Starting phenix.real_space_refine on Sat Feb 24 02:41:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdv_31926/02_2024/7vdv_31926_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdv_31926/02_2024/7vdv_31926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdv_31926/02_2024/7vdv_31926.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdv_31926/02_2024/7vdv_31926.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdv_31926/02_2024/7vdv_31926_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdv_31926/02_2024/7vdv_31926_updated.pdb" } resolution = 3.4 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 976 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 274 5.49 5 Mg 1 5.21 5 S 173 5.16 5 Be 1 3.05 5 C 24443 2.51 5 N 7154 2.21 5 O 7979 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 17": "NH1" <-> "NH2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D ASP 68": "OD1" <-> "OD2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E ASP 77": "OD1" <-> "OD2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 68": "OD1" <-> "OD2" Residue "H TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "H TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 181": "NH1" <-> "NH2" Residue "A TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 441": "NH1" <-> "NH2" Residue "A ARG 444": "NH1" <-> "NH2" Residue "A GLU 454": "OE1" <-> "OE2" Residue "A TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 485": "OD1" <-> "OD2" Residue "A TYR 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 801": "NH1" <-> "NH2" Residue "A TYR 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 821": "OE1" <-> "OE2" Residue "A ARG 842": "NH1" <-> "NH2" Residue "A ARG 849": "NH1" <-> "NH2" Residue "A GLU 861": "OE1" <-> "OE2" Residue "A ARG 874": "NH1" <-> "NH2" Residue "A GLU 882": "OE1" <-> "OE2" Residue "A TYR 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 955": "OD1" <-> "OD2" Residue "A ARG 966": "NH1" <-> "NH2" Residue "A ARG 967": "NH1" <-> "NH2" Residue "A ARG 973": "NH1" <-> "NH2" Residue "A PHE 975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 979": "NH1" <-> "NH2" Residue "A GLU 993": "OE1" <-> "OE2" Residue "A ASP 999": "OD1" <-> "OD2" Residue "A ARG 1005": "NH1" <-> "NH2" Residue "A TYR 1008": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1043": "NH1" <-> "NH2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1056": "OE1" <-> "OE2" Residue "A ASP 1074": "OD1" <-> "OD2" Residue "A PHE 1116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1119": "NH1" <-> "NH2" Residue "A PHE 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "A GLU 1148": "OE1" <-> "OE2" Residue "A PHE 1174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1177": "OD1" <-> "OD2" Residue "A ARG 1189": "NH1" <-> "NH2" Residue "A ARG 1192": "NH1" <-> "NH2" Residue "A GLU 1198": "OE1" <-> "OE2" Residue "A ARG 1200": "NH1" <-> "NH2" Residue "A GLU 1212": "OE1" <-> "OE2" Residue "A TYR 1220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1260": "OE1" <-> "OE2" Residue "A GLU 1279": "OE1" <-> "OE2" Residue "A GLU 1307": "OE1" <-> "OE2" Residue "A PHE 1334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1336": "NH1" <-> "NH2" Residue "A ARG 1341": "NH1" <-> "NH2" Residue "A ASP 1345": "OD1" <-> "OD2" Residue "A TYR 1346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 80": "OE1" <-> "OE2" Residue "N GLU 114": "OE1" <-> "OE2" Residue "N GLU 300": "OE1" <-> "OE2" Residue "P GLU 125": "OE1" <-> "OE2" Residue "P GLU 167": "OE1" <-> "OE2" Residue "P GLU 205": "OE1" <-> "OE2" Residue "P PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 334": "OE1" <-> "OE2" Residue "Q GLU 44": "OE1" <-> "OE2" Residue "Q PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 95": "NH1" <-> "NH2" Residue "Q TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 110": "OD1" <-> "OD2" Residue "Q ASP 111": "OD1" <-> "OD2" Residue "Q GLU 112": "OE1" <-> "OE2" Residue "Q TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 140": "OD1" <-> "OD2" Residue "Q ASP 174": "OD1" <-> "OD2" Residue "Q PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 224": "OE1" <-> "OE2" Residue "Q GLU 227": "OE1" <-> "OE2" Residue "Q ARG 231": "NH1" <-> "NH2" Residue "Q ASP 242": "OD1" <-> "OD2" Residue "Q PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 366": "NH1" <-> "NH2" Residue "Q PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 396": "OD1" <-> "OD2" Residue "Q TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 427": "OE1" <-> "OE2" Residue "Q ASP 430": "OD1" <-> "OD2" Residue "Q ASP 453": "OD1" <-> "OD2" Residue "Q PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 1758": "OD1" <-> "OD2" Residue "R TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 209": "OE1" <-> "OE2" Residue "R ARG 216": "NH1" <-> "NH2" Residue "R TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 264": "OE1" <-> "OE2" Residue "R GLU 285": "OE1" <-> "OE2" Residue "T GLU 132": "OE1" <-> "OE2" Residue "T ARG 145": "NH1" <-> "NH2" Residue "T ASP 151": "OD1" <-> "OD2" Residue "T PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 162": "OD1" <-> "OD2" Residue "T PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 214": "OE1" <-> "OE2" Residue "T TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 390": "OE1" <-> "OE2" Residue "T ARG 393": "NH1" <-> "NH2" Residue "T TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 540": "OE1" <-> "OE2" Residue "T PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 548": "OE1" <-> "OE2" Residue "T GLU 558": "OE1" <-> "OE2" Residue "T ARG 563": "NH1" <-> "NH2" Residue "T TYR 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 595": "OE1" <-> "OE2" Residue "T ASP 604": "OD1" <-> "OD2" Residue "T ARG 612": "NH1" <-> "NH2" Residue "V ARG 158": "NH1" <-> "NH2" Residue "V PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 170": "OD1" <-> "OD2" Residue "V ARG 190": "NH1" <-> "NH2" Residue "V ASP 192": "OD1" <-> "OD2" Residue "V ARG 201": "NH1" <-> "NH2" Residue "V PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 261": "NH1" <-> "NH2" Residue "V PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 282": "OD1" <-> "OD2" Residue "V GLU 287": "OE1" <-> "OE2" Residue "V GLU 330": "OE1" <-> "OE2" Residue "V ASP 347": "OD1" <-> "OD2" Residue "V ASP 358": "OD1" <-> "OD2" Residue "W PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 443": "NH1" <-> "NH2" Residue "W PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 487": "NH1" <-> "NH2" Residue "W TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 599": "NH1" <-> "NH2" Residue "W ASP 619": "OD1" <-> "OD2" Residue "W ARG 630": "NH1" <-> "NH2" Residue "W GLU 900": "OE1" <-> "OE2" Residue "W ASP 914": "OD1" <-> "OD2" Residue "W ARG 917": "NH1" <-> "NH2" Residue "W PHE 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 937": "OE1" <-> "OE2" Residue "X PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 466": "NH1" <-> "NH2" Residue "X TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 505": "OE1" <-> "OE2" Residue "X GLU 517": "OE1" <-> "OE2" Residue "X TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 645": "OE1" <-> "OE2" Residue "X ARG 882": "NH1" <-> "NH2" Residue "X GLU 910": "OE1" <-> "OE2" Residue "X ASP 914": "OD1" <-> "OD2" Residue "Y GLU 154": "OE1" <-> "OE2" Residue "Y ARG 155": "NH1" <-> "NH2" Residue "Y ASP 158": "OD1" <-> "OD2" Residue "Y ARG 163": "NH1" <-> "NH2" Residue "Y GLU 426": "OE1" <-> "OE2" Residue "Y ARG 446": "NH1" <-> "NH2" Residue "Y ASP 462": "OD1" <-> "OD2" Residue "Y PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 489": "OE1" <-> "OE2" Residue "Y TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 502": "NH1" <-> "NH2" Residue "Y ARG 503": "NH1" <-> "NH2" Residue "Z ARG 195": "NH1" <-> "NH2" Residue "Z ARG 198": "NH1" <-> "NH2" Residue "Z ARG 201": "NH1" <-> "NH2" Residue "Z ARG 223": "NH1" <-> "NH2" Residue "Z GLU 242": "OE1" <-> "OE2" Residue "Z GLU 249": "OE1" <-> "OE2" Residue "Z GLU 261": "OE1" <-> "OE2" Residue "a PHE 1594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 1620": "OE1" <-> "OE2" Residue "a ASP 1628": "OD1" <-> "OD2" Residue "a ARG 1636": "NH1" <-> "NH2" Residue "a ARG 1670": "NH1" <-> "NH2" Residue "a ASP 1671": "OD1" <-> "OD2" Residue "K TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 105": "OE1" <-> "OE2" Residue "K ASP 106": "OD1" <-> "OD2" Residue "K ASP 123": "OD1" <-> "OD2" Residue "K GLU 133": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 40028 Number of models: 1 Model: "" Number of chains: 25 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 717 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2752 Classifications: {'DNA': 135} Link IDs: {'rna3p': 134} Chain: "J" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2827 Classifications: {'DNA': 137} Link IDs: {'rna3p': 136} Chain: "A" Number of atoms: 6652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6652 Classifications: {'peptide': 809} Link IDs: {'PTRANS': 26, 'TRANS': 782} Chain breaks: 5 Chain: "N" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2612 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 15, 'TRANS': 318} Chain breaks: 4 Chain: "P" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2482 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain breaks: 3 Chain: "Q" Number of atoms: 3981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3981 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 14, 'TRANS': 485} Chain breaks: 4 Chain: "R" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 771 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 8, 'TRANS': 83} Chain: "T" Number of atoms: 2166 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 267, 2147 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 15, 'TRANS': 251} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 267, 2147 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 15, 'TRANS': 251} Chain breaks: 2 bond proxies already assigned to first conformer: 2164 Chain: "U" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 35 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Chain: "V" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1910 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 13, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "W" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 2056 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 6, 'TRANS': 241} Chain breaks: 2 Chain: "X" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2072 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 14, 'TRANS': 237} Chain breaks: 2 Chain: "Y" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 2057 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 14, 'TRANS': 230} Chain breaks: 2 Chain: "Z" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 757 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "a" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 750 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER T 239 " occ=0.35 ... (10 atoms not shown) pdb=" OG BSER T 239 " occ=0.65 residue: pdb=" N ASER T 243 " occ=0.43 ... (10 atoms not shown) pdb=" OG BSER T 243 " occ=0.57 Time building chain proxies: 21.00, per 1000 atoms: 0.52 Number of scatterers: 40028 At special positions: 0 Unit cell: (238.15, 184.025, 227.325, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 173 16.00 P 274 15.00 Mg 1 11.99 F 3 9.00 O 7979 8.00 N 7154 7.00 C 24443 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.21 Conformation dependent library (CDL) restraints added in 7.0 seconds 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8178 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 193 helices and 12 sheets defined 55.2% alpha, 3.2% beta 109 base pairs and 187 stacking pairs defined. Time for finding SS restraints: 17.80 Creating SS restraints... Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 50 through 76 Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.438A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'D' and resid 38 through 48 Processing helix chain 'D' and resid 56 through 83 Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.598A pdb=" N LYS D 108 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER D 123 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.946A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.026A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 114 removed outlier: 3.583A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 50 through 76 Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.468A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 56 through 83 Processing helix chain 'H' and resid 91 through 101 Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.903A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 192 removed outlier: 4.153A pdb=" N LEU A 180 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 363 through 386 Processing helix chain 'A' and resid 395 through 422 removed outlier: 3.510A pdb=" N ILE A 402 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N PHE A 412 " --> pdb=" O ARG A 408 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 515 removed outlier: 4.289A pdb=" N GLU A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LYS A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN A 459 " --> pdb=" O LYS A 455 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN A 473 " --> pdb=" O ARG A 469 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 479 " --> pdb=" O TYR A 475 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR A 511 " --> pdb=" O TYR A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 removed outlier: 3.528A pdb=" N ALA A 551 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR A 552 " --> pdb=" O LYS A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 735 No H-bonds generated for 'chain 'A' and resid 732 through 735' Processing helix chain 'A' and resid 756 through 771 removed outlier: 3.509A pdb=" N LEU A 765 " --> pdb=" O GLY A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 798 Processing helix chain 'A' and resid 812 through 824 removed outlier: 4.256A pdb=" N SER A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN A 817 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 850 removed outlier: 3.508A pdb=" N ALA A 843 " --> pdb=" O ALA A 839 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE A 844 " --> pdb=" O ALA A 840 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL A 845 " --> pdb=" O ARG A 841 " (cutoff:3.500A) Proline residue: A 846 - end of helix Processing helix chain 'A' and resid 860 through 865 Processing helix chain 'A' and resid 867 through 870 No H-bonds generated for 'chain 'A' and resid 867 through 870' Processing helix chain 'A' and resid 883 through 886 Processing helix chain 'A' and resid 892 through 900 Processing helix chain 'A' and resid 918 through 928 removed outlier: 3.998A pdb=" N LEU A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 925 " --> pdb=" O LEU A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 933 No H-bonds generated for 'chain 'A' and resid 930 through 933' Processing helix chain 'A' and resid 963 through 971 Processing helix chain 'A' and resid 973 through 975 No H-bonds generated for 'chain 'A' and resid 973 through 975' Processing helix chain 'A' and resid 981 through 984 No H-bonds generated for 'chain 'A' and resid 981 through 984' Processing helix chain 'A' and resid 1002 through 1013 removed outlier: 3.567A pdb=" N VAL A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1047 Processing helix chain 'A' and resid 1050 through 1052 No H-bonds generated for 'chain 'A' and resid 1050 through 1052' Processing helix chain 'A' and resid 1054 through 1062 removed outlier: 3.627A pdb=" N SER A1058 " --> pdb=" O HIS A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1078 Processing helix chain 'A' and resid 1080 through 1095 removed outlier: 3.564A pdb=" N LEU A1084 " --> pdb=" O GLY A1080 " (cutoff:3.500A) Proline residue: A1090 - end of helix Processing helix chain 'A' and resid 1106 through 1118 removed outlier: 3.591A pdb=" N ILE A1111 " --> pdb=" O SER A1107 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A1117 " --> pdb=" O GLU A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1143 removed outlier: 3.966A pdb=" N GLY A1136 " --> pdb=" O ALA A1132 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET A1137 " --> pdb=" O GLU A1133 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS A1140 " --> pdb=" O GLY A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1159 No H-bonds generated for 'chain 'A' and resid 1156 through 1159' Processing helix chain 'A' and resid 1180 through 1189 removed outlier: 3.537A pdb=" N ASP A1188 " --> pdb=" O LEU A1184 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A1189 " --> pdb=" O GLN A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1228 removed outlier: 3.506A pdb=" N ASN A1223 " --> pdb=" O LYS A1219 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL A1224 " --> pdb=" O TYR A1220 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASP A1225 " --> pdb=" O LYS A1221 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN A1226 " --> pdb=" O LEU A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1254 removed outlier: 3.619A pdb=" N ALA A1249 " --> pdb=" O ALA A1245 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A1250 " --> pdb=" O PHE A1246 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU A1251 " --> pdb=" O LEU A1247 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLU A1252 " --> pdb=" O GLN A1248 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N HIS A1253 " --> pdb=" O ALA A1249 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU A1254 " --> pdb=" O ILE A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1273 Processing helix chain 'A' and resid 1277 through 1291 removed outlier: 3.669A pdb=" N ARG A1285 " --> pdb=" O ASP A1281 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET A1286 " --> pdb=" O LEU A1282 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU A1288 " --> pdb=" O MET A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1296 No H-bonds generated for 'chain 'A' and resid 1294 through 1296' Processing helix chain 'A' and resid 1307 through 1309 No H-bonds generated for 'chain 'A' and resid 1307 through 1309' Processing helix chain 'A' and resid 1311 through 1314 No H-bonds generated for 'chain 'A' and resid 1311 through 1314' Processing helix chain 'N' and resid 73 through 76 Processing helix chain 'N' and resid 96 through 109 removed outlier: 3.562A pdb=" N ALA N 101 " --> pdb=" O ASP N 97 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS N 108 " --> pdb=" O ASP N 104 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 141 removed outlier: 3.614A pdb=" N MET N 140 " --> pdb=" O LEU N 136 " (cutoff:3.500A) Processing helix chain 'N' and resid 154 through 162 Processing helix chain 'N' and resid 199 through 212 Processing helix chain 'N' and resid 248 through 265 removed outlier: 3.522A pdb=" N MET N 254 " --> pdb=" O TRP N 250 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N CYS N 255 " --> pdb=" O HIS N 251 " (cutoff:3.500A) Processing helix chain 'N' and resid 300 through 302 No H-bonds generated for 'chain 'N' and resid 300 through 302' Processing helix chain 'N' and resid 304 through 309 Processing helix chain 'N' and resid 325 through 334 Processing helix chain 'N' and resid 341 through 346 Processing helix chain 'N' and resid 353 through 356 Processing helix chain 'N' and resid 361 through 370 removed outlier: 3.556A pdb=" N ARG N 366 " --> pdb=" O ASP N 362 " (cutoff:3.500A) Processing helix chain 'N' and resid 387 through 389 No H-bonds generated for 'chain 'N' and resid 387 through 389' Processing helix chain 'N' and resid 392 through 400 Processing helix chain 'N' and resid 405 through 408 No H-bonds generated for 'chain 'N' and resid 405 through 408' Processing helix chain 'P' and resid 3 through 6 No H-bonds generated for 'chain 'P' and resid 3 through 6' Processing helix chain 'P' and resid 80 through 90 removed outlier: 3.610A pdb=" N THR P 89 " --> pdb=" O ILE P 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 113 through 124 removed outlier: 3.601A pdb=" N THR P 120 " --> pdb=" O ARG P 116 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN P 121 " --> pdb=" O GLU P 117 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET P 123 " --> pdb=" O MET P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 145 removed outlier: 3.524A pdb=" N ALA P 144 " --> pdb=" O LEU P 140 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER P 145 " --> pdb=" O SER P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 182 through 193 removed outlier: 3.509A pdb=" N LEU P 193 " --> pdb=" O LEU P 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 203 through 215 removed outlier: 3.659A pdb=" N ILE P 208 " --> pdb=" O ALA P 204 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL P 209 " --> pdb=" O GLU P 205 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ARG P 210 " --> pdb=" O ARG P 206 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASP P 211 " --> pdb=" O GLU P 207 " (cutoff:3.500A) Processing helix chain 'P' and resid 223 through 230 Processing helix chain 'P' and resid 253 through 261 Proline residue: P 258 - end of helix removed outlier: 4.951A pdb=" N LEU P 261 " --> pdb=" O CYS P 257 " (cutoff:3.500A) Processing helix chain 'P' and resid 264 through 267 No H-bonds generated for 'chain 'P' and resid 264 through 267' Processing helix chain 'P' and resid 274 through 284 removed outlier: 3.615A pdb=" N MET P 283 " --> pdb=" O PHE P 279 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS P 284 " --> pdb=" O ASN P 280 " (cutoff:3.500A) Processing helix chain 'P' and resid 290 through 294 Processing helix chain 'P' and resid 302 through 304 No H-bonds generated for 'chain 'P' and resid 302 through 304' Processing helix chain 'P' and resid 309 through 320 Processing helix chain 'P' and resid 338 through 346 removed outlier: 3.524A pdb=" N GLY P 343 " --> pdb=" O VAL P 339 " (cutoff:3.500A) Processing helix chain 'P' and resid 353 through 355 No H-bonds generated for 'chain 'P' and resid 353 through 355' Processing helix chain 'P' and resid 359 through 365 removed outlier: 3.692A pdb=" N ASP P 363 " --> pdb=" O LYS P 359 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU P 364 " --> pdb=" O GLN P 360 " (cutoff:3.500A) Processing helix chain 'P' and resid 367 through 370 Processing helix chain 'Q' and resid 20 through 29 Processing helix chain 'Q' and resid 53 through 56 No H-bonds generated for 'chain 'Q' and resid 53 through 56' Processing helix chain 'Q' and resid 60 through 66 removed outlier: 3.827A pdb=" N GLU Q 65 " --> pdb=" O ALA Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 76 removed outlier: 4.079A pdb=" N GLU Q 74 " --> pdb=" O GLU Q 71 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU Q 75 " --> pdb=" O ILE Q 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 97 removed outlier: 3.626A pdb=" N TYR Q 96 " --> pdb=" O TYR Q 92 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 103 Processing helix chain 'Q' and resid 133 through 136 removed outlier: 3.704A pdb=" N HIS Q 136 " --> pdb=" O TYR Q 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 133 through 136' Processing helix chain 'Q' and resid 141 through 146 Processing helix chain 'Q' and resid 159 through 167 Processing helix chain 'Q' and resid 170 through 184 Processing helix chain 'Q' and resid 199 through 207 Processing helix chain 'Q' and resid 223 through 229 Processing helix chain 'Q' and resid 233 through 240 Processing helix chain 'Q' and resid 244 through 250 removed outlier: 4.260A pdb=" N LEU Q 249 " --> pdb=" O GLU Q 245 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE Q 250 " --> pdb=" O VAL Q 246 " (cutoff:3.500A) Processing helix chain 'Q' and resid 281 through 298 removed outlier: 3.566A pdb=" N VAL Q 291 " --> pdb=" O LEU Q 287 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE Q 292 " --> pdb=" O GLN Q 288 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU Q 293 " --> pdb=" O ILE Q 289 " (cutoff:3.500A) Processing helix chain 'Q' and resid 300 through 308 removed outlier: 3.929A pdb=" N LYS Q 304 " --> pdb=" O GLU Q 300 " (cutoff:3.500A) Processing helix chain 'Q' and resid 311 through 320 Processing helix chain 'Q' and resid 325 through 340 removed outlier: 3.822A pdb=" N LEU Q 330 " --> pdb=" O SER Q 326 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA Q 340 " --> pdb=" O GLY Q 336 " (cutoff:3.500A) Processing helix chain 'Q' and resid 349 through 360 Processing helix chain 'Q' and resid 368 through 381 removed outlier: 3.637A pdb=" N ILE Q 377 " --> pdb=" O ARG Q 373 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU Q 378 " --> pdb=" O GLY Q 374 " (cutoff:3.500A) Processing helix chain 'Q' and resid 390 through 392 No H-bonds generated for 'chain 'Q' and resid 390 through 392' Processing helix chain 'Q' and resid 400 through 408 removed outlier: 4.164A pdb=" N LEU Q 407 " --> pdb=" O ILE Q 403 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR Q 408 " --> pdb=" O ILE Q 404 " (cutoff:3.500A) Processing helix chain 'Q' and resid 412 through 428 removed outlier: 3.781A pdb=" N VAL Q 421 " --> pdb=" O SER Q 417 " (cutoff:3.500A) Processing helix chain 'Q' and resid 430 through 438 removed outlier: 4.703A pdb=" N ALA Q 437 " --> pdb=" O CYS Q 433 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS Q 438 " --> pdb=" O THR Q 434 " (cutoff:3.500A) Processing helix chain 'Q' and resid 443 through 451 Processing helix chain 'Q' and resid 461 through 464 removed outlier: 3.914A pdb=" N ALA Q 464 " --> pdb=" O ALA Q 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 461 through 464' Processing helix chain 'Q' and resid 1763 through 1781 removed outlier: 3.861A pdb=" N LEU Q1776 " --> pdb=" O ALA Q1772 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1784 through 1803 removed outlier: 3.868A pdb=" N ARG Q1788 " --> pdb=" O GLU Q1784 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU Q1789 " --> pdb=" O CYS Q1785 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ARG Q1792 " --> pdb=" O ARG Q1788 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N HIS Q1793 " --> pdb=" O LEU Q1789 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU Q1794 " --> pdb=" O LEU Q1790 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASN Q1795 " --> pdb=" O LYS Q1791 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ASN Q1796 " --> pdb=" O ARG Q1792 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU Q1800 " --> pdb=" O ASN Q1796 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1808 through 1820 removed outlier: 3.871A pdb=" N LYS Q1813 " --> pdb=" O SER Q1809 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU Q1815 " --> pdb=" O LEU Q1811 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR Q1816 " --> pdb=" O ALA Q1812 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU Q1817 " --> pdb=" O LYS Q1813 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 218 removed outlier: 3.592A pdb=" N GLU R 217 " --> pdb=" O ASN R 213 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG R 218 " --> pdb=" O LEU R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 239 No H-bonds generated for 'chain 'R' and resid 237 through 239' Processing helix chain 'R' and resid 271 through 276 removed outlier: 3.649A pdb=" N TYR R 276 " --> pdb=" O ASP R 272 " (cutoff:3.500A) Processing helix chain 'T' and resid 135 through 150 removed outlier: 3.557A pdb=" N LEU T 143 " --> pdb=" O ALA T 139 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 171 No H-bonds generated for 'chain 'T' and resid 168 through 171' Processing helix chain 'T' and resid 178 through 187 removed outlier: 3.872A pdb=" N GLU T 183 " --> pdb=" O SER T 179 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS T 186 " --> pdb=" O LYS T 182 " (cutoff:3.500A) Processing helix chain 'T' and resid 193 through 210 removed outlier: 3.513A pdb=" N CYS T 204 " --> pdb=" O PHE T 200 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN T 206 " --> pdb=" O LEU T 202 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA T 207 " --> pdb=" O MET T 203 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET T 208 " --> pdb=" O CYS T 204 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE T 209 " --> pdb=" O THR T 205 " (cutoff:3.500A) Processing helix chain 'T' and resid 216 through 220 removed outlier: 3.547A pdb=" N ALA T 220 " --> pdb=" O TYR T 217 " (cutoff:3.500A) Processing helix chain 'T' and resid 222 through 231 Processing helix chain 'T' and resid 234 through 247 removed outlier: 3.712A pdb=" N ASER T 243 " --> pdb=" O ASER T 239 " (cutoff:3.500A) Processing helix chain 'T' and resid 370 through 372 No H-bonds generated for 'chain 'T' and resid 370 through 372' Processing helix chain 'T' and resid 423 through 431 removed outlier: 3.919A pdb=" N TYR T 430 " --> pdb=" O SER T 426 " (cutoff:3.500A) Processing helix chain 'T' and resid 537 through 565 removed outlier: 3.503A pdb=" N SER T 565 " --> pdb=" O ASN T 561 " (cutoff:3.500A) Processing helix chain 'T' and resid 580 through 598 removed outlier: 3.698A pdb=" N GLN T 598 " --> pdb=" O LYS T 594 " (cutoff:3.500A) Processing helix chain 'V' and resid 138 through 142 Processing helix chain 'V' and resid 160 through 162 No H-bonds generated for 'chain 'V' and resid 160 through 162' Processing helix chain 'V' and resid 168 through 170 No H-bonds generated for 'chain 'V' and resid 168 through 170' Processing helix chain 'V' and resid 173 through 181 Processing helix chain 'V' and resid 215 through 226 Processing helix chain 'V' and resid 230 through 247 Proline residue: V 235 - end of helix removed outlier: 3.776A pdb=" N GLU V 246 " --> pdb=" O ARG V 242 " (cutoff:3.500A) Processing helix chain 'V' and resid 290 through 301 Processing helix chain 'V' and resid 305 through 325 removed outlier: 3.811A pdb=" N THR V 310 " --> pdb=" O PHE V 307 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA V 312 " --> pdb=" O THR V 309 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE V 315 " --> pdb=" O ALA V 312 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU V 319 " --> pdb=" O ARG V 316 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER V 320 " --> pdb=" O GLY V 317 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN V 323 " --> pdb=" O SER V 320 " (cutoff:3.500A) Processing helix chain 'V' and resid 347 through 349 No H-bonds generated for 'chain 'V' and resid 347 through 349' Processing helix chain 'V' and resid 358 through 380 removed outlier: 4.038A pdb=" N ASP V 369 " --> pdb=" O ILE V 365 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG V 370 " --> pdb=" O ARG V 366 " (cutoff:3.500A) Processing helix chain 'W' and resid 440 through 445 Processing helix chain 'W' and resid 447 through 450 Processing helix chain 'W' and resid 459 through 476 removed outlier: 4.058A pdb=" N LEU W 463 " --> pdb=" O PRO W 459 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA W 464 " --> pdb=" O GLU W 460 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN W 476 " --> pdb=" O THR W 472 " (cutoff:3.500A) Processing helix chain 'W' and resid 483 through 487 Processing helix chain 'W' and resid 494 through 506 Processing helix chain 'W' and resid 603 through 616 removed outlier: 4.411A pdb=" N MET W 615 " --> pdb=" O GLU W 611 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR W 616 " --> pdb=" O ALA W 612 " (cutoff:3.500A) Processing helix chain 'W' and resid 620 through 627 Processing helix chain 'W' and resid 632 through 641 Processing helix chain 'W' and resid 646 through 649 No H-bonds generated for 'chain 'W' and resid 646 through 649' Processing helix chain 'W' and resid 859 through 949 removed outlier: 3.567A pdb=" N GLU W 881 " --> pdb=" O ALA W 877 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL W 892 " --> pdb=" O VAL W 888 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU W 893 " --> pdb=" O ALA W 889 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS W 905 " --> pdb=" O ILE W 901 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG W 915 " --> pdb=" O THR W 911 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG W 917 " --> pdb=" O MET W 913 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU W 918 " --> pdb=" O ASP W 914 " (cutoff:3.500A) Processing helix chain 'X' and resid 440 through 445 Processing helix chain 'X' and resid 447 through 451 Processing helix chain 'X' and resid 459 through 476 removed outlier: 3.542A pdb=" N ARG X 466 " --> pdb=" O TYR X 462 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN X 467 " --> pdb=" O LEU X 463 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE X 468 " --> pdb=" O ALA X 464 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASN X 476 " --> pdb=" O THR X 472 " (cutoff:3.500A) Processing helix chain 'X' and resid 483 through 487 Processing helix chain 'X' and resid 494 through 506 Processing helix chain 'X' and resid 603 through 616 removed outlier: 3.809A pdb=" N LEU X 613 " --> pdb=" O LEU X 609 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU X 614 " --> pdb=" O LEU X 610 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET X 615 " --> pdb=" O GLU X 611 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N TYR X 616 " --> pdb=" O ALA X 612 " (cutoff:3.500A) Processing helix chain 'X' and resid 624 through 627 No H-bonds generated for 'chain 'X' and resid 624 through 627' Processing helix chain 'X' and resid 632 through 641 Processing helix chain 'X' and resid 869 through 913 removed outlier: 3.636A pdb=" N ALA X 878 " --> pdb=" O LYS X 874 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL X 879 " --> pdb=" O HIS X 875 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU X 880 " --> pdb=" O LEU X 876 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG X 882 " --> pdb=" O ALA X 878 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS X 883 " --> pdb=" O VAL X 879 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE X 884 " --> pdb=" O GLU X 880 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE X 906 " --> pdb=" O LYS X 902 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU X 907 " --> pdb=" O LEU X 903 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU X 908 " --> pdb=" O ARG X 904 " (cutoff:3.500A) Processing helix chain 'X' and resid 915 through 946 removed outlier: 3.852A pdb=" N HIS X 935 " --> pdb=" O ARG X 931 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET X 936 " --> pdb=" O GLN X 932 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU X 937 " --> pdb=" O ALA X 933 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 140 removed outlier: 3.796A pdb=" N LEU Y 140 " --> pdb=" O ARG Y 136 " (cutoff:3.500A) Processing helix chain 'Y' and resid 144 through 171 removed outlier: 3.501A pdb=" N MET Y 148 " --> pdb=" O SER Y 144 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET Y 162 " --> pdb=" O ASP Y 158 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG Y 163 " --> pdb=" O GLN Y 159 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU Y 170 " --> pdb=" O LEU Y 166 " (cutoff:3.500A) Processing helix chain 'Y' and resid 299 through 305 removed outlier: 3.646A pdb=" N LEU Y 304 " --> pdb=" O ARG Y 300 " (cutoff:3.500A) Processing helix chain 'Y' and resid 312 through 326 removed outlier: 3.670A pdb=" N ILE Y 316 " --> pdb=" O ARG Y 312 " (cutoff:3.500A) Processing helix chain 'Y' and resid 357 through 362 Processing helix chain 'Y' and resid 400 through 413 removed outlier: 3.802A pdb=" N PHE Y 407 " --> pdb=" O MET Y 404 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR Y 411 " --> pdb=" O LEU Y 408 " (cutoff:3.500A) Processing helix chain 'Y' and resid 416 through 446 removed outlier: 3.607A pdb=" N GLN Y 437 " --> pdb=" O GLN Y 433 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG Y 438 " --> pdb=" O LEU Y 434 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU Y 439 " --> pdb=" O LYS Y 435 " (cutoff:3.500A) Processing helix chain 'Y' and resid 448 through 465 Processing helix chain 'Y' and resid 479 through 483 Processing helix chain 'Y' and resid 485 through 510 removed outlier: 4.023A pdb=" N VAL Y 491 " --> pdb=" O GLN Y 488 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG Y 493 " --> pdb=" O ALA Y 490 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN Y 501 " --> pdb=" O LYS Y 498 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG Y 503 " --> pdb=" O GLN Y 500 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLN Y 504 " --> pdb=" O GLN Y 501 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 199 removed outlier: 3.503A pdb=" N ALA Z 192 " --> pdb=" O LYS Z 189 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR Z 193 " --> pdb=" O HIS Z 190 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG Z 195 " --> pdb=" O ALA Z 192 " (cutoff:3.500A) Processing helix chain 'Z' and resid 221 through 275 removed outlier: 3.589A pdb=" N MET Z 235 " --> pdb=" O VAL Z 231 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA Z 243 " --> pdb=" O ARG Z 239 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU Z 244 " --> pdb=" O LYS Z 240 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN Z 253 " --> pdb=" O GLU Z 249 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY Z 275 " --> pdb=" O LYS Z 271 " (cutoff:3.500A) Processing helix chain 'a' and resid 1602 through 1615 Processing helix chain 'a' and resid 1627 through 1632 Processing helix chain 'a' and resid 1643 through 1646 No H-bonds generated for 'chain 'a' and resid 1643 through 1646' Processing helix chain 'a' and resid 1650 through 1652 No H-bonds generated for 'chain 'a' and resid 1650 through 1652' Processing helix chain 'a' and resid 1663 through 1678 removed outlier: 4.013A pdb=" N ASP a1671 " --> pdb=" O TRP a1667 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU a1672 " --> pdb=" O ARG a1668 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR a1677 " --> pdb=" O MET a1673 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 54 removed outlier: 4.237A pdb=" N GLU K 50 " --> pdb=" O VAL K 46 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE K 51 " --> pdb=" O ALA K 47 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG K 52 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG K 53 " --> pdb=" O ARG K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 78 removed outlier: 4.279A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE K 78 " --> pdb=" O ILE K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 114 removed outlier: 3.877A pdb=" N ASP K 106 " --> pdb=" O ALA K 102 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS K 113 " --> pdb=" O LEU K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 131 Processing helix chain 'M' and resid 312 through 325 removed outlier: 3.691A pdb=" N UNK M 325 " --> pdb=" O UNK M 321 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 905 through 908 removed outlier: 6.812A pdb=" N LEU A 807 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU A 856 " --> pdb=" O ILE A 808 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL A 810 " --> pdb=" O LEU A 856 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N THR A 858 " --> pdb=" O VAL A 810 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 992 through 996 removed outlier: 7.914A pdb=" N VAL A1171 " --> pdb=" O LEU A1202 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU A1204 " --> pdb=" O VAL A1171 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE A1173 " --> pdb=" O LEU A1204 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE A1152 " --> pdb=" O VAL A1099 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER A1155 " --> pdb=" O LEU A1126 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'N' and resid 119 through 121 removed outlier: 3.655A pdb=" N PHE N 37 " --> pdb=" O VAL N 23 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'N' and resid 41 through 43 Processing sheet with id= E, first strand: chain 'N' and resid 348 through 351 removed outlier: 6.596A pdb=" N LEU N 168 " --> pdb=" O ILE N 349 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ALA N 351 " --> pdb=" O LEU N 168 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU N 170 " --> pdb=" O ALA N 351 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR N 177 " --> pdb=" O SER N 195 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'P' and resid 8 through 11 Processing sheet with id= G, first strand: chain 'P' and resid 103 through 107 removed outlier: 3.550A pdb=" N TYR P 133 " --> pdb=" O VAL P 103 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'P' and resid 297 through 300 removed outlier: 6.701A pdb=" N ILE P 151 " --> pdb=" O VAL P 298 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N SER P 300 " --> pdb=" O ILE P 151 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N MET P 153 " --> pdb=" O SER P 300 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR P 160 " --> pdb=" O LEU P 178 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'R' and resid 224 through 226 Processing sheet with id= J, first strand: chain 'V' and resid 186 through 191 Processing sheet with id= K, first strand: chain 'V' and resid 262 through 270 Processing sheet with id= L, first strand: chain 'Y' and resid 336 through 338 1467 hydrogen bonds defined for protein. 4138 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 257 hydrogen bonds 470 hydrogen bond angles 0 basepair planarities 109 basepair parallelities 187 stacking parallelities Total time for adding SS restraints: 19.16 Time building geometry restraints manager: 20.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8412 1.33 - 1.45: 10550 1.45 - 1.57: 21532 1.57 - 1.70: 546 1.70 - 1.82: 298 Bond restraints: 41338 Sorted by residual: bond pdb=" BE BEF A1701 " pdb=" F2 BEF A1701 " ideal model delta sigma weight residual 1.476 1.710 -0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" BE BEF A1701 " pdb=" F1 BEF A1701 " ideal model delta sigma weight residual 1.476 1.702 -0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" BE BEF A1701 " pdb=" F3 BEF A1701 " ideal model delta sigma weight residual 1.476 1.689 -0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" CA PRO N 373 " pdb=" C PRO N 373 " ideal model delta sigma weight residual 1.514 1.539 -0.024 5.50e-03 3.31e+04 1.94e+01 bond pdb=" CA PRO Q 272 " pdb=" C PRO Q 272 " ideal model delta sigma weight residual 1.517 1.545 -0.028 6.70e-03 2.23e+04 1.73e+01 ... (remaining 41333 not shown) Histogram of bond angle deviations from ideal: 96.34 - 104.23: 1518 104.23 - 112.13: 21372 112.13 - 120.02: 16857 120.02 - 127.92: 16591 127.92 - 135.81: 644 Bond angle restraints: 56982 Sorted by residual: angle pdb=" F1 BEF A1701 " pdb=" BE BEF A1701 " pdb=" F3 BEF A1701 " ideal model delta sigma weight residual 120.12 97.82 22.30 3.00e+00 1.11e-01 5.52e+01 angle pdb=" N GLU F 63 " pdb=" CA GLU F 63 " pdb=" CB GLU F 63 " ideal model delta sigma weight residual 110.12 119.04 -8.92 1.47e+00 4.63e-01 3.68e+01 angle pdb=" C GLU F 63 " pdb=" CA GLU F 63 " pdb=" CB GLU F 63 " ideal model delta sigma weight residual 110.79 101.78 9.01 1.66e+00 3.63e-01 2.94e+01 angle pdb=" F2 BEF A1701 " pdb=" BE BEF A1701 " pdb=" F3 BEF A1701 " ideal model delta sigma weight residual 119.96 104.93 15.03 3.00e+00 1.11e-01 2.51e+01 angle pdb=" C LEU F 62 " pdb=" N GLU F 63 " pdb=" CA GLU F 63 " ideal model delta sigma weight residual 120.28 113.80 6.48 1.34e+00 5.57e-01 2.34e+01 ... (remaining 56977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 22874 35.59 - 71.19: 1556 71.19 - 106.78: 60 106.78 - 142.37: 3 142.37 - 177.96: 2 Dihedral angle restraints: 24495 sinusoidal: 11929 harmonic: 12566 Sorted by residual: dihedral pdb=" O2A ADP A1703 " pdb=" O3A ADP A1703 " pdb=" PA ADP A1703 " pdb=" PB ADP A1703 " ideal model delta sinusoidal sigma weight residual 300.00 133.13 166.87 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O1B ADP A1703 " pdb=" O3A ADP A1703 " pdb=" PB ADP A1703 " pdb=" PA ADP A1703 " ideal model delta sinusoidal sigma weight residual -60.00 70.10 -130.10 1 2.00e+01 2.50e-03 3.95e+01 dihedral pdb=" CA GLY Q 49 " pdb=" C GLY Q 49 " pdb=" N LEU Q 50 " pdb=" CA LEU Q 50 " ideal model delta harmonic sigma weight residual 180.00 150.69 29.31 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 24492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 5861 0.087 - 0.174: 507 0.174 - 0.261: 16 0.261 - 0.348: 0 0.348 - 0.436: 1 Chirality restraints: 6385 Sorted by residual: chirality pdb=" CA ARG A1300 " pdb=" N ARG A1300 " pdb=" C ARG A1300 " pdb=" CB ARG A1300 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" CB ILE Q 454 " pdb=" CA ILE Q 454 " pdb=" CG1 ILE Q 454 " pdb=" CG2 ILE Q 454 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA LYS A1301 " pdb=" N LYS A1301 " pdb=" C LYS A1301 " pdb=" CB LYS A1301 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 6382 not shown) Planarity restraints: 6351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU a1648 " -0.059 5.00e-02 4.00e+02 8.98e-02 1.29e+01 pdb=" N PRO a1649 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO a1649 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO a1649 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY Q 458 " -0.049 5.00e-02 4.00e+02 7.15e-02 8.19e+00 pdb=" N PRO Q 459 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO Q 459 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO Q 459 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE V 164 " 0.019 2.00e-02 2.50e+03 2.03e-02 7.24e+00 pdb=" CG PHE V 164 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE V 164 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE V 164 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE V 164 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE V 164 " 0.015 2.00e-02 2.50e+03 pdb=" CZ PHE V 164 " -0.003 2.00e-02 2.50e+03 ... (remaining 6348 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 394 2.47 - 3.07: 30638 3.07 - 3.68: 66841 3.68 - 4.29: 95206 4.29 - 4.90: 145225 Nonbonded interactions: 338304 Sorted by model distance: nonbonded pdb=" OG1 THR V 357 " pdb=" OE1 GLU V 360 " model vdw 1.858 2.440 nonbonded pdb="MG MG A1702 " pdb=" O2B ADP A1703 " model vdw 1.891 2.170 nonbonded pdb="MG MG A1702 " pdb=" O1A ADP A1703 " model vdw 1.899 2.170 nonbonded pdb=" O ARG T 377 " pdb=" CD2 LEU T 378 " model vdw 1.959 3.460 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 1.991 2.440 ... (remaining 338299 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 'B' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name \ O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 17 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 117 or (resid 118 and (name N or \ name CA or name C or name O or name CB )))) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 32 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 56 or (resid 57 through 58 and (na \ me N or name CA or name C or name O or name CB )) or resid 59 through 124)) } ncs_group { reference = chain 'E' selection = (chain 'K' and resid 40 through 134) } ncs_group { reference = (chain 'W' and (resid 423 through 598 or resid 600 through 647 or resid 868 thro \ ugh 947)) selection = (chain 'X' and (resid 423 through 515 or resid 537 or resid 600 through 947)) } 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=0.21 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: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.260 Construct map_model_manager: 0.030 Extract box with map and model: 11.830 Check model and map are aligned: 0.620 Set scattering table: 0.360 Process input model: 121.380 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.234 41338 Z= 0.600 Angle : 0.911 22.298 56982 Z= 0.501 Chirality : 0.051 0.436 6385 Planarity : 0.005 0.090 6351 Dihedral : 20.103 177.963 16317 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 24.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.47 % Favored : 92.43 % Rotamer: Outliers : 0.03 % Allowed : 0.62 % Favored : 99.36 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % 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: -1.78 (0.12), residues: 4170 helix: -0.72 (0.10), residues: 2231 sheet: -1.56 (0.37), residues: 183 loop : -1.64 (0.15), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP a1667 HIS 0.018 0.002 HIS F 75 PHE 0.045 0.003 PHE V 164 TYR 0.033 0.003 TYR T 414 ARG 0.016 0.002 ARG V 366 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 296 time to evaluate : 4.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 886 MET cc_start: 0.8926 (mpp) cc_final: 0.8598 (mpp) REVERT: N 282 MET cc_start: 0.0140 (ptm) cc_final: -0.0394 (ptp) REVERT: N 295 CYS cc_start: 0.5716 (m) cc_final: 0.4571 (t) REVERT: N 327 HIS cc_start: 0.5622 (m90) cc_final: 0.5312 (t-90) REVERT: N 335 MET cc_start: 0.1317 (tpp) cc_final: 0.0757 (ptm) REVERT: P 269 MET cc_start: 0.2252 (ttm) cc_final: 0.1916 (mtp) REVERT: Q 375 MET cc_start: 0.9577 (mtm) cc_final: 0.9326 (mtp) REVERT: Q 456 MET cc_start: 0.8229 (tmm) cc_final: 0.7935 (tmm) REVERT: Y 162 MET cc_start: 0.8013 (mmp) cc_final: 0.7466 (mmm) outliers start: 1 outliers final: 0 residues processed: 297 average time/residue: 0.5312 time to fit residues: 261.9464 Evaluate side-chains 216 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 4.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 373 optimal weight: 9.9990 chunk 335 optimal weight: 0.9990 chunk 185 optimal weight: 0.1980 chunk 114 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 178 optimal weight: 50.0000 chunk 346 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 210 optimal weight: 40.0000 chunk 257 optimal weight: 0.9990 chunk 401 optimal weight: 3.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 GLN ** A 508 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1185 GLN ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 397 GLN ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 895 GLN ** Y 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 253 GLN ** Z 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a1606 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 41338 Z= 0.254 Angle : 0.710 15.028 56982 Z= 0.383 Chirality : 0.043 0.199 6385 Planarity : 0.005 0.045 6351 Dihedral : 22.606 176.407 7658 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.03 % Favored : 93.95 % Rotamer: Outliers : 0.64 % Allowed : 6.63 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.03 (0.13), residues: 4170 helix: 0.02 (0.10), residues: 2389 sheet: -1.28 (0.36), residues: 186 loop : -1.59 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP N 394 HIS 0.010 0.001 HIS A1048 PHE 0.027 0.002 PHE A1082 TYR 0.036 0.002 TYR X 465 ARG 0.006 0.001 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 275 time to evaluate : 4.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 777 LEU cc_start: 0.9189 (tp) cc_final: 0.8803 (tt) REVERT: A 886 MET cc_start: 0.8802 (mpp) cc_final: 0.8422 (mmm) REVERT: N 282 MET cc_start: 0.0540 (ptm) cc_final: 0.0159 (ptp) REVERT: N 295 CYS cc_start: 0.5768 (m) cc_final: 0.4589 (t) REVERT: N 335 MET cc_start: 0.1290 (tpp) cc_final: 0.0747 (ptm) REVERT: Q 45 LEU cc_start: 0.8504 (tp) cc_final: 0.8256 (tt) REVERT: Q 372 MET cc_start: 0.9592 (pmm) cc_final: 0.8998 (pmm) REVERT: Q 375 MET cc_start: 0.9403 (mtm) cc_final: 0.8877 (mtp) REVERT: V 279 PHE cc_start: 0.8703 (p90) cc_final: 0.8437 (p90) REVERT: W 645 GLU cc_start: 0.7441 (tp30) cc_final: 0.6752 (tp30) REVERT: Y 162 MET cc_start: 0.7695 (mmp) cc_final: 0.7368 (mmm) outliers start: 24 outliers final: 9 residues processed: 287 average time/residue: 0.4782 time to fit residues: 234.6558 Evaluate side-chains 244 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 235 time to evaluate : 4.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 1261 ASP Chi-restraints excluded: chain Q residue 1814 CYS Chi-restraints excluded: chain W residue 642 LEU Chi-restraints excluded: chain W residue 906 PHE Chi-restraints excluded: chain Z residue 191 THR Chi-restraints excluded: chain Z residue 276 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 223 optimal weight: 0.6980 chunk 124 optimal weight: 9.9990 chunk 334 optimal weight: 0.0170 chunk 273 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 402 optimal weight: 0.0980 chunk 434 optimal weight: 3.9990 chunk 358 optimal weight: 30.0000 chunk 398 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 322 optimal weight: 4.9990 overall best weight: 1.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN H 67 ASN ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN A 508 HIS ** A 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 179 ASN ** V 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41338 Z= 0.238 Angle : 0.629 10.994 56982 Z= 0.340 Chirality : 0.040 0.161 6385 Planarity : 0.004 0.042 6351 Dihedral : 22.259 179.940 7658 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.05 % Favored : 93.92 % Rotamer: Outliers : 1.05 % Allowed : 9.13 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.59 (0.13), residues: 4170 helix: 0.43 (0.10), residues: 2375 sheet: -1.43 (0.36), residues: 196 loop : -1.45 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.002 TRP N 394 HIS 0.010 0.001 HIS A1048 PHE 0.023 0.002 PHE Z 259 TYR 0.029 0.002 TYR X 465 ARG 0.007 0.001 ARG X 917 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 261 time to evaluate : 4.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.7664 (t0) cc_final: 0.7449 (t0) REVERT: A 201 GLN cc_start: 0.3415 (OUTLIER) cc_final: 0.2812 (mm-40) REVERT: A 777 LEU cc_start: 0.9136 (tp) cc_final: 0.8782 (tt) REVERT: A 886 MET cc_start: 0.8819 (mpp) cc_final: 0.8414 (mmm) REVERT: N 282 MET cc_start: 0.0547 (ptm) cc_final: 0.0254 (ptp) REVERT: N 295 CYS cc_start: 0.5580 (m) cc_final: 0.4238 (t) REVERT: N 335 MET cc_start: 0.1449 (tpp) cc_final: 0.0805 (ptm) REVERT: N 376 MET cc_start: -0.2566 (mtt) cc_final: -0.2816 (mtm) REVERT: P 325 MET cc_start: 0.1091 (ptt) cc_final: 0.0864 (ptt) REVERT: Q 372 MET cc_start: 0.9668 (OUTLIER) cc_final: 0.9010 (pmm) REVERT: Q 375 MET cc_start: 0.9343 (mtm) cc_final: 0.8670 (mtp) REVERT: V 279 PHE cc_start: 0.8703 (p90) cc_final: 0.8458 (p90) REVERT: X 913 MET cc_start: 0.6582 (ppp) cc_final: 0.6240 (ppp) REVERT: Y 162 MET cc_start: 0.7661 (mmp) cc_final: 0.7345 (mmm) REVERT: Z 188 MET cc_start: 0.9165 (tmm) cc_final: 0.8620 (tmm) outliers start: 39 outliers final: 18 residues processed: 284 average time/residue: 0.5400 time to fit residues: 262.5403 Evaluate side-chains 258 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 238 time to evaluate : 4.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 1261 ASP Chi-restraints excluded: chain A residue 1344 VAL Chi-restraints excluded: chain N residue 251 HIS Chi-restraints excluded: chain P residue 305 MET Chi-restraints excluded: chain Q residue 150 MET Chi-restraints excluded: chain Q residue 372 MET Chi-restraints excluded: chain T residue 583 MET Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 300 GLU Chi-restraints excluded: chain W residue 642 LEU Chi-restraints excluded: chain W residue 906 PHE Chi-restraints excluded: chain Z residue 258 LYS Chi-restraints excluded: chain Z residue 276 LEU Chi-restraints excluded: chain a residue 1630 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 397 optimal weight: 7.9990 chunk 302 optimal weight: 6.9990 chunk 208 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 191 optimal weight: 20.0000 chunk 270 optimal weight: 1.9990 chunk 403 optimal weight: 30.0000 chunk 427 optimal weight: 0.0870 chunk 210 optimal weight: 40.0000 chunk 382 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 overall best weight: 5.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN G 89 ASN H 84 ASN ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN ** A 736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 854 ASN ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 148 GLN ** T 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 344 GLN ** Y 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 41338 Z= 0.446 Angle : 0.709 10.599 56982 Z= 0.381 Chirality : 0.044 0.197 6385 Planarity : 0.005 0.052 6351 Dihedral : 22.428 176.884 7658 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.13 % Favored : 92.84 % Rotamer: Outliers : 1.26 % Allowed : 11.60 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.76 (0.13), residues: 4170 helix: 0.28 (0.10), residues: 2388 sheet: -1.11 (0.38), residues: 170 loop : -1.57 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.003 TRP N 394 HIS 0.012 0.002 HIS A1048 PHE 0.042 0.002 PHE Z 259 TYR 0.026 0.002 TYR W 512 ARG 0.020 0.001 ARG Q 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 239 time to evaluate : 4.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 GLN cc_start: 0.3356 (OUTLIER) cc_final: 0.2839 (mm-40) REVERT: A 886 MET cc_start: 0.8799 (mpp) cc_final: 0.8583 (mmm) REVERT: A 1197 ASN cc_start: 0.8049 (OUTLIER) cc_final: 0.7793 (t0) REVERT: N 295 CYS cc_start: 0.5634 (m) cc_final: 0.4493 (t) REVERT: N 335 MET cc_start: 0.1236 (tpp) cc_final: 0.0673 (ptm) REVERT: P 132 MET cc_start: -0.1695 (OUTLIER) cc_final: -0.2348 (ttp) REVERT: Q 372 MET cc_start: 0.9618 (OUTLIER) cc_final: 0.9118 (pmm) REVERT: Q 375 MET cc_start: 0.9380 (mtm) cc_final: 0.8736 (mtp) REVERT: W 645 GLU cc_start: 0.7557 (tp30) cc_final: 0.7347 (tp30) REVERT: Y 162 MET cc_start: 0.7779 (mmp) cc_final: 0.7393 (mmm) REVERT: Z 188 MET cc_start: 0.9169 (tmm) cc_final: 0.8961 (tmm) outliers start: 47 outliers final: 29 residues processed: 268 average time/residue: 0.4892 time to fit residues: 224.7336 Evaluate side-chains 255 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 222 time to evaluate : 4.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1197 ASN Chi-restraints excluded: chain A residue 1261 ASP Chi-restraints excluded: chain P residue 132 MET Chi-restraints excluded: chain Q residue 154 SER Chi-restraints excluded: chain Q residue 360 THR Chi-restraints excluded: chain Q residue 372 MET Chi-restraints excluded: chain Q residue 467 LEU Chi-restraints excluded: chain Q residue 1764 ILE Chi-restraints excluded: chain R residue 242 VAL Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain T residue 583 MET Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 298 CYS Chi-restraints excluded: chain V residue 300 GLU Chi-restraints excluded: chain V residue 308 VAL Chi-restraints excluded: chain W residue 642 LEU Chi-restraints excluded: chain W residue 906 PHE Chi-restraints excluded: chain X residue 937 GLU Chi-restraints excluded: chain Y residue 491 VAL Chi-restraints excluded: chain Z residue 191 THR Chi-restraints excluded: chain Z residue 258 LYS Chi-restraints excluded: chain Z residue 276 LEU Chi-restraints excluded: chain a residue 1630 THR Chi-restraints excluded: chain a residue 1639 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 355 optimal weight: 8.9990 chunk 242 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 318 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 chunk 364 optimal weight: 10.0000 chunk 295 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 218 optimal weight: 20.0000 chunk 383 optimal weight: 30.0000 chunk 107 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 91 GLN ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 199 ASN ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 632 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 950 HIS ** X 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 169 GLN ** Y 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 41338 Z= 0.484 Angle : 0.720 9.787 56982 Z= 0.388 Chirality : 0.045 0.204 6385 Planarity : 0.005 0.052 6351 Dihedral : 22.550 175.795 7658 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 1.99 % Allowed : 14.37 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.90 (0.13), residues: 4170 helix: 0.21 (0.10), residues: 2380 sheet: -1.35 (0.37), residues: 174 loop : -1.68 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP N 394 HIS 0.013 0.002 HIS R 231 PHE 0.019 0.002 PHE N 391 TYR 0.028 0.002 TYR W 512 ARG 0.007 0.001 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 234 time to evaluate : 4.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.6780 (mmm) cc_final: 0.6569 (mmm) REVERT: A 201 GLN cc_start: 0.3291 (OUTLIER) cc_final: 0.2670 (mm-40) REVERT: A 877 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7020 (t80) REVERT: N 295 CYS cc_start: 0.5271 (m) cc_final: 0.4072 (t) REVERT: N 335 MET cc_start: 0.1141 (tpp) cc_final: 0.0560 (ptm) REVERT: P 242 LEU cc_start: 0.4254 (mt) cc_final: 0.4035 (mp) REVERT: Q 375 MET cc_start: 0.9391 (mtm) cc_final: 0.8718 (mtp) REVERT: Q 428 MET cc_start: 0.8351 (ttp) cc_final: 0.8148 (mtp) REVERT: R 276 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7090 (m-80) REVERT: X 615 MET cc_start: 0.4735 (ttm) cc_final: 0.4115 (tpp) REVERT: Y 162 MET cc_start: 0.7730 (mmp) cc_final: 0.7311 (mmm) REVERT: Y 439 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8607 (mm-30) REVERT: Z 188 MET cc_start: 0.9185 (tmm) cc_final: 0.8809 (tmm) REVERT: Z 259 PHE cc_start: 0.6573 (m-80) cc_final: 0.6356 (m-80) outliers start: 74 outliers final: 42 residues processed: 288 average time/residue: 0.4884 time to fit residues: 239.7384 Evaluate side-chains 265 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 219 time to evaluate : 4.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 877 TYR Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1261 ASP Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain P residue 304 THR Chi-restraints excluded: chain Q residue 19 PHE Chi-restraints excluded: chain Q residue 154 SER Chi-restraints excluded: chain Q residue 186 GLU Chi-restraints excluded: chain Q residue 302 ASN Chi-restraints excluded: chain Q residue 372 MET Chi-restraints excluded: chain Q residue 382 CYS Chi-restraints excluded: chain Q residue 467 LEU Chi-restraints excluded: chain Q residue 1764 ILE Chi-restraints excluded: chain R residue 242 VAL Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain T residue 572 MET Chi-restraints excluded: chain T residue 583 MET Chi-restraints excluded: chain V residue 208 MET Chi-restraints excluded: chain V residue 298 CYS Chi-restraints excluded: chain V residue 300 GLU Chi-restraints excluded: chain W residue 463 LEU Chi-restraints excluded: chain W residue 642 LEU Chi-restraints excluded: chain W residue 906 PHE Chi-restraints excluded: chain X residue 627 VAL Chi-restraints excluded: chain X residue 879 VAL Chi-restraints excluded: chain X residue 937 GLU Chi-restraints excluded: chain Y residue 439 GLU Chi-restraints excluded: chain Y residue 491 VAL Chi-restraints excluded: chain Z residue 258 LYS Chi-restraints excluded: chain Z residue 276 LEU Chi-restraints excluded: chain a residue 1630 THR Chi-restraints excluded: chain a residue 1639 HIS Chi-restraints excluded: chain a residue 1655 SER Chi-restraints excluded: chain K residue 45 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 143 optimal weight: 5.9990 chunk 384 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 250 optimal weight: 0.9990 chunk 105 optimal weight: 20.0000 chunk 427 optimal weight: 20.0000 chunk 355 optimal weight: 7.9990 chunk 198 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 141 optimal weight: 0.9980 chunk 224 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 214 ASN ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 260 GLN ** W 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 159 GLN ** Y 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 41338 Z= 0.251 Angle : 0.619 10.489 56982 Z= 0.332 Chirality : 0.040 0.180 6385 Planarity : 0.004 0.049 6351 Dihedral : 22.348 177.640 7658 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.99 % Allowed : 15.15 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.13), residues: 4170 helix: 0.55 (0.11), residues: 2385 sheet: -1.30 (0.36), residues: 179 loop : -1.51 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP N 394 HIS 0.007 0.001 HIS A1048 PHE 0.019 0.001 PHE V 218 TYR 0.020 0.001 TYR Q 158 ARG 0.004 0.000 ARG a1675 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 244 time to evaluate : 4.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 GLN cc_start: 0.3331 (OUTLIER) cc_final: 0.2757 (mm-40) REVERT: A 1000 MET cc_start: 0.7101 (tmm) cc_final: 0.6887 (tmm) REVERT: A 1233 MET cc_start: 0.7045 (mpp) cc_final: 0.6762 (mpp) REVERT: A 1282 LEU cc_start: 0.9212 (mp) cc_final: 0.8780 (tp) REVERT: N 295 CYS cc_start: 0.5005 (m) cc_final: 0.4335 (t) REVERT: N 327 HIS cc_start: 0.5754 (m90) cc_final: 0.5290 (t-90) REVERT: N 335 MET cc_start: 0.1120 (tpp) cc_final: 0.0523 (ptm) REVERT: P 132 MET cc_start: -0.2858 (mtp) cc_final: -0.3173 (ttp) REVERT: P 325 MET cc_start: -0.0158 (ptt) cc_final: -0.1995 (pmm) REVERT: Q 375 MET cc_start: 0.9340 (mtm) cc_final: 0.8650 (mtp) REVERT: Q 428 MET cc_start: 0.8512 (ttp) cc_final: 0.8251 (tmm) REVERT: V 246 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.8943 (pm20) REVERT: X 615 MET cc_start: 0.4704 (ttm) cc_final: 0.4080 (tpp) REVERT: X 905 HIS cc_start: 0.9137 (OUTLIER) cc_final: 0.8907 (t-90) REVERT: X 913 MET cc_start: 0.6079 (ppp) cc_final: 0.5702 (ppp) REVERT: Y 162 MET cc_start: 0.7684 (mmp) cc_final: 0.7164 (mmm) REVERT: Y 439 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8604 (mm-30) REVERT: Z 188 MET cc_start: 0.9267 (tmm) cc_final: 0.8825 (tmm) REVERT: a 1655 SER cc_start: 0.7140 (OUTLIER) cc_final: 0.6622 (p) outliers start: 74 outliers final: 40 residues processed: 296 average time/residue: 0.4878 time to fit residues: 244.5934 Evaluate side-chains 278 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 233 time to evaluate : 4.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain N residue 251 HIS Chi-restraints excluded: chain P residue 304 THR Chi-restraints excluded: chain Q residue 150 MET Chi-restraints excluded: chain Q residue 186 GLU Chi-restraints excluded: chain Q residue 282 GLU Chi-restraints excluded: chain Q residue 302 ASN Chi-restraints excluded: chain Q residue 372 MET Chi-restraints excluded: chain Q residue 420 GLU Chi-restraints excluded: chain Q residue 1764 ILE Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain T residue 572 MET Chi-restraints excluded: chain T residue 583 MET Chi-restraints excluded: chain V residue 246 GLU Chi-restraints excluded: chain V residue 265 LYS Chi-restraints excluded: chain V residue 298 CYS Chi-restraints excluded: chain V residue 300 GLU Chi-restraints excluded: chain V residue 308 VAL Chi-restraints excluded: chain W residue 442 GLU Chi-restraints excluded: chain W residue 463 LEU Chi-restraints excluded: chain W residue 631 THR Chi-restraints excluded: chain W residue 642 LEU Chi-restraints excluded: chain W residue 906 PHE Chi-restraints excluded: chain X residue 879 VAL Chi-restraints excluded: chain X residue 905 HIS Chi-restraints excluded: chain X residue 937 GLU Chi-restraints excluded: chain Y residue 439 GLU Chi-restraints excluded: chain Z residue 191 THR Chi-restraints excluded: chain Z residue 258 LYS Chi-restraints excluded: chain Z residue 276 LEU Chi-restraints excluded: chain a residue 1639 HIS Chi-restraints excluded: chain a residue 1655 SER Chi-restraints excluded: chain K residue 45 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 412 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 243 optimal weight: 5.9990 chunk 312 optimal weight: 10.0000 chunk 241 optimal weight: 9.9990 chunk 359 optimal weight: 6.9990 chunk 238 optimal weight: 10.0000 chunk 426 optimal weight: 9.9990 chunk 266 optimal weight: 0.9990 chunk 259 optimal weight: 3.9990 chunk 196 optimal weight: 30.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 HIS N 214 ASN ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 41338 Z= 0.269 Angle : 0.623 10.510 56982 Z= 0.333 Chirality : 0.040 0.162 6385 Planarity : 0.004 0.048 6351 Dihedral : 22.264 178.135 7658 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.72 % Allowed : 16.08 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.13), residues: 4170 helix: 0.62 (0.11), residues: 2397 sheet: -1.39 (0.36), residues: 191 loop : -1.47 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP Q 225 HIS 0.008 0.001 HIS A1048 PHE 0.019 0.002 PHE Q 221 TYR 0.017 0.001 TYR X 465 ARG 0.010 0.000 ARG A 448 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 244 time to evaluate : 4.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 GLN cc_start: 0.8435 (mp10) cc_final: 0.8086 (mp10) REVERT: A 201 GLN cc_start: 0.3307 (OUTLIER) cc_final: 0.2719 (mm-40) REVERT: A 410 LEU cc_start: 0.7899 (mt) cc_final: 0.7636 (mt) REVERT: A 1000 MET cc_start: 0.7210 (tmm) cc_final: 0.6848 (tmm) REVERT: A 1040 MET cc_start: 0.8891 (tpp) cc_final: 0.8619 (tpp) REVERT: N 295 CYS cc_start: 0.5992 (m) cc_final: 0.5165 (t) REVERT: N 327 HIS cc_start: 0.5876 (m90) cc_final: 0.5405 (t-90) REVERT: N 335 MET cc_start: 0.1217 (tpp) cc_final: 0.0578 (ptm) REVERT: P 325 MET cc_start: -0.0001 (ptt) cc_final: -0.0304 (ptt) REVERT: Q 375 MET cc_start: 0.9354 (mtm) cc_final: 0.8624 (mtp) REVERT: Q 428 MET cc_start: 0.8505 (ttp) cc_final: 0.8100 (tmm) REVERT: T 174 HIS cc_start: 0.5782 (m90) cc_final: 0.4925 (p90) REVERT: X 615 MET cc_start: 0.4774 (ttm) cc_final: 0.4244 (tpp) REVERT: X 905 HIS cc_start: 0.9034 (OUTLIER) cc_final: 0.8614 (t-90) REVERT: X 913 MET cc_start: 0.5811 (ppp) cc_final: 0.5551 (ppp) REVERT: Y 162 MET cc_start: 0.7659 (mmp) cc_final: 0.7328 (mmm) REVERT: Y 439 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8595 (mm-30) REVERT: Z 188 MET cc_start: 0.9270 (tmm) cc_final: 0.9012 (tmm) REVERT: Z 256 LYS cc_start: 0.8270 (pptt) cc_final: 0.8034 (pttp) REVERT: Z 259 PHE cc_start: 0.6801 (m-80) cc_final: 0.6596 (m-80) REVERT: a 1655 SER cc_start: 0.7167 (OUTLIER) cc_final: 0.6640 (p) outliers start: 64 outliers final: 45 residues processed: 292 average time/residue: 0.4781 time to fit residues: 239.4298 Evaluate side-chains 283 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 234 time to evaluate : 4.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1261 ASP Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain P residue 304 THR Chi-restraints excluded: chain Q residue 19 PHE Chi-restraints excluded: chain Q residue 28 HIS Chi-restraints excluded: chain Q residue 150 MET Chi-restraints excluded: chain Q residue 186 GLU Chi-restraints excluded: chain Q residue 203 LEU Chi-restraints excluded: chain Q residue 302 ASN Chi-restraints excluded: chain Q residue 372 MET Chi-restraints excluded: chain Q residue 420 GLU Chi-restraints excluded: chain Q residue 1764 ILE Chi-restraints excluded: chain Q residue 1805 MET Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain T residue 583 MET Chi-restraints excluded: chain V residue 265 LYS Chi-restraints excluded: chain V residue 298 CYS Chi-restraints excluded: chain V residue 300 GLU Chi-restraints excluded: chain V residue 308 VAL Chi-restraints excluded: chain V residue 357 THR Chi-restraints excluded: chain W residue 442 GLU Chi-restraints excluded: chain W residue 463 LEU Chi-restraints excluded: chain W residue 631 THR Chi-restraints excluded: chain W residue 642 LEU Chi-restraints excluded: chain X residue 879 VAL Chi-restraints excluded: chain X residue 905 HIS Chi-restraints excluded: chain X residue 937 GLU Chi-restraints excluded: chain X residue 939 LEU Chi-restraints excluded: chain Y residue 439 GLU Chi-restraints excluded: chain Z residue 191 THR Chi-restraints excluded: chain Z residue 258 LYS Chi-restraints excluded: chain Z residue 276 LEU Chi-restraints excluded: chain a residue 1639 HIS Chi-restraints excluded: chain a residue 1655 SER Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 48 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 263 optimal weight: 4.9990 chunk 170 optimal weight: 40.0000 chunk 254 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 270 optimal weight: 0.9990 chunk 290 optimal weight: 30.0000 chunk 210 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 334 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 HIS ** N 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 472 ASN ** Z 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 41338 Z= 0.294 Angle : 0.630 10.299 56982 Z= 0.336 Chirality : 0.040 0.155 6385 Planarity : 0.004 0.048 6351 Dihedral : 22.274 177.790 7658 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.88 % Allowed : 16.30 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.40 (0.13), residues: 4170 helix: 0.65 (0.11), residues: 2397 sheet: -1.44 (0.37), residues: 191 loop : -1.50 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP Q 225 HIS 0.008 0.001 HIS A1048 PHE 0.035 0.002 PHE X 906 TYR 0.016 0.001 TYR Q 158 ARG 0.006 0.000 ARG a1675 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 238 time to evaluate : 4.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 GLN cc_start: 0.8393 (mp10) cc_final: 0.8138 (mp10) REVERT: A 201 GLN cc_start: 0.3439 (OUTLIER) cc_final: 0.2940 (mm-40) REVERT: A 410 LEU cc_start: 0.7954 (mt) cc_final: 0.7714 (mt) REVERT: A 1000 MET cc_start: 0.7255 (tmm) cc_final: 0.6823 (tmm) REVERT: N 295 CYS cc_start: 0.5434 (m) cc_final: 0.4595 (t) REVERT: N 327 HIS cc_start: 0.5902 (m90) cc_final: 0.5461 (t70) REVERT: N 335 MET cc_start: 0.1256 (tpp) cc_final: 0.0611 (ptm) REVERT: P 325 MET cc_start: 0.0120 (ptt) cc_final: -0.0168 (ptt) REVERT: Q 375 MET cc_start: 0.9357 (mtm) cc_final: 0.8624 (mtp) REVERT: Q 428 MET cc_start: 0.8538 (ttp) cc_final: 0.8119 (tmm) REVERT: T 174 HIS cc_start: 0.5786 (m90) cc_final: 0.4927 (p90) REVERT: W 913 MET cc_start: 0.5494 (mmm) cc_final: 0.5116 (ttt) REVERT: X 615 MET cc_start: 0.4799 (ttm) cc_final: 0.4278 (tpp) REVERT: X 905 HIS cc_start: 0.8917 (OUTLIER) cc_final: 0.8698 (t-90) REVERT: Y 162 MET cc_start: 0.7580 (mmp) cc_final: 0.7233 (mmm) REVERT: Y 439 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8657 (mp0) REVERT: Z 188 MET cc_start: 0.9267 (tmm) cc_final: 0.9008 (tmm) REVERT: a 1655 SER cc_start: 0.7019 (OUTLIER) cc_final: 0.6544 (p) REVERT: a 1675 ARG cc_start: 0.8063 (tpm170) cc_final: 0.7840 (tpm170) outliers start: 70 outliers final: 53 residues processed: 287 average time/residue: 0.4943 time to fit residues: 241.8795 Evaluate side-chains 290 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 233 time to evaluate : 4.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1261 ASP Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1344 VAL Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 304 THR Chi-restraints excluded: chain Q residue 19 PHE Chi-restraints excluded: chain Q residue 28 HIS Chi-restraints excluded: chain Q residue 154 SER Chi-restraints excluded: chain Q residue 186 GLU Chi-restraints excluded: chain Q residue 203 LEU Chi-restraints excluded: chain Q residue 302 ASN Chi-restraints excluded: chain Q residue 372 MET Chi-restraints excluded: chain Q residue 420 GLU Chi-restraints excluded: chain Q residue 1764 ILE Chi-restraints excluded: chain Q residue 1805 MET Chi-restraints excluded: chain R residue 242 VAL Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain T residue 572 MET Chi-restraints excluded: chain T residue 583 MET Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 265 LYS Chi-restraints excluded: chain V residue 298 CYS Chi-restraints excluded: chain V residue 300 GLU Chi-restraints excluded: chain V residue 308 VAL Chi-restraints excluded: chain V residue 357 THR Chi-restraints excluded: chain W residue 442 GLU Chi-restraints excluded: chain W residue 463 LEU Chi-restraints excluded: chain W residue 631 THR Chi-restraints excluded: chain W residue 642 LEU Chi-restraints excluded: chain X residue 879 VAL Chi-restraints excluded: chain X residue 905 HIS Chi-restraints excluded: chain X residue 937 GLU Chi-restraints excluded: chain X residue 939 LEU Chi-restraints excluded: chain Y residue 439 GLU Chi-restraints excluded: chain Z residue 191 THR Chi-restraints excluded: chain Z residue 258 LYS Chi-restraints excluded: chain Z residue 276 LEU Chi-restraints excluded: chain a residue 1630 THR Chi-restraints excluded: chain a residue 1639 HIS Chi-restraints excluded: chain a residue 1655 SER Chi-restraints excluded: chain K residue 45 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 387 optimal weight: 5.9990 chunk 408 optimal weight: 0.0570 chunk 372 optimal weight: 5.9990 chunk 396 optimal weight: 8.9990 chunk 238 optimal weight: 8.9990 chunk 172 optimal weight: 6.9990 chunk 311 optimal weight: 10.0000 chunk 121 optimal weight: 0.5980 chunk 358 optimal weight: 20.0000 chunk 375 optimal weight: 5.9990 chunk 395 optimal weight: 0.0270 overall best weight: 2.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 HIS ** N 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 91 GLN ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 41338 Z= 0.260 Angle : 0.627 12.213 56982 Z= 0.333 Chirality : 0.039 0.298 6385 Planarity : 0.004 0.047 6351 Dihedral : 22.225 178.183 7658 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.72 % Allowed : 16.94 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.13), residues: 4170 helix: 0.75 (0.11), residues: 2390 sheet: -1.63 (0.38), residues: 179 loop : -1.42 (0.16), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP Q 225 HIS 0.008 0.001 HIS A1048 PHE 0.046 0.002 PHE Z 259 TYR 0.016 0.001 TYR X 465 ARG 0.006 0.000 ARG A 448 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 233 time to evaluate : 4.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 24 GLN cc_start: 0.8476 (mp10) cc_final: 0.8242 (mp10) REVERT: A 178 HIS cc_start: 0.5525 (OUTLIER) cc_final: 0.4625 (m-70) REVERT: A 198 ASP cc_start: 0.7553 (t0) cc_final: 0.7140 (m-30) REVERT: A 201 GLN cc_start: 0.3460 (OUTLIER) cc_final: 0.3213 (mm-40) REVERT: A 410 LEU cc_start: 0.7998 (mt) cc_final: 0.7763 (mt) REVERT: N 295 CYS cc_start: 0.5444 (m) cc_final: 0.4586 (t) REVERT: N 327 HIS cc_start: 0.5978 (m90) cc_final: 0.5545 (t70) REVERT: N 335 MET cc_start: 0.1260 (tpp) cc_final: 0.0608 (ptm) REVERT: P 325 MET cc_start: 0.0106 (ptt) cc_final: -0.0140 (ptt) REVERT: Q 375 MET cc_start: 0.9352 (mtm) cc_final: 0.8623 (mtp) REVERT: Q 428 MET cc_start: 0.8551 (ttp) cc_final: 0.8154 (tmm) REVERT: T 174 HIS cc_start: 0.5781 (m90) cc_final: 0.4928 (p90) REVERT: X 615 MET cc_start: 0.4381 (ttm) cc_final: 0.3917 (tpp) REVERT: X 905 HIS cc_start: 0.8871 (OUTLIER) cc_final: 0.8546 (t-90) REVERT: Y 162 MET cc_start: 0.7533 (mmp) cc_final: 0.7186 (mmm) REVERT: Y 439 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8657 (mp0) REVERT: Z 256 LYS cc_start: 0.8348 (pptt) cc_final: 0.8045 (mmmt) REVERT: a 1675 ARG cc_start: 0.8029 (tpm170) cc_final: 0.7798 (tpm170) outliers start: 64 outliers final: 52 residues processed: 277 average time/residue: 0.4849 time to fit residues: 231.1057 Evaluate side-chains 284 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 228 time to evaluate : 4.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1261 ASP Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1344 VAL Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 304 THR Chi-restraints excluded: chain Q residue 19 PHE Chi-restraints excluded: chain Q residue 28 HIS Chi-restraints excluded: chain Q residue 186 GLU Chi-restraints excluded: chain Q residue 203 LEU Chi-restraints excluded: chain Q residue 302 ASN Chi-restraints excluded: chain Q residue 372 MET Chi-restraints excluded: chain Q residue 420 GLU Chi-restraints excluded: chain Q residue 1764 ILE Chi-restraints excluded: chain Q residue 1797 LEU Chi-restraints excluded: chain Q residue 1805 MET Chi-restraints excluded: chain R residue 232 VAL Chi-restraints excluded: chain R residue 242 VAL Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain T residue 583 MET Chi-restraints excluded: chain V residue 265 LYS Chi-restraints excluded: chain V residue 298 CYS Chi-restraints excluded: chain V residue 300 GLU Chi-restraints excluded: chain V residue 308 VAL Chi-restraints excluded: chain V residue 357 THR Chi-restraints excluded: chain W residue 442 GLU Chi-restraints excluded: chain W residue 463 LEU Chi-restraints excluded: chain W residue 631 THR Chi-restraints excluded: chain W residue 642 LEU Chi-restraints excluded: chain X residue 879 VAL Chi-restraints excluded: chain X residue 905 HIS Chi-restraints excluded: chain X residue 937 GLU Chi-restraints excluded: chain X residue 939 LEU Chi-restraints excluded: chain Y residue 439 GLU Chi-restraints excluded: chain Z residue 191 THR Chi-restraints excluded: chain Z residue 258 LYS Chi-restraints excluded: chain Z residue 276 LEU Chi-restraints excluded: chain a residue 1630 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 48 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 260 optimal weight: 10.0000 chunk 419 optimal weight: 9.9990 chunk 256 optimal weight: 0.7980 chunk 199 optimal weight: 9.9990 chunk 291 optimal weight: 9.9990 chunk 440 optimal weight: 0.4980 chunk 405 optimal weight: 5.9990 chunk 350 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 270 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 91 GLN ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 199 ASN ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 626 HIS W 905 HIS ** X 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 41338 Z= 0.325 Angle : 0.655 11.604 56982 Z= 0.348 Chirality : 0.041 0.278 6385 Planarity : 0.004 0.048 6351 Dihedral : 22.305 177.291 7658 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.72 % Allowed : 17.02 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.35 (0.13), residues: 4170 helix: 0.68 (0.11), residues: 2399 sheet: -1.62 (0.39), residues: 179 loop : -1.43 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP Y 486 HIS 0.008 0.001 HIS A1048 PHE 0.025 0.002 PHE X 906 TYR 0.016 0.002 TYR Q 158 ARG 0.005 0.000 ARG A 448 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 230 time to evaluate : 4.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 HIS cc_start: 0.5569 (OUTLIER) cc_final: 0.4792 (m-70) REVERT: A 198 ASP cc_start: 0.7498 (t0) cc_final: 0.7045 (m-30) REVERT: A 877 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.6997 (t80) REVERT: N 295 CYS cc_start: 0.5503 (m) cc_final: 0.4693 (t) REVERT: N 327 HIS cc_start: 0.5974 (m90) cc_final: 0.5573 (t70) REVERT: N 335 MET cc_start: 0.1316 (tpp) cc_final: 0.0650 (ptm) REVERT: P 325 MET cc_start: 0.0120 (ptt) cc_final: -0.0093 (ptt) REVERT: Q 375 MET cc_start: 0.9403 (mtm) cc_final: 0.8678 (mtp) REVERT: Q 428 MET cc_start: 0.8549 (ttp) cc_final: 0.8259 (mtp) REVERT: T 174 HIS cc_start: 0.5782 (m90) cc_final: 0.4926 (p90) REVERT: W 646 ASP cc_start: 0.7571 (t70) cc_final: 0.7273 (t0) REVERT: X 615 MET cc_start: 0.4645 (ttm) cc_final: 0.4170 (tpp) REVERT: X 905 HIS cc_start: 0.8856 (OUTLIER) cc_final: 0.8603 (t-90) REVERT: Y 162 MET cc_start: 0.7505 (mmp) cc_final: 0.7156 (mmm) REVERT: Y 439 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8581 (mp0) REVERT: Z 188 MET cc_start: 0.9063 (tmm) cc_final: 0.8745 (tmm) outliers start: 64 outliers final: 53 residues processed: 274 average time/residue: 0.4805 time to fit residues: 225.6145 Evaluate side-chains 285 residues out of total 3733 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 228 time to evaluate : 4.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 877 TYR Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 1103 CYS Chi-restraints excluded: chain A residue 1261 ASP Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1344 VAL Chi-restraints excluded: chain N residue 104 ASP Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain P residue 304 THR Chi-restraints excluded: chain Q residue 19 PHE Chi-restraints excluded: chain Q residue 28 HIS Chi-restraints excluded: chain Q residue 154 SER Chi-restraints excluded: chain Q residue 186 GLU Chi-restraints excluded: chain Q residue 203 LEU Chi-restraints excluded: chain Q residue 302 ASN Chi-restraints excluded: chain Q residue 372 MET Chi-restraints excluded: chain Q residue 420 GLU Chi-restraints excluded: chain Q residue 1764 ILE Chi-restraints excluded: chain Q residue 1797 LEU Chi-restraints excluded: chain Q residue 1805 MET Chi-restraints excluded: chain R residue 242 VAL Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 276 TYR Chi-restraints excluded: chain T residue 583 MET Chi-restraints excluded: chain V residue 265 LYS Chi-restraints excluded: chain V residue 298 CYS Chi-restraints excluded: chain V residue 300 GLU Chi-restraints excluded: chain V residue 308 VAL Chi-restraints excluded: chain V residue 357 THR Chi-restraints excluded: chain W residue 442 GLU Chi-restraints excluded: chain W residue 463 LEU Chi-restraints excluded: chain W residue 631 THR Chi-restraints excluded: chain W residue 642 LEU Chi-restraints excluded: chain X residue 879 VAL Chi-restraints excluded: chain X residue 905 HIS Chi-restraints excluded: chain X residue 937 GLU Chi-restraints excluded: chain X residue 939 LEU Chi-restraints excluded: chain Y residue 439 GLU Chi-restraints excluded: chain Z residue 191 THR Chi-restraints excluded: chain Z residue 276 LEU Chi-restraints excluded: chain a residue 1630 THR Chi-restraints excluded: chain a residue 1639 HIS Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 48 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 442 random chunks: chunk 278 optimal weight: 4.9990 chunk 373 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 323 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 351 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 360 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 626 HIS ** X 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.101680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.069233 restraints weight = 320979.523| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 7.57 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 41338 Z= 0.258 Angle : 0.632 12.507 56982 Z= 0.334 Chirality : 0.039 0.280 6385 Planarity : 0.004 0.046 6351 Dihedral : 22.216 178.061 7658 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.69 % Allowed : 17.21 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.24 (0.13), residues: 4170 helix: 0.78 (0.11), residues: 2402 sheet: -1.66 (0.38), residues: 185 loop : -1.39 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP Y 486 HIS 0.008 0.001 HIS A1048 PHE 0.025 0.001 PHE X 906 TYR 0.037 0.001 TYR A 475 ARG 0.013 0.000 ARG Z 257 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7985.96 seconds wall clock time: 146 minutes 54.25 seconds (8814.25 seconds total)