 0.349 2070 Planarity : 0.004 0.041 2194 Dihedral : 10.636 155.172 2105 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.41 % Allowed : 24.03 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.22), residues: 1556 helix: 0.86 (0.18), residues: 869 sheet: -0.44 (0.41), residues: 138 loop : -1.25 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1382 HIS 0.004 0.001 HIS C 136 PHE 0.023 0.001 PHE A 733 TYR 0.025 0.001 TYR B 32 ARG 0.007 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 219 time to evaluate : 1.413 Fit side-chains revert: symmetry clash REVERT: A 128 PHE cc_start: 0.8140 (t80) cc_final: 0.7770 (t80) REVERT: A 157 TYR cc_start: 0.7907 (m-80) cc_final: 0.7411 (t80) REVERT: A 163 TYR cc_start: 0.7036 (m-80) cc_final: 0.6661 (m-80) REVERT: A 362 TYR cc_start: 0.8875 (t80) cc_final: 0.8610 (t80) REVERT: A 790 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7730 (tp30) REVERT: A 791 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7044 (tpt) REVERT: A 798 MET cc_start: 0.7271 (ppp) cc_final: 0.6885 (ppp) REVERT: A 1474 MET cc_start: 0.7608 (mtp) cc_final: 0.6970 (ttm) REVERT: A 1482 TYR cc_start: 0.7760 (t80) cc_final: 0.7391 (t80) REVERT: A 1762 ASN cc_start: 0.8700 (t0) cc_final: 0.8448 (t0) REVERT: B 184 LYS cc_start: 0.9164 (tptp) cc_final: 0.8914 (tptp) REVERT: C 113 MET cc_start: 0.2364 (mmt) cc_final: 0.1863 (ttp) REVERT: C 135 ARG cc_start: 0.6939 (mmp80) cc_final: 0.6677 (mpt-90) outliers start: 34 outliers final: 22 residues processed: 239 average time/residue: 0.2161 time to fit residues: 79.6223 Evaluate side-chains 237 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 214 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1510 ASP Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 107 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 135 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 HIS ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 13403 Z= 0.183 Angle : 0.598 12.232 18110 Z= 0.308 Chirality : 0.043 0.344 2070 Planarity : 0.004 0.041 2194 Dihedral : 10.468 154.935 2105 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.27 % Allowed : 23.95 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.22), residues: 1556 helix: 0.91 (0.18), residues: 867 sheet: -0.28 (0.41), residues: 136 loop : -1.20 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1382 HIS 0.003 0.001 HIS C 136 PHE 0.023 0.001 PHE A 733 TYR 0.026 0.001 TYR B 32 ARG 0.007 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 224 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 PHE cc_start: 0.8094 (t80) cc_final: 0.7734 (t80) REVERT: A 157 TYR cc_start: 0.7922 (m-80) cc_final: 0.7429 (t80) REVERT: A 163 TYR cc_start: 0.7065 (m-80) cc_final: 0.6659 (m-80) REVERT: A 190 TRP cc_start: 0.8154 (m100) cc_final: 0.7889 (m100) REVERT: A 790 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7703 (tp30) REVERT: A 791 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7067 (tpt) REVERT: A 798 MET cc_start: 0.7217 (ppp) cc_final: 0.6933 (ppp) REVERT: A 1474 MET cc_start: 0.7666 (mtp) cc_final: 0.7093 (ttm) REVERT: A 1614 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8068 (mp) REVERT: A 1639 MET cc_start: 0.8331 (mmp) cc_final: 0.8069 (tpp) REVERT: B 184 LYS cc_start: 0.9148 (tptp) cc_final: 0.8890 (tptp) REVERT: C 113 MET cc_start: 0.2501 (mmt) cc_final: 0.1949 (ttp) REVERT: C 135 ARG cc_start: 0.6933 (mmp80) cc_final: 0.6707 (mpt-90) outliers start: 32 outliers final: 24 residues processed: 244 average time/residue: 0.2233 time to fit residues: 82.7405 Evaluate side-chains 241 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 215 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1510 ASP Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 107 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 20.0000 chunk 130 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 125 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN A 765 HIS A1762 ASN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13403 Z= 0.175 Angle : 0.610 12.538 18110 Z= 0.312 Chirality : 0.043 0.355 2070 Planarity : 0.004 0.041 2194 Dihedral : 10.333 154.691 2105 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.20 % Allowed : 24.59 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.22), residues: 1556 helix: 0.90 (0.18), residues: 866 sheet: -0.25 (0.42), residues: 136 loop : -1.17 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1382 HIS 0.008 0.001 HIS C 136 PHE 0.023 0.001 PHE A 733 TYR 0.026 0.001 TYR B 32 ARG 0.007 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 222 time to evaluate : 1.434 Fit side-chains revert: symmetry clash REVERT: A 128 PHE cc_start: 0.8097 (t80) cc_final: 0.7782 (t80) REVERT: A 157 TYR cc_start: 0.7913 (m-80) cc_final: 0.7418 (t80) REVERT: A 163 TYR cc_start: 0.7057 (m-80) cc_final: 0.6699 (m-80) REVERT: A 190 TRP cc_start: 0.8156 (m100) cc_final: 0.7900 (m100) REVERT: A 362 TYR cc_start: 0.8855 (t80) cc_final: 0.8578 (t80) REVERT: A 398 LEU cc_start: 0.8332 (mp) cc_final: 0.7971 (tt) REVERT: A 790 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7678 (tp30) REVERT: A 791 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7144 (tpt) REVERT: A 798 MET cc_start: 0.7225 (ppp) cc_final: 0.6918 (ppp) REVERT: A 1474 MET cc_start: 0.7626 (mtp) cc_final: 0.7045 (ttm) REVERT: A 1614 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8036 (mp) REVERT: A 1639 MET cc_start: 0.8479 (mmp) cc_final: 0.8040 (tpp) REVERT: B 184 LYS cc_start: 0.9167 (tptp) cc_final: 0.8907 (tptp) REVERT: C 113 MET cc_start: 0.2397 (mmt) cc_final: 0.1900 (ttp) REVERT: C 135 ARG cc_start: 0.6991 (mmp80) cc_final: 0.6718 (mpt-90) outliers start: 31 outliers final: 25 residues processed: 240 average time/residue: 0.2222 time to fit residues: 81.5782 Evaluate side-chains 242 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 215 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1510 ASP Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1762 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 107 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 20.0000 chunk 89 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 chunk 154 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 HIS ** A1762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13403 Z= 0.312 Angle : 0.673 14.771 18110 Z= 0.343 Chirality : 0.045 0.355 2070 Planarity : 0.005 0.040 2194 Dihedral : 10.561 154.201 2105 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.22 % Favored : 94.72 % Rotamer: Outliers : 2.20 % Allowed : 24.95 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.21), residues: 1556 helix: 0.75 (0.18), residues: 870 sheet: -0.38 (0.41), residues: 141 loop : -1.23 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1382 HIS 0.005 0.001 HIS B 134 PHE 0.033 0.002 PHE A1509 TYR 0.027 0.002 TYR B 32 ARG 0.007 0.001 ARG B 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 218 time to evaluate : 1.507 Fit side-chains revert: symmetry clash REVERT: A 128 PHE cc_start: 0.8248 (t80) cc_final: 0.7922 (t80) REVERT: A 157 TYR cc_start: 0.7944 (m-80) cc_final: 0.7483 (t80) REVERT: A 163 TYR cc_start: 0.7124 (m-80) cc_final: 0.6777 (m-80) REVERT: A 190 TRP cc_start: 0.8188 (m100) cc_final: 0.7979 (m100) REVERT: A 790 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7717 (tp30) REVERT: A 791 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7247 (tpt) REVERT: A 1639 MET cc_start: 0.8433 (mmp) cc_final: 0.8164 (tpp) REVERT: B 48 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.7883 (pm20) REVERT: B 184 LYS cc_start: 0.9143 (tptp) cc_final: 0.8886 (tptp) REVERT: C 113 MET cc_start: 0.2331 (mmt) cc_final: 0.1931 (ttp) REVERT: C 135 ARG cc_start: 0.7090 (mmp80) cc_final: 0.6789 (mpt-90) outliers start: 31 outliers final: 27 residues processed: 237 average time/residue: 0.2175 time to fit residues: 80.0992 Evaluate side-chains 242 residues out of total 1407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 213 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 278 ASN Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1510 ASP Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1695 THR Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 107 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 HIS ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.151889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.107791 restraints weight = 40466.820| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.80 r_work: 0.3345 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13403 Z= 0.192 Angle : 0.643 15.120 18110 Z= 0.324 Chirality : 0.044 0.375 2070 Planarity : 0.004 0.041 2194 Dihedral : 10.409 155.062 2105 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.27 % Allowed : 24.73 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.22), residues: 1556 helix: 0.81 (0.18), residues: 868 sheet: -0.39 (0.41), residues: 142 loop : -1.18 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1382 HIS 0.015 0.002 HIS A 765 PHE 0.047 0.001 PHE A1452 TYR 0.027 0.001 TYR B 32 ARG 0.007 0.001 ARG B 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3189.56 seconds wall clock time: 57 minutes 23.08 seconds (3443.08 seconds total)