Starting phenix.real_space_refine on Sat Mar 23 04:19:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wuh_32832/03_2024/7wuh_32832.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wuh_32832/03_2024/7wuh_32832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wuh_32832/03_2024/7wuh_32832.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wuh_32832/03_2024/7wuh_32832.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wuh_32832/03_2024/7wuh_32832.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wuh_32832/03_2024/7wuh_32832.pdb" } resolution = 4.7 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= -0.005 sd= 0.385 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 22517 2.51 5 N 5779 2.21 5 O 7129 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 340": "OE1" <-> "OE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 364": "OD1" <-> "OD2" Residue "E PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 428": "OD1" <-> "OD2" Residue "E TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 516": "OE1" <-> "OE2" Residue "E TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 979": "OD1" <-> "OD2" Residue "E PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 176": "OD1" <-> "OD2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 61": "OE1" <-> "OE2" Residue "I ASP 76": "OD1" <-> "OD2" Residue "I PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 171": "OE1" <-> "OE2" Residue "K TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35569 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 8062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8062 Classifications: {'peptide': 1038} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 49, 'TRANS': 988} Chain breaks: 6 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 8072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8072 Classifications: {'peptide': 1038} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 48, 'TRANS': 989} Chain breaks: 5 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 8123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8123 Classifications: {'peptide': 1044} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 51, 'TRANS': 992} Chain breaks: 7 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1641 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 206} Chain: "F" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1705 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 6, 'TRANS': 209} Chain: "H" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1641 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 206} Chain: "I" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1705 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 6, 'TRANS': 209} Chain: "K" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1641 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 206} Chain: "L" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1705 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 6, 'TRANS': 209} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "g" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 19.70, per 1000 atoms: 0.55 Number of scatterers: 35569 At special positions: 0 Unit cell: (161.02, 151.06, 231.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 7129 8.00 N 5779 7.00 C 22517 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=1.98 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.04 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 146 " - pdb=" SG CYS D 202 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 94 " distance=2.03 Simple disulfide: pdb=" SG CYS F 140 " - pdb=" SG CYS F 200 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 94 " distance=2.03 Simple disulfide: pdb=" SG CYS I 140 " - pdb=" SG CYS I 200 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 146 " - pdb=" SG CYS K 202 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Simple disulfide: pdb=" SG CYS L 140 " - pdb=" SG CYS L 200 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA W 3 " - " MAN W 4 " " BMA d 3 " - " MAN d 4 " " BMA f 3 " - " MAN f 4 " " MAN f 4 " - " MAN f 5 " ALPHA1-6 " BMA J 3 " - " MAN J 4 " " BMA S 3 " - " MAN S 5 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 5 " " BMA W 3 " - " MAN W 5 " " BMA Y 3 " - " MAN Y 4 " " MAN d 4 " - " MAN d 6 " " MAN f 4 " - " MAN f 6 " BETA1-2 " MAN d 4 " - " NAG d 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG G 1 " - " NAG G 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " BETA1-6 " NAG B 1 " - " FUC B 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG a 1 " - " FUC a 4 " " NAG b 1 " - " FUC b 3 " " NAG c 1 " - " FUC c 2 " " NAG g 1 " - " FUC g 4 " NAG-ASN " NAG A1301 " - " ASN A 657 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A1098 " " NAG A1304 " - " ASN A 61 " " NAG A1305 " - " ASN A 616 " " NAG B 1 " - " ASN A 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 74 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1098 " " NAG E1301 " - " ASN E1098 " " NAG E1302 " - " ASN E 61 " " NAG E1303 " - " ASN E 165 " " NAG E1304 " - " ASN E 122 " " NAG E1305 " - " ASN E 234 " " NAG G 1 " - " ASN A 234 " " NAG J 1 " - " ASN A 282 " " NAG K 301 " - " ASN K 102 " " NAG M 1 " - " ASN A 331 " " NAG N 1 " - " ASN A 717 " " NAG O 1 " - " ASN A 801 " " NAG P 1 " - " ASN A 122 " " NAG Q 1 " - " ASN A1074 " " NAG R 1 " - " ASN C 149 " " NAG S 1 " - " ASN C 331 " " NAG T 1 " - " ASN C 122 " " NAG U 1 " - " ASN C 165 " " NAG V 1 " - " ASN C 709 " " NAG W 1 " - " ASN C 717 " " NAG X 1 " - " ASN C 801 " " NAG Y 1 " - " ASN C 282 " " NAG Z 1 " - " ASN E 282 " " NAG a 1 " - " ASN E 717 " " NAG b 1 " - " ASN E 149 " " NAG c 1 " - " ASN E 603 " " NAG d 1 " - " ASN E 331 " " NAG e 1 " - " ASN E 801 " " NAG f 1 " - " ASN E1074 " " NAG g 1 " - " ASN H 102 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.58 Conformation dependent library (CDL) restraints added in 6.1 seconds 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8280 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 67 sheets defined 18.4% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.654A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.920A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.868A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.582A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.244A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 885 through 890 Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 902 through 910 removed outlier: 3.958A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 940 removed outlier: 3.849A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 968 removed outlier: 3.994A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.589A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.063A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN C 409 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 Processing helix chain 'C' and resid 757 through 783 Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 883 Processing helix chain 'C' and resid 884 through 891 removed outlier: 3.620A pdb=" N THR C 887 " --> pdb=" O SER C 884 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.940A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 939 removed outlier: 4.513A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 944 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 977 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.709A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 365 through 372 removed outlier: 3.773A pdb=" N ALA E 372 " --> pdb=" O TYR E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 408 removed outlier: 3.591A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 506 Processing helix chain 'E' and resid 746 through 757 removed outlier: 3.987A pdb=" N GLN E 755 " --> pdb=" O ASN E 751 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR E 756 " --> pdb=" O LEU E 752 " (cutoff:3.500A) Processing helix chain 'E' and resid 757 through 782 Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 866 through 884 Processing helix chain 'E' and resid 885 through 891 removed outlier: 3.842A pdb=" N GLY E 889 " --> pdb=" O TRP E 886 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 908 removed outlier: 4.097A pdb=" N ALA E 903 " --> pdb=" O ALA E 899 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR E 904 " --> pdb=" O MET E 900 " (cutoff:3.500A) Processing helix chain 'E' and resid 913 through 940 removed outlier: 7.195A pdb=" N LYS E 921 " --> pdb=" O TYR E 917 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU E 922 " --> pdb=" O GLU E 918 " (cutoff:3.500A) Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 968 removed outlier: 4.010A pdb=" N LEU E 966 " --> pdb=" O LEU E 962 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER E 967 " --> pdb=" O VAL E 963 " (cutoff:3.500A) Processing helix chain 'E' and resid 977 through 984 removed outlier: 4.072A pdb=" N LEU E 981 " --> pdb=" O LEU E 977 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU E 984 " --> pdb=" O ILE E 980 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 1033 removed outlier: 3.890A pdb=" N ARG E 995 " --> pdb=" O VAL E 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'F' and resid 32 through 36 removed outlier: 4.615A pdb=" N LYS F 36 " --> pdb=" O SER F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.910A pdb=" N LEU F 89 " --> pdb=" O ALA F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 133 Processing helix chain 'F' and resid 188 through 195 removed outlier: 3.702A pdb=" N GLU F 193 " --> pdb=" O LYS F 189 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 65 Processing helix chain 'H' and resid 160 through 164 Processing helix chain 'I' and resid 85 through 89 removed outlier: 3.526A pdb=" N LEU I 89 " --> pdb=" O ALA I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 132 removed outlier: 3.666A pdb=" N LYS I 132 " --> pdb=" O ASP I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 195 removed outlier: 3.945A pdb=" N TYR I 192 " --> pdb=" O SER I 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 4.114A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 65 removed outlier: 3.959A pdb=" N LYS K 65 " --> pdb=" O GLN K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'K' and resid 191 through 195 removed outlier: 4.001A pdb=" N LEU K 195 " --> pdb=" O SER K 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 36 removed outlier: 3.510A pdb=" N GLN L 35 " --> pdb=" O SER L 32 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS L 36 " --> pdb=" O SER L 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 32 through 36' Processing helix chain 'L' and resid 128 through 133 removed outlier: 3.520A pdb=" N LYS L 132 " --> pdb=" O GLU L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 193 removed outlier: 3.518A pdb=" N TYR L 192 " --> pdb=" O SER L 188 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU L 193 " --> pdb=" O LYS L 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 188 through 193' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.860A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 209 removed outlier: 4.664A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 189 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 120 removed outlier: 3.546A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 204 through 205 removed outlier: 3.720A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.710A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.814A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 583 through 586 removed outlier: 4.506A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 566 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N PHE A 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 610 through 611 removed outlier: 3.669A pdb=" N LEU A 650 " --> pdb=" O PHE A 643 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 653 through 654 removed outlier: 7.455A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 9.636A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 727 removed outlier: 3.959A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR A1066 " --> pdb=" O SER A 721 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 723 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS A1064 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A1061 " --> pdb=" O GLN A1054 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A1054 " --> pdb=" O VAL A1061 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 789 removed outlier: 7.197A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1077 through 1078 removed outlier: 3.807A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1088 through 1089 removed outlier: 3.699A pdb=" N PHE A1089 " --> pdb=" O PHE A1121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 90 through 92 removed outlier: 4.308A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.712A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 104 through 107 removed outlier: 3.533A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 239 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 118 through 122 removed outlier: 3.546A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN C 122 " --> pdb=" O ASN C 125 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN C 125 " --> pdb=" O ASN C 122 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 275 through 279 removed outlier: 4.210A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 313 through 316 removed outlier: 7.284A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 325 through 327 removed outlier: 6.290A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU C 546 " --> pdb=" O PHE C 543 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.637A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.971A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.938A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 643 through 645 Processing sheet with id=AD1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.442A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 718 through 723 removed outlier: 3.564A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1053 through 1056 Processing sheet with id=AD4, first strand: chain 'C' and resid 1088 through 1089 Processing sheet with id=AD5, first strand: chain 'C' and resid 1094 through 1095 removed outlier: 3.607A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'E' and resid 29 through 31 Processing sheet with id=AD7, first strand: chain 'E' and resid 51 through 55 removed outlier: 3.870A pdb=" N THR E 51 " --> pdb=" O PHE E 275 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.698A pdb=" N LEU E 84 " --> pdb=" O PHE E 238 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 189 through 191 Processing sheet with id=AE1, first strand: chain 'E' and resid 195 through 197 removed outlier: 4.344A pdb=" N LYS E 195 " --> pdb=" O LYS E 202 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS E 202 " --> pdb=" O LYS E 195 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE E 197 " --> pdb=" O TYR E 200 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL E 227 " --> pdb=" O ILE E 203 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 311 through 316 removed outlier: 3.556A pdb=" N GLY E 311 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR E 599 " --> pdb=" O GLY E 311 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL E 597 " --> pdb=" O TYR E 313 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR E 315 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 377 through 380 removed outlier: 4.179A pdb=" N CYS E 432 " --> pdb=" O LEU E 513 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU E 513 " --> pdb=" O CYS E 432 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE E 402 " --> pdb=" O TYR E 508 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 551 through 553 Processing sheet with id=AE5, first strand: chain 'E' and resid 643 through 645 removed outlier: 3.566A pdb=" N LEU E 650 " --> pdb=" O PHE E 643 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 665 through 667 removed outlier: 6.543A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 718 through 720 Processing sheet with id=AE8, first strand: chain 'E' and resid 726 through 727 removed outlier: 3.627A pdb=" N VAL E1060 " --> pdb=" O LEU E 727 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 1077 through 1078 removed outlier: 3.764A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN E1106 " --> pdb=" O GLU E1111 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N GLU E1111 " --> pdb=" O GLN E1106 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 34 through 37 removed outlier: 4.307A pdb=" N TYR D 35 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA D 97 " --> pdb=" O TYR D 35 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 39 through 40 removed outlier: 3.572A pdb=" N SER D 40 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'F' and resid 6 through 7 removed outlier: 3.622A pdb=" N SER F 7 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER F 22 " --> pdb=" O SER F 7 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N CYS F 23 " --> pdb=" O PHE F 77 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N PHE F 77 " --> pdb=" O CYS F 23 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER F 71 " --> pdb=" O THR F 78 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 59 through 60 removed outlier: 4.179A pdb=" N SER F 59 " --> pdb=" O TYR F 55 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR F 55 " --> pdb=" O SER F 59 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP F 41 " --> pdb=" O LEU F 53 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR F 55 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU F 39 " --> pdb=" O TYR F 55 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA F 40 " --> pdb=" O GLN F 95 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR F 42 " --> pdb=" O TYR F 93 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 138 through 140 removed outlier: 3.764A pdb=" N VAL F 138 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU F 185 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N CYS F 140 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER F 183 " --> pdb=" O CYS F 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'F' and resid 153 through 155 removed outlier: 3.612A pdb=" N GLN F 153 " --> pdb=" O GLU F 201 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS F 155 " --> pdb=" O ALA F 199 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA F 199 " --> pdb=" O LYS F 155 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.758A pdb=" N GLN H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS H 23 " --> pdb=" O GLN H 5 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 46 through 51 removed outlier: 5.321A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE H 34 " --> pdb=" O ILE H 51 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 72 through 73 removed outlier: 3.919A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 148 through 151 removed outlier: 4.068A pdb=" N ASP H 150 " --> pdb=" O TYR H 182 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 39 through 40 removed outlier: 3.747A pdb=" N GLN I 95 " --> pdb=" O ALA I 40 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 142 through 143 removed outlier: 4.204A pdb=" N LEU I 142 " --> pdb=" O LEU I 181 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU I 181 " --> pdb=" O LEU I 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'K' and resid 46 through 49 removed outlier: 7.234A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 126 through 129 removed outlier: 3.921A pdb=" N SER K 126 " --> pdb=" O LYS K 149 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS K 149 " --> pdb=" O SER K 126 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 159 through 160 removed outlier: 3.559A pdb=" N ASN K 203 " --> pdb=" O SER K 159 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.611A pdb=" N SER L 5 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS L 24 " --> pdb=" O SER L 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.492A pdb=" N LEU L 11 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR L 108 " --> pdb=" O TYR L 92 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 39 through 41 removed outlier: 4.222A pdb=" N ALA L 40 " --> pdb=" O GLN L 95 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN L 95 " --> pdb=" O ALA L 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'L' and resid 54 through 55 Processing sheet with id=AH2, first strand: chain 'L' and resid 71 through 73 removed outlier: 4.002A pdb=" N SER L 71 " --> pdb=" O THR L 78 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR L 78 " --> pdb=" O SER L 71 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 140 through 145 removed outlier: 5.401A pdb=" N LEU L 141 " --> pdb=" O SER L 183 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N SER L 183 " --> pdb=" O LEU L 141 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASN L 143 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU L 181 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 159 through 160 removed outlier: 4.011A pdb=" N GLN L 153 " --> pdb=" O GLU L 201 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU L 201 " --> pdb=" O GLN L 153 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS L 155 " --> pdb=" O ALA L 199 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA L 199 " --> pdb=" O LYS L 155 " (cutoff:3.500A) 739 hydrogen bonds defined for protein. 1944 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.35 Time building geometry restraints manager: 16.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6162 1.32 - 1.45: 10368 1.45 - 1.58: 19636 1.58 - 1.71: 1 1.71 - 1.83: 182 Bond restraints: 36349 Sorted by residual: bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1 BMA f 3 " pdb=" C2 BMA f 3 " ideal model delta sigma weight residual 1.519 1.581 -0.062 2.00e-02 2.50e+03 9.53e+00 bond pdb=" C ASN C 282 " pdb=" O ASN C 282 " ideal model delta sigma weight residual 1.236 1.198 0.038 1.31e-02 5.83e+03 8.52e+00 ... (remaining 36344 not shown) Histogram of bond angle deviations from ideal: 96.68 - 105.07: 661 105.07 - 113.46: 20790 113.46 - 121.85: 19834 121.85 - 130.24: 8068 130.24 - 138.63: 106 Bond angle restraints: 49459 Sorted by residual: angle pdb=" C ARG I 99 " pdb=" N TYR I 100 " pdb=" CA TYR I 100 " ideal model delta sigma weight residual 120.49 130.63 -10.14 1.42e+00 4.96e-01 5.10e+01 angle pdb=" CA ASN C 282 " pdb=" CB ASN C 282 " pdb=" CG ASN C 282 " ideal model delta sigma weight residual 112.60 119.60 -7.00 1.00e+00 1.00e+00 4.90e+01 angle pdb=" CA ARG C 995 " pdb=" CB ARG C 995 " pdb=" CG ARG C 995 " ideal model delta sigma weight residual 114.10 126.15 -12.05 2.00e+00 2.50e-01 3.63e+01 angle pdb=" N ASN C 148 " pdb=" CA ASN C 148 " pdb=" C ASN C 148 " ideal model delta sigma weight residual 110.91 117.86 -6.95 1.17e+00 7.31e-01 3.53e+01 angle pdb=" C SER C 155 " pdb=" CA SER C 155 " pdb=" CB SER C 155 " ideal model delta sigma weight residual 117.23 109.39 7.84 1.36e+00 5.41e-01 3.33e+01 ... (remaining 49454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.45: 21291 23.45 - 46.90: 1210 46.90 - 70.35: 198 70.35 - 93.80: 123 93.80 - 117.25: 79 Dihedral angle restraints: 22901 sinusoidal: 10003 harmonic: 12898 Sorted by residual: dihedral pdb=" CB CYS E1032 " pdb=" SG CYS E1032 " pdb=" SG CYS E1043 " pdb=" CB CYS E1043 " ideal model delta sinusoidal sigma weight residual 93.00 -176.61 -90.39 1 1.00e+01 1.00e-02 9.67e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 4.24 88.76 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 8.12 84.88 1 1.00e+01 1.00e-02 8.74e+01 ... (remaining 22898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 5819 0.146 - 0.291: 83 0.291 - 0.437: 11 0.437 - 0.583: 3 0.583 - 0.728: 3 Chirality restraints: 5919 Sorted by residual: chirality pdb=" C1 BMA Y 3 " pdb=" O4 NAG Y 2 " pdb=" C2 BMA Y 3 " pdb=" O5 BMA Y 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-02 2.50e+03 9.22e+02 chirality pdb=" C1 MAN U 4 " pdb=" O6 BMA U 3 " pdb=" C2 MAN U 4 " pdb=" O5 MAN U 4 " both_signs ideal model delta sigma weight residual False 2.40 1.94 0.46 2.00e-02 2.50e+03 5.21e+02 chirality pdb=" C1 MAN Y 4 " pdb=" O6 BMA Y 3 " pdb=" C2 MAN Y 4 " pdb=" O5 MAN Y 4 " both_signs ideal model delta sigma weight residual False 2.40 2.17 0.23 2.00e-02 2.50e+03 1.31e+02 ... (remaining 5916 not shown) Planarity restraints: 6254 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 2 " -0.296 2.00e-02 2.50e+03 2.61e-01 8.50e+02 pdb=" C7 NAG Y 2 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG Y 2 " -0.064 2.00e-02 2.50e+03 pdb=" N2 NAG Y 2 " 0.467 2.00e-02 2.50e+03 pdb=" O7 NAG Y 2 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1305 " 0.298 2.00e-02 2.50e+03 2.50e-01 7.83e+02 pdb=" C7 NAG A1305 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG A1305 " 0.188 2.00e-02 2.50e+03 pdb=" N2 NAG A1305 " -0.428 2.00e-02 2.50e+03 pdb=" O7 NAG A1305 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " -0.278 2.00e-02 2.50e+03 2.37e-01 7.00e+02 pdb=" C7 NAG A1304 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " -0.169 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " 0.411 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " -0.031 2.00e-02 2.50e+03 ... (remaining 6251 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 767 2.61 - 3.18: 34232 3.18 - 3.76: 56071 3.76 - 4.33: 74856 4.33 - 4.90: 114006 Nonbonded interactions: 279932 Sorted by model distance: nonbonded pdb=" OG1 THR K 24 " pdb=" O SER K 77 " model vdw 2.038 2.440 nonbonded pdb=" O PHE H 105 " pdb=" OH TYR I 42 " model vdw 2.071 2.440 nonbonded pdb=" O ALA E 706 " pdb=" OG SER E 711 " model vdw 2.077 2.440 nonbonded pdb=" O GLU A 309 " pdb=" OH TYR A 313 " model vdw 2.095 2.440 nonbonded pdb=" O ALA C 958 " pdb=" OG1 THR C 961 " model vdw 2.096 2.440 ... (remaining 279927 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 'A' and (resid 26 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB )) or resid 33 through 69 or resid 78 through 210 or resi \ d 214 through 245 or (resid 265 and (name N or name CA or name C or name O or na \ me CB )) or resid 266 through 621 or resid 641 through 679 or resid 689 through \ 828 or resid 852 or resid 854 through 1134 or resid 1301 through 1305)) selection = (chain 'C' and (resid 26 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 40 or (resid 41 and (name N or nam \ e CA or name C or name O or name CB )) or resid 42 through 69 or resid 78 or (re \ sid 79 and (name N or name CA or name C or name O or name CB )) or resid 80 thro \ ugh 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or \ resid 98 through 112 or (resid 113 and (name N or name CA or name C or name O or \ name CB )) or resid 114 through 139 or (resid 140 and (name N or name CA or nam \ e C or name O or name CB )) or resid 141 through 152 or (resid 153 through 154 a \ nd (name N or name CA or name C or name O or name CB )) or resid 155 through 167 \ or (resid 168 and (name N or name CA or name C or name O or name CB )) or resid \ 169 through 210 or resid 214 through 217 or (resid 218 and (name N or name CA o \ r name C or name O or name CB )) or resid 219 through 245 or resid 265 through 5 \ 27 or (resid 528 and (name N or name CA or name C or name O or name CB )) or res \ id 529 through 621 or resid 641 through 679 or resid 689 through 1134 or resid 1 \ 304 through 1308)) selection = (chain 'E' and (resid 26 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB )) or resid 33 through 36 or (resid 37 and (name N or nam \ e CA or name C or name O or name CB )) or resid 38 through 40 or (resid 41 and ( \ name N or name CA or name C or name O or name CB )) or resid 42 through 69 or re \ sid 78 or (resid 79 and (name N or name CA or name C or name O or name CB )) or \ resid 80 through 96 or (resid 97 and (name N or name CA or name C or name O or n \ ame CB )) or resid 98 through 112 or (resid 113 and (name N or name CA or name C \ or name O or name CB )) or resid 114 through 139 or (resid 140 and (name N or n \ ame CA or name C or name O or name CB )) or resid 141 through 152 or (resid 153 \ through 154 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 5 through 217 or (resid 218 and (name N or name CA or name C or name O or name C \ B )) or resid 219 through 245 or (resid 265 and (name N or name CA or name C or \ name O or name CB )) or resid 266 through 527 or (resid 528 and (name N or name \ CA or name C or name O or name CB )) or resid 529 through 621 or resid 641 throu \ gh 679 or resid 689 through 828 or resid 831 or resid 854 through 1134 or resid \ 1301 through 1305)) } ncs_group { reference = (chain 'B' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) } ncs_group { reference = chain 'D' selection = chain 'H' selection = (chain 'K' and resid 1 through 218) } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'L' } ncs_group { reference = (chain 'G' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'c' and resid 1) } ncs_group { reference = (chain 'J' and resid 1 through 3) selection = (chain 'Y' and resid 1 through 3) selection = (chain 'a' and resid 1 through 3) selection = (chain 'g' and resid 1 through 3) } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = (chain 'd' and (resid 1 through 4 or resid 6)) selection = (chain 'f' and (resid 1 through 4 or resid 6)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 14.210 Check model and map are aligned: 0.560 Set scattering table: 0.330 Process input model: 92.260 Find NCS groups from input model: 3.030 Set up NCS constraints: 0.350 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: 0.020 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 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 : 0.005 0.080 36349 Z= 0.331 Angle : 0.932 13.986 49459 Z= 0.507 Chirality : 0.058 0.728 5919 Planarity : 0.008 0.261 6211 Dihedral : 17.314 117.249 14477 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 27.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.13 % Favored : 87.71 % Rotamer: Outliers : 0.13 % Allowed : 0.47 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.10 (0.12), residues: 4377 helix: -1.21 (0.19), residues: 650 sheet: -1.60 (0.22), residues: 547 loop : -2.52 (0.10), residues: 3180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP L 41 HIS 0.018 0.002 HIS C1048 PHE 0.050 0.002 PHE C 55 TYR 0.040 0.002 TYR C 707 ARG 0.013 0.001 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 511 time to evaluate : 4.231 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8640 (tp30) cc_final: 0.8106 (tp30) REVERT: A 314 GLN cc_start: 0.7739 (tm-30) cc_final: 0.7132 (tm-30) REVERT: A 770 ILE cc_start: 0.9471 (mt) cc_final: 0.9175 (mt) REVERT: A 1005 GLN cc_start: 0.8014 (tp40) cc_final: 0.7661 (tp-100) REVERT: A 1009 THR cc_start: 0.8792 (m) cc_final: 0.8357 (m) REVERT: A 1010 GLN cc_start: 0.7920 (mp10) cc_final: 0.7612 (mp10) REVERT: C 354 ASN cc_start: 0.9545 (t0) cc_final: 0.9135 (t0) REVERT: C 765 ARG cc_start: 0.8423 (tmt-80) cc_final: 0.8042 (ptm-80) REVERT: C 790 LYS cc_start: 0.7854 (mmpt) cc_final: 0.7465 (mmmt) REVERT: C 817 PHE cc_start: 0.8067 (t80) cc_final: 0.7577 (t80) REVERT: C 883 THR cc_start: 0.7548 (p) cc_final: 0.7269 (p) REVERT: C 954 GLN cc_start: 0.8711 (pm20) cc_final: 0.8242 (pm20) REVERT: C 1007 TYR cc_start: 0.8314 (t80) cc_final: 0.7969 (t80) REVERT: C 1052 PHE cc_start: 0.8184 (m-10) cc_final: 0.6668 (m-10) REVERT: C 1082 CYS cc_start: 0.8041 (m) cc_final: 0.7741 (m) REVERT: C 1103 PHE cc_start: 0.8262 (m-10) cc_final: 0.8055 (m-80) REVERT: C 1109 PHE cc_start: 0.8988 (t80) cc_final: 0.8495 (t80) REVERT: E 53 ASP cc_start: 0.6752 (t70) cc_final: 0.6368 (t70) REVERT: E 737 ASP cc_start: 0.7464 (p0) cc_final: 0.7057 (p0) REVERT: E 800 PHE cc_start: 0.6994 (m-80) cc_final: 0.6504 (m-80) REVERT: E 925 ASN cc_start: 0.8650 (m110) cc_final: 0.8252 (m-40) REVERT: E 1010 GLN cc_start: 0.7907 (tp-100) cc_final: 0.7585 (tp40) REVERT: E 1121 PHE cc_start: 0.6606 (p90) cc_final: 0.6251 (p90) REVERT: H 47 TRP cc_start: 0.5742 (t60) cc_final: 0.4582 (t60) REVERT: H 81 MET cc_start: -0.1531 (ttp) cc_final: -0.2418 (ttp) REVERT: H 82 GLU cc_start: 0.4124 (pm20) cc_final: 0.3725 (pm20) REVERT: I 92 TYR cc_start: 0.9054 (m-10) cc_final: 0.8711 (m-10) REVERT: L 4 MET cc_start: 0.3641 (mtp) cc_final: 0.0457 (mpp) REVERT: L 42 TYR cc_start: 0.6074 (m-80) cc_final: 0.5083 (m-80) outliers start: 5 outliers final: 2 residues processed: 515 average time/residue: 0.4347 time to fit residues: 371.8739 Evaluate side-chains 413 residues out of total 3863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 411 time to evaluate : 3.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 368 optimal weight: 7.9990 chunk 330 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 chunk 176 optimal weight: 6.9990 chunk 341 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 254 optimal weight: 20.0000 chunk 395 optimal weight: 0.0570 overall best weight: 5.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 954 GLN ** C1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 GLN I 144 ASN K 41 HIS L 130 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 36349 Z= 0.332 Angle : 0.814 13.605 49459 Z= 0.415 Chirality : 0.052 0.445 5919 Planarity : 0.006 0.078 6211 Dihedral : 14.223 103.800 6735 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 30.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.23 % Favored : 86.63 % Rotamer: Outliers : 0.23 % Allowed : 7.71 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.21 % 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: -3.28 (0.11), residues: 4377 helix: -1.42 (0.18), residues: 683 sheet: -1.81 (0.21), residues: 556 loop : -2.62 (0.10), residues: 3138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 436 HIS 0.016 0.002 HIS C1048 PHE 0.025 0.002 PHE C 898 TYR 0.031 0.002 TYR E 707 ARG 0.010 0.001 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 505 time to evaluate : 4.260 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8650 (tp30) cc_final: 0.8172 (tp30) REVERT: A 740 MET cc_start: 0.7166 (tpt) cc_final: 0.6778 (tpt) REVERT: A 953 ASN cc_start: 0.7982 (m110) cc_final: 0.7756 (m110) REVERT: A 993 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7669 (mp) REVERT: A 1005 GLN cc_start: 0.8125 (tp40) cc_final: 0.7656 (tp-100) REVERT: A 1009 THR cc_start: 0.8868 (m) cc_final: 0.8270 (m) REVERT: C 312 ILE cc_start: 0.9165 (pt) cc_final: 0.8950 (pt) REVERT: C 354 ASN cc_start: 0.9590 (t0) cc_final: 0.9226 (t0) REVERT: C 663 ASP cc_start: 0.8525 (p0) cc_final: 0.7811 (p0) REVERT: C 697 MET cc_start: 0.8553 (tmm) cc_final: 0.8245 (tmm) REVERT: C 790 LYS cc_start: 0.8021 (mmpt) cc_final: 0.7611 (mmmt) REVERT: C 817 PHE cc_start: 0.8132 (t80) cc_final: 0.7717 (t80) REVERT: C 957 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8393 (tm-30) REVERT: C 996 LEU cc_start: 0.8212 (mm) cc_final: 0.7932 (mm) REVERT: C 1018 ILE cc_start: 0.9120 (mt) cc_final: 0.8449 (mt) REVERT: C 1052 PHE cc_start: 0.8402 (m-10) cc_final: 0.6967 (m-10) REVERT: C 1103 PHE cc_start: 0.8304 (m-10) cc_final: 0.8104 (m-80) REVERT: E 53 ASP cc_start: 0.6554 (t70) cc_final: 0.6312 (t70) REVERT: E 737 ASP cc_start: 0.7809 (p0) cc_final: 0.7334 (p0) REVERT: E 800 PHE cc_start: 0.7119 (m-80) cc_final: 0.6524 (m-80) REVERT: E 925 ASN cc_start: 0.8831 (m110) cc_final: 0.8533 (m-40) REVERT: E 949 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8801 (pm20) REVERT: E 950 ASP cc_start: 0.8101 (m-30) cc_final: 0.7401 (m-30) REVERT: E 1007 TYR cc_start: 0.7742 (t80) cc_final: 0.7082 (t80) REVERT: F 21 MET cc_start: 0.6955 (mpp) cc_final: 0.6512 (mpp) REVERT: H 47 TRP cc_start: 0.5919 (t60) cc_final: 0.4666 (t60) REVERT: H 81 MET cc_start: -0.1395 (ttp) cc_final: -0.1866 (ttp) REVERT: I 92 TYR cc_start: 0.9092 (m-10) cc_final: 0.8759 (m-10) REVERT: K 101 TYR cc_start: 0.7482 (p90) cc_final: 0.7191 (p90) REVERT: L 4 MET cc_start: 0.4251 (mtp) cc_final: 0.1169 (mpp) outliers start: 9 outliers final: 5 residues processed: 511 average time/residue: 0.4335 time to fit residues: 373.9214 Evaluate side-chains 416 residues out of total 3863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 409 time to evaluate : 3.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 220 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 329 optimal weight: 0.2980 chunk 269 optimal weight: 1.9990 chunk 109 optimal weight: 20.0000 chunk 396 optimal weight: 10.0000 chunk 428 optimal weight: 50.0000 chunk 353 optimal weight: 7.9990 chunk 393 optimal weight: 10.0000 chunk 135 optimal weight: 20.0000 chunk 318 optimal weight: 0.9980 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 540 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 ASN ** C1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 777 ASN ** E 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 928 ASN ** E 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1010 GLN ** E1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN ** F 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 36349 Z= 0.288 Angle : 0.781 9.882 49459 Z= 0.397 Chirality : 0.052 0.405 5919 Planarity : 0.006 0.081 6211 Dihedral : 12.801 104.210 6735 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 28.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.86 % Favored : 87.02 % Rotamer: Outliers : 0.13 % Allowed : 5.71 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.28 (0.11), residues: 4377 helix: -1.42 (0.18), residues: 686 sheet: -1.78 (0.21), residues: 551 loop : -2.63 (0.10), residues: 3140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 436 HIS 0.014 0.002 HIS A 655 PHE 0.020 0.002 PHE A 906 TYR 0.031 0.002 TYR E 707 ARG 0.007 0.001 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 530 time to evaluate : 3.701 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8627 (tp30) cc_final: 0.8184 (tp30) REVERT: A 312 ILE cc_start: 0.8967 (pt) cc_final: 0.8719 (pt) REVERT: A 314 GLN cc_start: 0.7525 (tm-30) cc_final: 0.7027 (tm-30) REVERT: A 993 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7591 (mp) REVERT: A 1005 GLN cc_start: 0.8166 (tp40) cc_final: 0.7631 (tp-100) REVERT: A 1009 THR cc_start: 0.8877 (m) cc_final: 0.8205 (m) REVERT: A 1017 GLU cc_start: 0.7953 (pp20) cc_final: 0.7702 (tm-30) REVERT: A 1028 LYS cc_start: 0.9338 (mmtp) cc_final: 0.8612 (mmtp) REVERT: A 1052 PHE cc_start: 0.8869 (m-10) cc_final: 0.8419 (m-10) REVERT: C 354 ASN cc_start: 0.9582 (t0) cc_final: 0.9216 (t0) REVERT: C 542 ASN cc_start: 0.6564 (m-40) cc_final: 0.6344 (m-40) REVERT: C 770 ILE cc_start: 0.9629 (mt) cc_final: 0.9290 (mt) REVERT: C 790 LYS cc_start: 0.8005 (mmpt) cc_final: 0.7669 (mmmt) REVERT: C 817 PHE cc_start: 0.8124 (t80) cc_final: 0.7700 (t80) REVERT: C 902 MET cc_start: 0.7996 (pmm) cc_final: 0.7565 (pmm) REVERT: C 957 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8406 (tm-30) REVERT: C 996 LEU cc_start: 0.8292 (mm) cc_final: 0.8040 (mm) REVERT: C 1018 ILE cc_start: 0.9191 (mt) cc_final: 0.8635 (mt) REVERT: C 1052 PHE cc_start: 0.8067 (m-10) cc_final: 0.6878 (m-10) REVERT: C 1103 PHE cc_start: 0.8299 (m-10) cc_final: 0.8098 (m-80) REVERT: E 53 ASP cc_start: 0.6573 (t70) cc_final: 0.6333 (t70) REVERT: E 205 SER cc_start: 0.7251 (p) cc_final: 0.6835 (m) REVERT: E 737 ASP cc_start: 0.7781 (p0) cc_final: 0.7259 (p0) REVERT: E 800 PHE cc_start: 0.7010 (m-80) cc_final: 0.6570 (m-80) REVERT: E 925 ASN cc_start: 0.8807 (m110) cc_final: 0.8403 (m-40) REVERT: E 950 ASP cc_start: 0.8088 (m-30) cc_final: 0.7580 (m-30) REVERT: E 1007 TYR cc_start: 0.7778 (t80) cc_final: 0.6878 (t80) REVERT: E 1010 GLN cc_start: 0.7769 (tp-100) cc_final: 0.7479 (tp40) REVERT: E 1014 ARG cc_start: 0.7783 (mmm160) cc_final: 0.7316 (mmm160) REVERT: E 1018 ILE cc_start: 0.9369 (mp) cc_final: 0.8839 (mp) REVERT: E 1019 ARG cc_start: 0.7872 (tmt170) cc_final: 0.7532 (tpt170) REVERT: E 1121 PHE cc_start: 0.6390 (p90) cc_final: 0.6032 (p90) REVERT: H 47 TRP cc_start: 0.5868 (t60) cc_final: 0.4614 (t60) REVERT: I 92 TYR cc_start: 0.8984 (m-10) cc_final: 0.8728 (m-10) REVERT: K 101 TYR cc_start: 0.7370 (p90) cc_final: 0.7150 (p90) REVERT: L 4 MET cc_start: 0.4489 (mtp) cc_final: 0.1519 (mpp) REVERT: L 109 LYS cc_start: 0.6756 (tttt) cc_final: 0.6256 (tptt) outliers start: 5 outliers final: 0 residues processed: 533 average time/residue: 0.4535 time to fit residues: 402.7734 Evaluate side-chains 412 residues out of total 3863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 411 time to evaluate : 4.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 391 optimal weight: 30.0000 chunk 298 optimal weight: 0.9990 chunk 205 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 189 optimal weight: 0.9990 chunk 266 optimal weight: 10.0000 chunk 398 optimal weight: 10.0000 chunk 421 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 377 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 679 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 804 GLN E 928 ASN E 955 ASN ** E 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 36349 Z= 0.250 Angle : 0.751 9.932 49459 Z= 0.379 Chirality : 0.051 0.411 5919 Planarity : 0.006 0.088 6211 Dihedral : 11.727 102.588 6735 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 26.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.59 % Favored : 87.30 % Rotamer: Outliers : 0.13 % Allowed : 4.33 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.21 (0.12), residues: 4377 helix: -1.30 (0.18), residues: 688 sheet: -1.85 (0.21), residues: 550 loop : -2.58 (0.10), residues: 3139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 154 HIS 0.011 0.002 HIS C1058 PHE 0.018 0.002 PHE E 759 TYR 0.027 0.002 TYR E 707 ARG 0.009 0.001 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 520 time to evaluate : 3.826 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8590 (tp30) cc_final: 0.8089 (tp30) REVERT: A 314 GLN cc_start: 0.7619 (tm-30) cc_final: 0.7073 (tm-30) REVERT: A 674 TYR cc_start: 0.7597 (t80) cc_final: 0.7347 (t80) REVERT: A 993 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7616 (mt) REVERT: A 1017 GLU cc_start: 0.7916 (pp20) cc_final: 0.7467 (tm-30) REVERT: A 1028 LYS cc_start: 0.9262 (mmtp) cc_final: 0.8405 (mmtm) REVERT: A 1052 PHE cc_start: 0.8885 (m-10) cc_final: 0.8499 (m-10) REVERT: C 354 ASN cc_start: 0.9590 (t0) cc_final: 0.9230 (t0) REVERT: C 396 TYR cc_start: 0.8427 (m-80) cc_final: 0.8130 (m-80) REVERT: C 498 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8275 (mm110) REVERT: C 542 ASN cc_start: 0.6433 (m-40) cc_final: 0.6194 (m-40) REVERT: C 765 ARG cc_start: 0.8480 (tmt-80) cc_final: 0.8081 (ptm-80) REVERT: C 790 LYS cc_start: 0.7879 (mmpt) cc_final: 0.7572 (mmmt) REVERT: C 817 PHE cc_start: 0.8027 (t80) cc_final: 0.7683 (t80) REVERT: C 902 MET cc_start: 0.7994 (pmm) cc_final: 0.7370 (pmm) REVERT: C 957 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8372 (tm-30) REVERT: C 996 LEU cc_start: 0.8211 (mm) cc_final: 0.7973 (mm) REVERT: C 1018 ILE cc_start: 0.9132 (mt) cc_final: 0.8582 (mt) REVERT: C 1050 MET cc_start: 0.6840 (ttt) cc_final: 0.6482 (ttt) REVERT: C 1052 PHE cc_start: 0.8406 (m-10) cc_final: 0.6675 (m-10) REVERT: C 1103 PHE cc_start: 0.8301 (m-10) cc_final: 0.8079 (m-80) REVERT: E 53 ASP cc_start: 0.6734 (t70) cc_final: 0.6434 (t70) REVERT: E 205 SER cc_start: 0.7262 (p) cc_final: 0.6711 (m) REVERT: E 567 ARG cc_start: 0.7902 (ttm110) cc_final: 0.7302 (ttm110) REVERT: E 737 ASP cc_start: 0.7754 (p0) cc_final: 0.7287 (p0) REVERT: E 800 PHE cc_start: 0.7015 (m-80) cc_final: 0.6455 (m-80) REVERT: E 925 ASN cc_start: 0.8826 (m110) cc_final: 0.8480 (m-40) REVERT: E 950 ASP cc_start: 0.8116 (m-30) cc_final: 0.7619 (m-30) REVERT: E 1007 TYR cc_start: 0.7762 (t80) cc_final: 0.6977 (t80) REVERT: E 1010 GLN cc_start: 0.7745 (tp-100) cc_final: 0.7466 (tp40) REVERT: E 1019 ARG cc_start: 0.7739 (tmt170) cc_final: 0.7446 (tpt170) REVERT: E 1050 MET cc_start: 0.7834 (ppp) cc_final: 0.6557 (ppp) REVERT: E 1121 PHE cc_start: 0.6232 (p90) cc_final: 0.5738 (p90) REVERT: I 92 TYR cc_start: 0.8992 (m-10) cc_final: 0.8700 (m-10) REVERT: K 81 MET cc_start: 0.4144 (tpt) cc_final: 0.3559 (tpt) REVERT: K 82 GLU cc_start: 0.5385 (pt0) cc_final: 0.5169 (pt0) REVERT: L 4 MET cc_start: 0.4552 (mtp) cc_final: 0.1578 (mpp) REVERT: L 109 LYS cc_start: 0.6779 (tttt) cc_final: 0.6501 (ptmt) outliers start: 5 outliers final: 0 residues processed: 522 average time/residue: 0.4446 time to fit residues: 386.2269 Evaluate side-chains 408 residues out of total 3863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 407 time to evaluate : 3.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 350 optimal weight: 40.0000 chunk 239 optimal weight: 0.9980 chunk 6 optimal weight: 0.0870 chunk 313 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 359 optimal weight: 6.9990 chunk 291 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 215 optimal weight: 30.0000 chunk 378 optimal weight: 9.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 955 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 762 GLN ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN E 901 GLN E 928 ASN E 955 ASN ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 GLN L 144 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36349 Z= 0.189 Angle : 0.721 11.175 49459 Z= 0.358 Chirality : 0.050 0.390 5919 Planarity : 0.005 0.085 6211 Dihedral : 10.462 100.560 6735 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.81 % Favored : 89.08 % Rotamer: Outliers : 0.08 % Allowed : 3.60 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.07 (0.12), residues: 4377 helix: -1.17 (0.18), residues: 682 sheet: -1.77 (0.20), residues: 600 loop : -2.47 (0.10), residues: 3095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 41 HIS 0.009 0.001 HIS C1058 PHE 0.026 0.002 PHE E 275 TYR 0.035 0.002 TYR C 873 ARG 0.013 0.001 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 553 time to evaluate : 3.656 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6585 (t80) cc_final: 0.6286 (t80) REVERT: A 298 GLU cc_start: 0.8527 (tp30) cc_final: 0.8018 (tp30) REVERT: A 314 GLN cc_start: 0.7459 (tm-30) cc_final: 0.6818 (tm-30) REVERT: A 770 ILE cc_start: 0.9213 (mt) cc_final: 0.8972 (mt) REVERT: A 1014 ARG cc_start: 0.8230 (tpp-160) cc_final: 0.7974 (tpp80) REVERT: A 1017 GLU cc_start: 0.7800 (pp20) cc_final: 0.7475 (tm-30) REVERT: A 1028 LYS cc_start: 0.9281 (mmtp) cc_final: 0.8387 (mmtm) REVERT: C 224 GLU cc_start: 0.6364 (pp20) cc_final: 0.6071 (pp20) REVERT: C 312 ILE cc_start: 0.9037 (pt) cc_final: 0.8672 (pt) REVERT: C 354 ASN cc_start: 0.9554 (t0) cc_final: 0.9234 (t0) REVERT: C 396 TYR cc_start: 0.8362 (m-80) cc_final: 0.7964 (m-80) REVERT: C 765 ARG cc_start: 0.8404 (tmt-80) cc_final: 0.7985 (ptm-80) REVERT: C 790 LYS cc_start: 0.7812 (mmpt) cc_final: 0.7599 (mmmt) REVERT: C 817 PHE cc_start: 0.7891 (t80) cc_final: 0.7649 (t80) REVERT: C 990 GLU cc_start: 0.7546 (mp0) cc_final: 0.7314 (mp0) REVERT: C 1050 MET cc_start: 0.6557 (ttt) cc_final: 0.6111 (ttt) REVERT: C 1052 PHE cc_start: 0.8219 (m-10) cc_final: 0.6813 (m-10) REVERT: C 1105 THR cc_start: 0.7200 (t) cc_final: 0.6870 (t) REVERT: E 53 ASP cc_start: 0.6666 (t70) cc_final: 0.6424 (t70) REVERT: E 104 TRP cc_start: 0.5514 (m100) cc_final: 0.5269 (m100) REVERT: E 106 PHE cc_start: 0.6300 (m-10) cc_final: 0.6023 (m-10) REVERT: E 205 SER cc_start: 0.7241 (p) cc_final: 0.6719 (m) REVERT: E 737 ASP cc_start: 0.7660 (p0) cc_final: 0.7275 (p0) REVERT: E 775 ASP cc_start: 0.8290 (p0) cc_final: 0.7774 (p0) REVERT: E 800 PHE cc_start: 0.6732 (m-80) cc_final: 0.6294 (m-80) REVERT: E 918 GLU cc_start: 0.9003 (tt0) cc_final: 0.8577 (tm-30) REVERT: E 925 ASN cc_start: 0.8808 (m110) cc_final: 0.8416 (m-40) REVERT: E 950 ASP cc_start: 0.7996 (m-30) cc_final: 0.7473 (m-30) REVERT: E 962 LEU cc_start: 0.9019 (tp) cc_final: 0.8796 (tp) REVERT: E 1007 TYR cc_start: 0.7606 (t80) cc_final: 0.6780 (t80) REVERT: E 1010 GLN cc_start: 0.7657 (tp-100) cc_final: 0.7305 (tp40) REVERT: E 1050 MET cc_start: 0.7812 (ppp) cc_final: 0.6541 (ppp) REVERT: I 92 TYR cc_start: 0.8952 (m-10) cc_final: 0.8712 (m-10) REVERT: I 98 TYR cc_start: 0.8462 (t80) cc_final: 0.7862 (t80) REVERT: L 4 MET cc_start: 0.4659 (mtp) cc_final: 0.2099 (mpp) REVERT: L 109 LYS cc_start: 0.6700 (tttt) cc_final: 0.6469 (ptmt) outliers start: 3 outliers final: 1 residues processed: 554 average time/residue: 0.4506 time to fit residues: 415.4438 Evaluate side-chains 430 residues out of total 3863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 429 time to evaluate : 3.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 141 optimal weight: 0.9980 chunk 379 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 247 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 421 optimal weight: 8.9990 chunk 350 optimal weight: 40.0000 chunk 195 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 955 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN A 965 GLN ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN ** E 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 928 ASN E 955 ASN ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36349 Z= 0.194 Angle : 0.711 16.157 49459 Z= 0.353 Chirality : 0.050 0.427 5919 Planarity : 0.005 0.090 6211 Dihedral : 9.821 96.807 6735 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.76 % Favored : 89.12 % Rotamer: Outliers : 0.05 % Allowed : 2.63 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.21 % 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: -2.98 (0.12), residues: 4377 helix: -1.06 (0.19), residues: 679 sheet: -1.70 (0.21), residues: 589 loop : -2.42 (0.10), residues: 3109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 47 HIS 0.011 0.001 HIS A1048 PHE 0.025 0.001 PHE A1075 TYR 0.027 0.002 TYR C 313 ARG 0.013 0.001 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 532 time to evaluate : 3.904 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8518 (tp30) cc_final: 0.8031 (tp30) REVERT: A 314 GLN cc_start: 0.7435 (tm-30) cc_final: 0.6830 (tm-30) REVERT: A 770 ILE cc_start: 0.9273 (mt) cc_final: 0.9053 (mt) REVERT: A 1010 GLN cc_start: 0.7547 (mp10) cc_final: 0.7329 (mp10) REVERT: A 1017 GLU cc_start: 0.7754 (pp20) cc_final: 0.7354 (tm-30) REVERT: A 1028 LYS cc_start: 0.9390 (mmtp) cc_final: 0.8494 (mmtm) REVERT: C 224 GLU cc_start: 0.6473 (pp20) cc_final: 0.6141 (pp20) REVERT: C 354 ASN cc_start: 0.9552 (t0) cc_final: 0.9217 (t0) REVERT: C 396 TYR cc_start: 0.8371 (m-80) cc_final: 0.8136 (m-80) REVERT: C 817 PHE cc_start: 0.7782 (t80) cc_final: 0.7547 (t80) REVERT: C 883 THR cc_start: 0.7687 (p) cc_final: 0.7424 (p) REVERT: C 1018 ILE cc_start: 0.9097 (mt) cc_final: 0.8482 (mt) REVERT: C 1052 PHE cc_start: 0.8106 (m-10) cc_final: 0.6935 (m-10) REVERT: C 1103 PHE cc_start: 0.8175 (m-10) cc_final: 0.7966 (m-80) REVERT: C 1105 THR cc_start: 0.7176 (t) cc_final: 0.6843 (t) REVERT: E 53 ASP cc_start: 0.6685 (t70) cc_final: 0.6388 (t70) REVERT: E 86 PHE cc_start: 0.5480 (t80) cc_final: 0.4545 (t80) REVERT: E 106 PHE cc_start: 0.6189 (m-10) cc_final: 0.5737 (m-10) REVERT: E 205 SER cc_start: 0.7137 (p) cc_final: 0.6681 (m) REVERT: E 737 ASP cc_start: 0.7518 (p0) cc_final: 0.7130 (p0) REVERT: E 772 VAL cc_start: 0.9316 (t) cc_final: 0.9102 (p) REVERT: E 775 ASP cc_start: 0.8324 (p0) cc_final: 0.7763 (p0) REVERT: E 776 LYS cc_start: 0.8982 (mtpp) cc_final: 0.8352 (tptp) REVERT: E 800 PHE cc_start: 0.6725 (m-80) cc_final: 0.6398 (m-80) REVERT: E 918 GLU cc_start: 0.8986 (tt0) cc_final: 0.8571 (tm-30) REVERT: E 925 ASN cc_start: 0.8841 (m110) cc_final: 0.8593 (m-40) REVERT: E 926 GLN cc_start: 0.9128 (pm20) cc_final: 0.8922 (pm20) REVERT: E 950 ASP cc_start: 0.8030 (m-30) cc_final: 0.7526 (m-30) REVERT: E 962 LEU cc_start: 0.9025 (tp) cc_final: 0.8771 (tp) REVERT: E 1007 TYR cc_start: 0.7599 (t80) cc_final: 0.6795 (t80) REVERT: E 1010 GLN cc_start: 0.7603 (tp-100) cc_final: 0.7308 (tp40) REVERT: E 1050 MET cc_start: 0.7678 (ppp) cc_final: 0.6338 (ppp) REVERT: I 92 TYR cc_start: 0.8924 (m-10) cc_final: 0.8673 (m-10) REVERT: I 98 TYR cc_start: 0.8390 (t80) cc_final: 0.7818 (t80) REVERT: L 4 MET cc_start: 0.4712 (mtp) cc_final: 0.2124 (mpp) REVERT: L 109 LYS cc_start: 0.6713 (tttt) cc_final: 0.6484 (ptmt) outliers start: 2 outliers final: 0 residues processed: 533 average time/residue: 0.4338 time to fit residues: 388.1263 Evaluate side-chains 430 residues out of total 3863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 3.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 406 optimal weight: 40.0000 chunk 47 optimal weight: 0.6980 chunk 240 optimal weight: 20.0000 chunk 308 optimal weight: 9.9990 chunk 238 optimal weight: 9.9990 chunk 355 optimal weight: 0.8980 chunk 235 optimal weight: 1.9990 chunk 420 optimal weight: 6.9990 chunk 262 optimal weight: 9.9990 chunk 256 optimal weight: 0.0870 chunk 194 optimal weight: 6.9990 overall best weight: 2.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN ** E 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 901 GLN ** E 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 928 ASN E 955 ASN ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 36349 Z= 0.213 Angle : 0.719 14.453 49459 Z= 0.359 Chirality : 0.050 0.443 5919 Planarity : 0.005 0.098 6211 Dihedral : 9.505 93.227 6735 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.26 % Favored : 88.65 % Rotamer: Outliers : 0.05 % Allowed : 2.06 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.21 % 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: -2.99 (0.12), residues: 4377 helix: -1.08 (0.18), residues: 684 sheet: -1.73 (0.21), residues: 589 loop : -2.42 (0.11), residues: 3104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP L 41 HIS 0.010 0.001 HIS A1048 PHE 0.024 0.002 PHE C 318 TYR 0.037 0.002 TYR E 707 ARG 0.013 0.001 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 531 time to evaluate : 3.714 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8540 (tp30) cc_final: 0.8053 (tp30) REVERT: A 314 GLN cc_start: 0.7500 (tm-30) cc_final: 0.7141 (tm-30) REVERT: A 725 GLU cc_start: 0.7457 (pt0) cc_final: 0.7141 (pt0) REVERT: A 770 ILE cc_start: 0.9320 (mt) cc_final: 0.9028 (mt) REVERT: A 1010 GLN cc_start: 0.7700 (mp10) cc_final: 0.7442 (mp10) REVERT: A 1014 ARG cc_start: 0.8312 (tpp-160) cc_final: 0.8026 (tpp80) REVERT: A 1017 GLU cc_start: 0.7864 (pp20) cc_final: 0.7504 (tm-30) REVERT: A 1028 LYS cc_start: 0.9310 (mmtp) cc_final: 0.8711 (mmtp) REVERT: A 1125 ASN cc_start: 0.5757 (p0) cc_final: 0.4380 (t0) REVERT: C 224 GLU cc_start: 0.6526 (pp20) cc_final: 0.6178 (pp20) REVERT: C 354 ASN cc_start: 0.9569 (t0) cc_final: 0.9324 (t0) REVERT: C 396 TYR cc_start: 0.8341 (m-80) cc_final: 0.8120 (m-80) REVERT: C 790 LYS cc_start: 0.7868 (mmpt) cc_final: 0.7637 (mmmt) REVERT: C 883 THR cc_start: 0.7759 (p) cc_final: 0.7550 (p) REVERT: C 1018 ILE cc_start: 0.9115 (mt) cc_final: 0.8593 (mt) REVERT: C 1052 PHE cc_start: 0.8187 (m-10) cc_final: 0.6966 (m-10) REVERT: C 1063 LEU cc_start: 0.8941 (mt) cc_final: 0.8725 (mp) REVERT: E 53 ASP cc_start: 0.6791 (t70) cc_final: 0.6475 (t70) REVERT: E 205 SER cc_start: 0.7262 (p) cc_final: 0.6805 (m) REVERT: E 737 ASP cc_start: 0.7504 (p0) cc_final: 0.7124 (p0) REVERT: E 775 ASP cc_start: 0.8358 (p0) cc_final: 0.8087 (p0) REVERT: E 800 PHE cc_start: 0.6784 (m-80) cc_final: 0.6518 (m-80) REVERT: E 925 ASN cc_start: 0.8839 (m110) cc_final: 0.8415 (m-40) REVERT: E 950 ASP cc_start: 0.8087 (m-30) cc_final: 0.7563 (m-30) REVERT: E 962 LEU cc_start: 0.9076 (tp) cc_final: 0.8839 (tp) REVERT: E 1007 TYR cc_start: 0.7623 (t80) cc_final: 0.6790 (t80) REVERT: E 1010 GLN cc_start: 0.7650 (tp-100) cc_final: 0.7357 (tp40) REVERT: I 92 TYR cc_start: 0.8950 (m-10) cc_final: 0.8696 (m-10) REVERT: I 98 TYR cc_start: 0.8411 (t80) cc_final: 0.7940 (t80) REVERT: K 81 MET cc_start: 0.3883 (tpt) cc_final: 0.3430 (tpt) REVERT: L 4 MET cc_start: 0.4631 (mtp) cc_final: 0.2083 (mpp) REVERT: L 109 LYS cc_start: 0.6728 (tttt) cc_final: 0.6488 (ptmt) outliers start: 2 outliers final: 0 residues processed: 533 average time/residue: 0.4469 time to fit residues: 393.8519 Evaluate side-chains 426 residues out of total 3863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 426 time to evaluate : 3.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 259 optimal weight: 7.9990 chunk 167 optimal weight: 1.9990 chunk 250 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 267 optimal weight: 8.9990 chunk 286 optimal weight: 0.4980 chunk 207 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 330 optimal weight: 8.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN A 965 GLN ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN ** E 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 901 GLN ** E 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 928 ASN E 955 ASN ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 36349 Z= 0.254 Angle : 0.765 14.140 49459 Z= 0.383 Chirality : 0.051 0.449 5919 Planarity : 0.006 0.101 6211 Dihedral : 9.426 82.869 6735 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 24.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.18 % Favored : 87.73 % Rotamer: Outliers : 0.03 % Allowed : 1.41 % Favored : 98.57 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 7.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.02 (0.12), residues: 4377 helix: -1.10 (0.19), residues: 681 sheet: -1.82 (0.20), residues: 640 loop : -2.42 (0.11), residues: 3056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 152 HIS 0.011 0.002 HIS C1048 PHE 0.028 0.002 PHE E1089 TYR 0.037 0.002 TYR E 707 ARG 0.017 0.001 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 523 time to evaluate : 3.916 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8546 (tp30) cc_final: 0.8094 (tp30) REVERT: A 314 GLN cc_start: 0.7663 (tm-30) cc_final: 0.7443 (tm-30) REVERT: A 406 GLU cc_start: 0.6198 (mt-10) cc_final: 0.5903 (mt-10) REVERT: A 725 GLU cc_start: 0.7575 (pt0) cc_final: 0.7125 (pt0) REVERT: A 1017 GLU cc_start: 0.7891 (pp20) cc_final: 0.7456 (tm-30) REVERT: A 1028 LYS cc_start: 0.9309 (mmtp) cc_final: 0.8783 (mmtp) REVERT: C 224 GLU cc_start: 0.6686 (pp20) cc_final: 0.6329 (pp20) REVERT: C 396 TYR cc_start: 0.8387 (m-80) cc_final: 0.8158 (m-80) REVERT: C 770 ILE cc_start: 0.9561 (mt) cc_final: 0.9336 (mt) REVERT: C 790 LYS cc_start: 0.7937 (mmpt) cc_final: 0.7710 (mmmt) REVERT: C 1018 ILE cc_start: 0.9038 (mt) cc_final: 0.8700 (mt) REVERT: C 1052 PHE cc_start: 0.7990 (m-10) cc_final: 0.6911 (m-10) REVERT: C 1063 LEU cc_start: 0.8988 (mt) cc_final: 0.8741 (mp) REVERT: E 53 ASP cc_start: 0.6837 (t70) cc_final: 0.6483 (t70) REVERT: E 205 SER cc_start: 0.7244 (p) cc_final: 0.6651 (m) REVERT: E 737 ASP cc_start: 0.7634 (p0) cc_final: 0.7250 (p0) REVERT: E 775 ASP cc_start: 0.8514 (p0) cc_final: 0.8300 (p0) REVERT: E 800 PHE cc_start: 0.6847 (m-80) cc_final: 0.6585 (m-80) REVERT: E 918 GLU cc_start: 0.8917 (tt0) cc_final: 0.8463 (tm-30) REVERT: E 925 ASN cc_start: 0.8899 (m110) cc_final: 0.8478 (m-40) REVERT: E 950 ASP cc_start: 0.8160 (m-30) cc_final: 0.7712 (m-30) REVERT: E 962 LEU cc_start: 0.9123 (tp) cc_final: 0.8911 (tp) REVERT: E 1007 TYR cc_start: 0.7658 (t80) cc_final: 0.6820 (t80) REVERT: E 1010 GLN cc_start: 0.7706 (tp-100) cc_final: 0.7411 (tp-100) REVERT: E 1050 MET cc_start: 0.7861 (ppp) cc_final: 0.7573 (ppp) REVERT: E 1121 PHE cc_start: 0.6304 (p90) cc_final: 0.5865 (p90) REVERT: I 92 TYR cc_start: 0.8986 (m-10) cc_final: 0.8739 (m-10) REVERT: I 98 TYR cc_start: 0.8454 (t80) cc_final: 0.7905 (t80) REVERT: K 81 MET cc_start: 0.4134 (tpt) cc_final: 0.3781 (tpt) REVERT: L 4 MET cc_start: 0.4710 (mtp) cc_final: 0.2073 (mpp) REVERT: L 109 LYS cc_start: 0.6726 (tttt) cc_final: 0.6506 (ptmt) outliers start: 1 outliers final: 0 residues processed: 524 average time/residue: 0.4433 time to fit residues: 386.2883 Evaluate side-chains 427 residues out of total 3863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 427 time to evaluate : 4.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 382 optimal weight: 8.9990 chunk 402 optimal weight: 7.9990 chunk 367 optimal weight: 5.9990 chunk 391 optimal weight: 8.9990 chunk 235 optimal weight: 10.0000 chunk 170 optimal weight: 0.9990 chunk 307 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 chunk 353 optimal weight: 0.5980 chunk 370 optimal weight: 9.9990 chunk 390 optimal weight: 4.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN ** E 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 901 GLN E 920 GLN E 928 ASN E 955 ASN ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 GLN K 6 GLN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 205 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 36349 Z= 0.300 Angle : 0.801 11.719 49459 Z= 0.407 Chirality : 0.052 0.452 5919 Planarity : 0.006 0.106 6211 Dihedral : 9.479 71.331 6735 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 28.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.23 % Favored : 86.68 % Rotamer: Outliers : 0.03 % Allowed : 1.12 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.11 (0.12), residues: 4377 helix: -1.17 (0.19), residues: 677 sheet: -1.91 (0.20), residues: 618 loop : -2.48 (0.11), residues: 3082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 152 HIS 0.012 0.002 HIS A1048 PHE 0.032 0.002 PHE E 275 TYR 0.035 0.002 TYR E 707 ARG 0.015 0.001 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 517 time to evaluate : 4.081 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8618 (tp30) cc_final: 0.8166 (tp30) REVERT: A 725 GLU cc_start: 0.7606 (pt0) cc_final: 0.7142 (pt0) REVERT: A 948 LEU cc_start: 0.9430 (mt) cc_final: 0.9226 (mt) REVERT: A 953 ASN cc_start: 0.8248 (m110) cc_final: 0.8035 (m110) REVERT: A 957 GLN cc_start: 0.8768 (mp10) cc_final: 0.8547 (pm20) REVERT: A 1017 GLU cc_start: 0.7916 (pp20) cc_final: 0.7578 (tm-30) REVERT: A 1028 LYS cc_start: 0.9332 (mmtp) cc_final: 0.8787 (mmtp) REVERT: C 224 GLU cc_start: 0.6682 (pp20) cc_final: 0.6347 (pp20) REVERT: C 396 TYR cc_start: 0.8412 (m-80) cc_final: 0.8181 (m-80) REVERT: C 790 LYS cc_start: 0.7752 (mmpt) cc_final: 0.7457 (mmmt) REVERT: C 902 MET cc_start: 0.8319 (pmm) cc_final: 0.7370 (pmm) REVERT: C 1052 PHE cc_start: 0.8362 (m-10) cc_final: 0.6955 (m-10) REVERT: C 1103 PHE cc_start: 0.8364 (m-80) cc_final: 0.8114 (m-80) REVERT: E 53 ASP cc_start: 0.6842 (t70) cc_final: 0.6413 (t70) REVERT: E 737 ASP cc_start: 0.7714 (p0) cc_final: 0.7298 (p0) REVERT: E 800 PHE cc_start: 0.6971 (m-80) cc_final: 0.6685 (m-80) REVERT: E 918 GLU cc_start: 0.8873 (tt0) cc_final: 0.8426 (tm-30) REVERT: E 925 ASN cc_start: 0.8880 (m110) cc_final: 0.8438 (m-40) REVERT: E 950 ASP cc_start: 0.8184 (m-30) cc_final: 0.7707 (m-30) REVERT: E 962 LEU cc_start: 0.9090 (tp) cc_final: 0.8868 (tp) REVERT: E 1007 TYR cc_start: 0.7819 (t80) cc_final: 0.6901 (t80) REVERT: E 1010 GLN cc_start: 0.7778 (tp-100) cc_final: 0.7551 (tp-100) REVERT: E 1121 PHE cc_start: 0.6479 (p90) cc_final: 0.6126 (p90) REVERT: F 41 TRP cc_start: 0.5096 (m100) cc_final: 0.4530 (m100) REVERT: H 81 MET cc_start: -0.1270 (tmm) cc_final: -0.1747 (tmm) REVERT: I 60 ARG cc_start: 0.4656 (ptt-90) cc_final: 0.3254 (pmt170) REVERT: I 92 TYR cc_start: 0.8992 (m-10) cc_final: 0.8726 (m-10) REVERT: I 98 TYR cc_start: 0.8495 (t80) cc_final: 0.8040 (t80) REVERT: K 11 MET cc_start: 0.5850 (tmm) cc_final: 0.5453 (tmm) REVERT: K 81 MET cc_start: 0.4342 (tpt) cc_final: 0.3877 (tpt) REVERT: L 4 MET cc_start: 0.4673 (mtp) cc_final: 0.2025 (mpp) REVERT: L 109 LYS cc_start: 0.6925 (tttt) cc_final: 0.6444 (tptt) outliers start: 1 outliers final: 0 residues processed: 518 average time/residue: 0.4543 time to fit residues: 390.6741 Evaluate side-chains 411 residues out of total 3863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 3.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 257 optimal weight: 1.9990 chunk 414 optimal weight: 20.0000 chunk 252 optimal weight: 2.9990 chunk 196 optimal weight: 5.9990 chunk 287 optimal weight: 0.9980 chunk 434 optimal weight: 7.9990 chunk 399 optimal weight: 3.9990 chunk 345 optimal weight: 8.9990 chunk 35 optimal weight: 0.0470 chunk 267 optimal weight: 7.9990 chunk 212 optimal weight: 6.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 960 ASN ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 954 GLN ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN ** E 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 901 GLN E 928 ASN E 955 ASN ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 36349 Z= 0.229 Angle : 0.759 12.112 49459 Z= 0.380 Chirality : 0.052 0.616 5919 Planarity : 0.006 0.107 6211 Dihedral : 9.092 69.645 6735 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 24.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.99 % Favored : 87.91 % Rotamer: Outliers : 0.08 % Allowed : 0.52 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.07 (0.12), residues: 4377 helix: -1.16 (0.19), residues: 683 sheet: -1.79 (0.21), residues: 604 loop : -2.47 (0.11), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP L 41 HIS 0.014 0.002 HIS A1048 PHE 0.030 0.002 PHE C 55 TYR 0.037 0.002 TYR C 873 ARG 0.012 0.001 ARG A 995 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 519 time to evaluate : 3.432 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8548 (tp30) cc_final: 0.8086 (tp30) REVERT: A 314 GLN cc_start: 0.7434 (tm-30) cc_final: 0.6871 (tm-30) REVERT: A 901 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8314 (tm-30) REVERT: A 953 ASN cc_start: 0.8203 (m110) cc_final: 0.7975 (m110) REVERT: A 1017 GLU cc_start: 0.7823 (pp20) cc_final: 0.7440 (tm-30) REVERT: A 1109 PHE cc_start: 0.8768 (t80) cc_final: 0.8310 (t80) REVERT: C 312 ILE cc_start: 0.9136 (pt) cc_final: 0.8923 (pt) REVERT: C 777 ASN cc_start: 0.8809 (m110) cc_final: 0.8595 (m110) REVERT: C 790 LYS cc_start: 0.7693 (mmpt) cc_final: 0.7361 (mmmt) REVERT: C 902 MET cc_start: 0.8206 (pmm) cc_final: 0.7456 (pmm) REVERT: C 1018 ILE cc_start: 0.9026 (mt) cc_final: 0.8598 (mt) REVERT: C 1052 PHE cc_start: 0.8253 (m-10) cc_final: 0.6944 (m-10) REVERT: C 1063 LEU cc_start: 0.9026 (mp) cc_final: 0.8796 (mt) REVERT: E 53 ASP cc_start: 0.6817 (t70) cc_final: 0.6403 (t70) REVERT: E 737 ASP cc_start: 0.7651 (p0) cc_final: 0.7277 (p0) REVERT: E 775 ASP cc_start: 0.8356 (p0) cc_final: 0.8065 (p0) REVERT: E 800 PHE cc_start: 0.6830 (m-80) cc_final: 0.6587 (m-80) REVERT: E 818 ILE cc_start: 0.9383 (pt) cc_final: 0.9168 (pt) REVERT: E 918 GLU cc_start: 0.8858 (tt0) cc_final: 0.8419 (tm-30) REVERT: E 950 ASP cc_start: 0.8119 (m-30) cc_final: 0.7680 (m-30) REVERT: E 962 LEU cc_start: 0.9087 (tp) cc_final: 0.8858 (tp) REVERT: E 1007 TYR cc_start: 0.7639 (t80) cc_final: 0.6741 (t80) REVERT: E 1010 GLN cc_start: 0.7595 (tp-100) cc_final: 0.7379 (tp-100) REVERT: E 1121 PHE cc_start: 0.6542 (p90) cc_final: 0.6035 (p90) REVERT: I 60 ARG cc_start: 0.4521 (ptt-90) cc_final: 0.3915 (mtt90) REVERT: I 92 TYR cc_start: 0.8976 (m-10) cc_final: 0.8731 (m-10) REVERT: I 98 TYR cc_start: 0.8405 (t80) cc_final: 0.7931 (t80) REVERT: K 11 MET cc_start: 0.5931 (tmm) cc_final: 0.5529 (tmm) REVERT: K 81 MET cc_start: 0.4120 (tpt) cc_final: 0.3724 (tpt) REVERT: L 4 MET cc_start: 0.4596 (mtp) cc_final: 0.2131 (mpp) REVERT: L 109 LYS cc_start: 0.6871 (tttt) cc_final: 0.6376 (tptt) outliers start: 3 outliers final: 0 residues processed: 522 average time/residue: 0.4328 time to fit residues: 373.9737 Evaluate side-chains 419 residues out of total 3863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 418 time to evaluate : 4.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.316 > 50: distance: 71 - 177: 38.373 distance: 74 - 174: 31.195 distance: 133 - 136: 33.693 distance: 136 - 137: 41.289 distance: 137 - 138: 66.166 distance: 137 - 140: 67.241 distance: 138 - 139: 56.663 distance: 138 - 148: 39.838 distance: 140 - 141: 41.136 distance: 141 - 142: 8.995 distance: 142 - 144: 28.950 distance: 143 - 145: 16.301 distance: 144 - 146: 40.678 distance: 145 - 146: 39.785 distance: 146 - 147: 28.676 distance: 148 - 149: 56.976 distance: 149 - 150: 57.308 distance: 149 - 152: 58.000 distance: 150 - 151: 16.392 distance: 150 - 159: 59.410 distance: 152 - 153: 14.326 distance: 153 - 155: 56.587 distance: 154 - 156: 7.992 distance: 156 - 158: 52.698 distance: 157 - 158: 48.932 distance: 159 - 160: 55.170 distance: 159 - 165: 29.227 distance: 160 - 161: 40.687 distance: 160 - 163: 42.768 distance: 161 - 162: 34.136 distance: 161 - 166: 40.587 distance: 163 - 164: 23.874 distance: 164 - 165: 47.488 distance: 166 - 167: 38.864 distance: 167 - 168: 40.766 distance: 167 - 170: 40.928 distance: 168 - 169: 40.532 distance: 168 - 174: 40.528 distance: 170 - 171: 52.819 distance: 171 - 172: 53.346 distance: 171 - 173: 60.584 distance: 174 - 175: 51.185 distance: 175 - 176: 56.605 distance: 175 - 178: 55.318 distance: 176 - 177: 40.841 distance: 176 - 183: 56.060 distance: 178 - 179: 49.209 distance: 179 - 180: 46.910 distance: 180 - 181: 38.515 distance: 180 - 182: 37.212 distance: 183 - 184: 39.907 distance: 184 - 185: 62.845 distance: 184 - 187: 55.417 distance: 185 - 186: 62.993 distance: 185 - 189: 13.848 distance: 187 - 188: 40.137 distance: 189 - 190: 55.586 distance: 190 - 193: 40.017 distance: 191 - 192: 39.106 distance: 191 - 201: 45.778 distance: 193 - 194: 34.717 distance: 194 - 196: 4.858 distance: 195 - 197: 32.486 distance: 196 - 198: 15.746 distance: 197 - 199: 40.274 distance: 198 - 199: 43.121 distance: 199 - 200: 35.295 distance: 201 - 202: 45.196 distance: 203 - 204: 56.074 distance: 203 - 205: 40.783 distance: 205 - 206: 39.372 distance: 206 - 207: 28.217 distance: 206 - 209: 40.584 distance: 207 - 208: 39.936 distance: 207 - 216: 36.241 distance: 210 - 211: 11.692 distance: 210 - 212: 39.077 distance: 211 - 213: 12.020 distance: 213 - 215: 55.627 distance: 214 - 215: 38.911 distance: 217 - 218: 57.843 distance: 217 - 220: 41.217 distance: 218 - 225: 29.275 distance: 220 - 221: 60.635 distance: 221 - 222: 59.969 distance: 222 - 224: 66.363