Starting phenix.real_space_refine on Tue Dec 12 04:10:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g85_29836/12_2023/8g85_29836.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g85_29836/12_2023/8g85_29836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g85_29836/12_2023/8g85_29836.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g85_29836/12_2023/8g85_29836.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g85_29836/12_2023/8g85_29836.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g85_29836/12_2023/8g85_29836.pdb" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.061 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 129 5.16 5 C 12577 2.51 5 N 3347 2.21 5 O 4037 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 92": "OE1" <-> "OE2" Residue "G PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 267": "OE1" <-> "OE2" Residue "G GLU 275": "OE1" <-> "OE2" Residue "G ASP 321": "OD1" <-> "OD2" Residue "G ASP 325": "OD1" <-> "OD2" Residue "G GLU 370": "OE1" <-> "OE2" Residue "G PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 457": "OD1" <-> "OD2" Residue "G ASP 474": "OD1" <-> "OD2" Residue "G ASP 477": "OD1" <-> "OD2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 657": "OE1" <-> "OE2" Residue "B ASP 659": "OD1" <-> "OD2" Residue "D ASP 107": "OD1" <-> "OD2" Residue "D PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 368": "OD1" <-> "OD2" Residue "D GLU 370": "OE1" <-> "OE2" Residue "D PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 381": "OE1" <-> "OE2" Residue "D PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 492": "OE1" <-> "OE2" Residue "E PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 632": "OD1" <-> "OD2" Residue "E TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 659": "OD1" <-> "OD2" Residue "J GLU 87": "OE1" <-> "OE2" Residue "J GLU 153": "OE1" <-> "OE2" Residue "J TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 368": "OD1" <-> "OD2" Residue "J GLU 370": "OE1" <-> "OE2" Residue "J PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 482": "OE1" <-> "OE2" Residue "K ASP 624": "OD1" <-> "OD2" Residue "K ASP 632": "OD1" <-> "OD2" Residue "K GLU 634": "OE1" <-> "OE2" Residue "K GLU 648": "OE1" <-> "OE2" Residue "K GLU 657": "OE1" <-> "OE2" Residue "K ASP 659": "OD1" <-> "OD2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 94": "NH1" <-> "NH2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ASP 60": "OD1" <-> "OD2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 82": "OD1" <-> "OD2" Residue "L ASP 85": "OD1" <-> "OD2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "A TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 66": "NH1" <-> "NH2" Residue "A ARG 94": "NH1" <-> "NH2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C ASP 60": "OD1" <-> "OD2" Residue "C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 82": "OD1" <-> "OD2" Residue "C ASP 85": "OD1" <-> "OD2" Residue "C TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "F TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 66": "NH1" <-> "NH2" Residue "F PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 94": "NH1" <-> "NH2" Residue "I ARG 18": "NH1" <-> "NH2" Residue "I ARG 54": "NH1" <-> "NH2" Residue "I ASP 60": "OD1" <-> "OD2" Residue "I PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 82": "OD1" <-> "OD2" Residue "I ASP 85": "OD1" <-> "OD2" Residue "I TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 105": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 20090 Number of models: 1 Model: "" Number of chains: 39 Chain: "G" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3468 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1059 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain breaks: 1 Chain: "D" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3468 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "E" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1059 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain breaks: 1 Chain: "J" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3468 Classifications: {'peptide': 441} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "K" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1059 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 1, 'TRANS': 133} Chain breaks: 1 Chain: "H" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 917 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "L" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 831 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 917 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "C" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 831 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 917 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "I" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 831 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "M" 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: 6 Unresolved non-hydrogen chiralities: 5 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: 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: "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: 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: 6 Unresolved non-hydrogen chiralities: 4 Chain: "T" 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: 6 Unresolved non-hydrogen chiralities: 5 Chain: "U" 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: "V" 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: 6 Unresolved non-hydrogen chiralities: 4 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: 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: "b" 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: 6 Unresolved non-hydrogen chiralities: 3 Chain: "c" 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: 6 Unresolved non-hydrogen chiralities: 3 Chain: "d" 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: 6 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" 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: "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: "h" 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: 6 Unresolved non-hydrogen chiralities: 3 Chain: "i" 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: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 9.89, per 1000 atoms: 0.49 Number of scatterers: 20090 At special positions: 0 Unit cell: (132.016, 145.969, 140.602, 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 129 16.00 O 4037 8.00 N 3347 7.00 C 12577 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.05 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 201 " - pdb=" SG CYS D 433 " distance=2.04 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.05 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 74 " distance=2.04 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.03 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.03 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 157 " distance=2.03 Simple disulfide: pdb=" SG CYS J 201 " - pdb=" SG CYS J 433 " distance=2.03 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.03 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.03 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.03 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.03 Simple disulfide: pdb=" SG CYS J 501 " - pdb=" SG CYS K 605 " distance=2.03 Simple disulfide: pdb=" SG CYS K 598 " - pdb=" SG CYS K 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " MAN M 4 " - " MAN M 5 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA d 3 " - " MAN d 4 " ALPHA1-6 " BMA M 3 " - " MAN M 4 " " BMA T 3 " - " MAN T 5 " " BMA V 3 " - " MAN V 4 " " BMA d 3 " - " MAN d 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " 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 T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " NAG-ASN " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG D 601 " - " ASN D 133 " " NAG D 602 " - " ASN D 156 " " NAG D 603 " - " ASN D 160 " " NAG D 604 " - " ASN D 197 " " NAG D 605 " - " ASN D 276 " " NAG D 606 " - " ASN D 301 " " NAG D 607 " - " ASN D 355 " " NAG D 608 " - " ASN D 339 " " NAG D 609 " - " ASN D 392 " " NAG D 610 " - " ASN D 234 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 637 " " NAG G 601 " - " ASN G 133 " " NAG G 602 " - " ASN G 156 " " NAG G 603 " - " ASN G 160 " " NAG G 604 " - " ASN G 197 " " NAG G 605 " - " ASN G 276 " " NAG G 606 " - " ASN G 301 " " NAG G 607 " - " ASN G 355 " " NAG G 608 " - " ASN G 339 " " NAG G 609 " - " ASN G 392 " " NAG G 610 " - " ASN G 234 " " NAG J 601 " - " ASN J 133 " " NAG J 602 " - " ASN J 156 " " NAG J 603 " - " ASN J 160 " " NAG J 604 " - " ASN J 197 " " NAG J 605 " - " ASN J 276 " " NAG J 606 " - " ASN J 301 " " NAG J 607 " - " ASN J 355 " " NAG J 608 " - " ASN J 339 " " NAG J 609 " - " ASN J 392 " " NAG J 610 " - " ASN J 234 " " NAG K 701 " - " ASN K 637 " " NAG M 1 " - " ASN G 262 " " NAG O 1 " - " ASN G 295 " " NAG P 1 " - " ASN G 332 " " NAG Q 1 " - " ASN G 363 " " NAG R 1 " - " ASN G 386 " " NAG S 1 " - " ASN G 448 " " NAG T 1 " - " ASN G 88 " " NAG U 1 " - " ASN D 88 " " NAG V 1 " - " ASN D 262 " " NAG X 1 " - " ASN D 295 " " NAG Y 1 " - " ASN D 332 " " NAG Z 1 " - " ASN D 363 " " NAG a 1 " - " ASN D 386 " " NAG b 1 " - " ASN D 448 " " NAG c 1 " - " ASN J 88 " " NAG d 1 " - " ASN J 262 " " NAG e 1 " - " ASN J 295 " " NAG f 1 " - " ASN J 332 " " NAG g 1 " - " ASN J 363 " " NAG h 1 " - " ASN J 386 " " NAG i 1 " - " ASN J 448 " Time building additional restraints: 8.71 Conformation dependent library (CDL) restraints added in 3.7 seconds 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 42 sheets defined 19.0% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'G' and resid 99 through 115 removed outlier: 3.504A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER G 110 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.681A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 122 through 126' Processing helix chain 'G' and resid 334 through 350 removed outlier: 3.794A pdb=" N GLN G 348 " --> pdb=" O LYS G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.820A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 391 removed outlier: 4.104A pdb=" N LEU G 390 " --> pdb=" O THR G 387 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE G 391 " --> pdb=" O SER G 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 387 through 391' Processing helix chain 'G' and resid 474 through 479 removed outlier: 3.761A pdb=" N ASP G 477 " --> pdb=" O ASP G 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 removed outlier: 3.788A pdb=" N ALA B 517 " --> pdb=" O GLY B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 3.818A pdb=" N ALA B 526 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 523 through 527' Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.699A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.945A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 633 removed outlier: 4.168A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 637 No H-bonds generated for 'chain 'B' and resid 635 through 637' Processing helix chain 'B' and resid 638 through 662 removed outlier: 4.060A pdb=" N LEU B 646 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 115 removed outlier: 4.274A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE D 109 " --> pdb=" O HIS D 105 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER D 115 " --> pdb=" O LEU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.558A pdb=" N LEU D 125 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS D 126 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL D 127 " --> pdb=" O PRO D 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 127' Processing helix chain 'D' and resid 139 through 151 removed outlier: 3.570A pdb=" N MET D 150 " --> pdb=" O THR D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 334 through 350 removed outlier: 3.543A pdb=" N LYS D 347 " --> pdb=" O GLY D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.887A pdb=" N THR D 373 " --> pdb=" O LEU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 481 removed outlier: 4.045A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 517 Processing helix chain 'E' and resid 531 through 535 removed outlier: 4.105A pdb=" N MET E 535 " --> pdb=" O ALA E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 542 removed outlier: 4.070A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA E 541 " --> pdb=" O LEU E 537 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG E 542 " --> pdb=" O THR E 538 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 536 through 542' Processing helix chain 'E' and resid 572 through 596 removed outlier: 3.913A pdb=" N TYR E 586 " --> pdb=" O ALA E 582 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU E 593 " --> pdb=" O ASP E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 622 removed outlier: 3.517A pdb=" N ILE E 622 " --> pdb=" O LEU E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 636 removed outlier: 4.087A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE E 635 " --> pdb=" O TRP E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 662 removed outlier: 3.679A pdb=" N LEU E 645 " --> pdb=" O ILE E 641 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU E 646 " --> pdb=" O ILE E 642 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU E 647 " --> pdb=" O TYR E 643 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN E 651 " --> pdb=" O GLU E 647 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS E 655 " --> pdb=" O ASN E 651 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN E 656 " --> pdb=" O GLN E 652 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU E 660 " --> pdb=" O ASN E 656 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 115 removed outlier: 4.102A pdb=" N GLU J 102 " --> pdb=" O ASN J 98 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE J 109 " --> pdb=" O HIS J 105 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER J 115 " --> pdb=" O LEU J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 127 removed outlier: 3.759A pdb=" N CYS J 126 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL J 127 " --> pdb=" O PRO J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 334 through 353 removed outlier: 3.977A pdb=" N LYS J 347 " --> pdb=" O GLY J 343 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN J 348 " --> pdb=" O LYS J 344 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS J 351 " --> pdb=" O LYS J 347 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS J 352 " --> pdb=" O GLN J 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 368 through 373 removed outlier: 3.787A pdb=" N THR J 373 " --> pdb=" O LEU J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 381 removed outlier: 4.135A pdb=" N GLY J 380 " --> pdb=" O ASN J 377 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU J 381 " --> pdb=" O CYS J 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 377 through 381' Processing helix chain 'J' and resid 474 through 482 removed outlier: 3.561A pdb=" N TRP J 479 " --> pdb=" O ARG J 476 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG J 480 " --> pdb=" O ASP J 477 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER J 481 " --> pdb=" O ASN J 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 513 through 517 removed outlier: 3.699A pdb=" N ALA K 517 " --> pdb=" O GLY K 514 " (cutoff:3.500A) Processing helix chain 'K' and resid 529 through 534 Processing helix chain 'K' and resid 575 through 596 removed outlier: 3.502A pdb=" N LEU K 592 " --> pdb=" O ARG K 588 " (cutoff:3.500A) Processing helix chain 'K' and resid 627 through 635 removed outlier: 3.533A pdb=" N TRP K 631 " --> pdb=" O THR K 627 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS K 633 " --> pdb=" O LEU K 629 " (cutoff:3.500A) Processing helix chain 'K' and resid 638 through 662 removed outlier: 3.689A pdb=" N ILE K 642 " --> pdb=" O TYR K 638 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY K 644 " --> pdb=" O GLN K 640 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU K 646 " --> pdb=" O ILE K 642 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLU K 647 " --> pdb=" O TYR K 643 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU K 648 " --> pdb=" O GLY K 644 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN K 652 " --> pdb=" O GLU K 648 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.524A pdb=" N ASP C 82 " --> pdb=" O GLN C 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'G' and resid 494 through 499 removed outlier: 3.551A pdb=" N CYS B 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 46 removed outlier: 3.899A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 91 through 93 removed outlier: 3.835A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 130 through 133 Processing sheet with id=AA5, first strand: chain 'G' and resid 181 through 182 Processing sheet with id=AA6, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.621A pdb=" N MET G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR G 297 " --> pdb=" O HIS G 330 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE G 383 " --> pdb=" O PHE G 376 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE G 376 " --> pdb=" O PHE G 383 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.621A pdb=" N MET G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.782A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.811A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.652A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.186A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.955A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 10.634A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 10.163A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.910A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 494 through 495 Processing sheet with id=AB1, first strand: chain 'D' and resid 494 through 495 Processing sheet with id=AB2, first strand: chain 'D' and resid 45 through 46 removed outlier: 3.918A pdb=" N ILE D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 75 through 76 removed outlier: 4.339A pdb=" N VAL D 75 " --> pdb=" O CYS D 54 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER D 56 " --> pdb=" O VAL D 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 91 through 93 removed outlier: 3.547A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 132 through 133 removed outlier: 3.690A pdb=" N VAL D 172 " --> pdb=" O PHE D 159 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 181 through 182 Processing sheet with id=AB7, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.337A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 10.007A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.235A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.647A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.609A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.033A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS D 330 " --> pdb=" O THR D 297 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL D 333 " --> pdb=" O ILE D 414 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE D 383 " --> pdb=" O PHE D 376 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE D 376 " --> pdb=" O PHE D 383 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 271 through 273 removed outlier: 3.503A pdb=" N LEU D 285 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 10.033A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.609A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.647A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.235A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.007A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER D 393 " --> pdb=" O PHE D 361 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 304 through 312 removed outlier: 6.843A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 494 through 499 removed outlier: 4.979A pdb=" N VAL J 36 " --> pdb=" O THR K 606 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 45 through 46 removed outlier: 3.787A pdb=" N ILE J 225 " --> pdb=" O VAL J 245 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 91 through 93 Processing sheet with id=AC4, first strand: chain 'J' and resid 130 through 133 Processing sheet with id=AC5, first strand: chain 'J' and resid 181 through 182 Processing sheet with id=AC6, first strand: chain 'J' and resid 259 through 261 removed outlier: 6.172A pdb=" N LEU J 260 " --> pdb=" O THR J 450 " (cutoff:3.500A) removed outlier: 10.514A pdb=" N VAL J 442 " --> pdb=" O CYS J 296 " (cutoff:3.500A) removed outlier: 11.451A pdb=" N CYS J 296 " --> pdb=" O VAL J 442 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N ARG J 444 " --> pdb=" O ILE J 294 " (cutoff:3.500A) removed outlier: 11.160A pdb=" N ILE J 294 " --> pdb=" O ARG J 444 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N VAL J 446 " --> pdb=" O VAL J 292 " (cutoff:3.500A) removed outlier: 10.896A pdb=" N VAL J 292 " --> pdb=" O VAL J 446 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ASN J 448 " --> pdb=" O THR J 290 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N THR J 290 " --> pdb=" O ASN J 448 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR J 450 " --> pdb=" O PHE J 288 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS J 330 " --> pdb=" O THR J 297 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL J 333 " --> pdb=" O ILE J 414 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE J 376 " --> pdb=" O PHE J 383 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 271 through 273 removed outlier: 3.934A pdb=" N MET J 271 " --> pdb=" O GLN J 287 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN J 287 " --> pdb=" O MET J 271 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU J 285 " --> pdb=" O ARG J 273 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR J 450 " --> pdb=" O PHE J 288 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N THR J 290 " --> pdb=" O ASN J 448 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N ASN J 448 " --> pdb=" O THR J 290 " (cutoff:3.500A) removed outlier: 10.896A pdb=" N VAL J 292 " --> pdb=" O VAL J 446 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N VAL J 446 " --> pdb=" O VAL J 292 " (cutoff:3.500A) removed outlier: 11.160A pdb=" N ILE J 294 " --> pdb=" O ARG J 444 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N ARG J 444 " --> pdb=" O ILE J 294 " (cutoff:3.500A) removed outlier: 11.451A pdb=" N CYS J 296 " --> pdb=" O VAL J 442 " (cutoff:3.500A) removed outlier: 10.514A pdb=" N VAL J 442 " --> pdb=" O CYS J 296 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG J 360 " --> pdb=" O PHE J 468 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER J 393 " --> pdb=" O PHE J 361 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 305 through 312 removed outlier: 6.840A pdb=" N GLN J 315 " --> pdb=" O ILE J 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 423 through 425 Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.563A pdb=" N GLN H 3 " --> pdb=" O THR H 25 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER H 68 " --> pdb=" O LYS H 81 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.674A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA H 88 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU H 95 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR H 34 " --> pdb=" O GLU H 95 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP H 35 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR H 50 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.674A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA H 88 " --> pdb=" O LEU H 109 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.504A pdb=" N THR L 5 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.336A pdb=" N MET L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR L 49 " --> pdb=" O THR L 53 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.553A pdb=" N PHE A 78 " --> pdb=" O CYS A 22 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.702A pdb=" N LEU A 109 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 88 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP A 35 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR A 50 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET A 48 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 38 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS A 44 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 58 " --> pdb=" O TYR A 50 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.702A pdb=" N LEU A 109 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 88 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AE1, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.553A pdb=" N MET C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR C 49 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR C 49 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR C 53 " --> pdb=" O TYR C 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.652A pdb=" N VAL F 12 " --> pdb=" O ILE F 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR F 107 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU F 109 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA F 88 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP F 35 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TYR F 50 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET F 48 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG F 38 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS F 44 " --> pdb=" O PHE F 40 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY F 58 " --> pdb=" O TYR F 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.652A pdb=" N VAL F 12 " --> pdb=" O ILE F 110 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR F 107 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU F 109 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA F 88 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AE6, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.616A pdb=" N MET I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TYR I 49 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR I 49 " --> pdb=" O THR I 53 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR I 53 " --> pdb=" O TYR I 49 " (cutoff:3.500A) 585 hydrogen bonds defined for protein. 1485 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: 6.67 Time building geometry restraints manager: 9.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6274 1.34 - 1.47: 5131 1.47 - 1.59: 8916 1.59 - 1.71: 0 1.71 - 1.83: 174 Bond restraints: 20495 Sorted by residual: bond pdb=" C1 NAG D 610 " pdb=" O5 NAG D 610 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C1 NAG G 610 " pdb=" O5 NAG G 610 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C1 NAG c 1 " pdb=" O5 NAG c 1 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C1 MAN M 5 " pdb=" C2 MAN M 5 " ideal model delta sigma weight residual 1.526 1.581 -0.055 2.00e-02 2.50e+03 7.46e+00 bond pdb=" C1 MAN M 5 " pdb=" O5 MAN M 5 " ideal model delta sigma weight residual 1.399 1.454 -0.055 2.00e-02 2.50e+03 7.46e+00 ... (remaining 20490 not shown) Histogram of bond angle deviations from ideal: 90.92 - 100.00: 10 100.00 - 109.07: 1807 109.07 - 118.14: 14351 118.14 - 127.21: 11402 127.21 - 136.28: 260 Bond angle restraints: 27830 Sorted by residual: angle pdb=" CG ARG H 94 " pdb=" CD ARG H 94 " pdb=" NE ARG H 94 " ideal model delta sigma weight residual 112.00 90.92 21.08 2.20e+00 2.07e-01 9.18e+01 angle pdb=" C ALA H 32 " pdb=" N TYR H 33 " pdb=" CA TYR H 33 " ideal model delta sigma weight residual 121.74 136.28 -14.54 1.58e+00 4.01e-01 8.47e+01 angle pdb=" CB ARG H 94 " pdb=" CG ARG H 94 " pdb=" CD ARG H 94 " ideal model delta sigma weight residual 111.30 128.66 -17.36 2.30e+00 1.89e-01 5.70e+01 angle pdb=" CA ARG H 94 " pdb=" CB ARG H 94 " pdb=" CG ARG H 94 " ideal model delta sigma weight residual 114.10 128.29 -14.19 2.00e+00 2.50e-01 5.03e+01 angle pdb=" C LYS H 64 " pdb=" CA LYS H 64 " pdb=" CB LYS H 64 " ideal model delta sigma weight residual 116.54 109.04 7.50 1.15e+00 7.56e-01 4.25e+01 ... (remaining 27825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.04: 12339 24.04 - 48.07: 677 48.07 - 72.11: 125 72.11 - 96.15: 15 96.15 - 120.18: 2 Dihedral angle restraints: 13158 sinusoidal: 6270 harmonic: 6888 Sorted by residual: dihedral pdb=" CB CYS G 218 " pdb=" SG CYS G 218 " pdb=" SG CYS G 247 " pdb=" CB CYS G 247 " ideal model delta sinusoidal sigma weight residual -86.00 -5.65 -80.35 1 1.00e+01 1.00e-02 7.99e+01 dihedral pdb=" CB CYS G 201 " pdb=" SG CYS G 201 " pdb=" SG CYS G 433 " pdb=" CB CYS G 433 " ideal model delta sinusoidal sigma weight residual -86.00 -16.38 -69.62 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CB CYS J 54 " pdb=" SG CYS J 54 " pdb=" SG CYS J 74 " pdb=" CB CYS J 74 " ideal model delta sinusoidal sigma weight residual -86.00 -16.88 -69.12 1 1.00e+01 1.00e-02 6.18e+01 ... (remaining 13155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3035 0.095 - 0.190: 333 0.190 - 0.285: 20 0.285 - 0.380: 5 0.380 - 0.474: 2 Chirality restraints: 3395 Sorted by residual: chirality pdb=" C1 NAG B 701 " pdb=" ND2 ASN B 611 " pdb=" C2 NAG B 701 " pdb=" O5 NAG B 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.63e+00 chirality pdb=" C1 NAG E 701 " pdb=" ND2 ASN E 611 " pdb=" C2 NAG E 701 " pdb=" O5 NAG E 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" C1 NAG D 605 " pdb=" ND2 ASN D 276 " pdb=" C2 NAG D 605 " pdb=" O5 NAG D 605 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 3392 not shown) Planarity restraints: 3472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 94 " 0.096 9.50e-02 1.11e+02 5.47e-02 1.54e+01 pdb=" NE ARG F 94 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG F 94 " 0.064 2.00e-02 2.50e+03 pdb=" NH1 ARG F 94 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG F 94 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA D 497 " -0.062 5.00e-02 4.00e+02 9.49e-02 1.44e+01 pdb=" N PRO D 498 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO D 498 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 498 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 42 " 0.042 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO G 43 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO G 43 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 43 " 0.036 5.00e-02 4.00e+02 ... (remaining 3469 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4061 2.79 - 3.32: 16698 3.32 - 3.84: 31260 3.84 - 4.37: 34508 4.37 - 4.90: 60633 Nonbonded interactions: 147160 Sorted by model distance: nonbonded pdb=" OG SER C 12 " pdb=" OE1 GLU C 105 " model vdw 2.259 2.440 nonbonded pdb=" O ILE J 277 " pdb=" NH2 ARG J 456 " model vdw 2.309 2.520 nonbonded pdb=" NZ LYS L 24 " pdb=" OD2 ASP L 70 " model vdw 2.315 2.520 nonbonded pdb=" OG SER G 264 " pdb=" OE2 GLU G 482 " model vdw 2.319 2.440 nonbonded pdb=" OD1 ASN G 283 " pdb=" OG1 THR G 455 " model vdw 2.327 2.440 ... (remaining 147155 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' selection = chain 'F' selection = chain 'H' } ncs_group { reference = (chain 'B' and (resid 512 through 662 or resid 701)) selection = (chain 'E' and (resid 512 through 662 or resid 701)) selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'M' selection = chain 'T' selection = chain 'd' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'S' selection = chain 'V' } ncs_group { reference = chain 'b' selection = chain 'c' selection = chain 'h' selection = chain 'i' } 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: 1.750 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: 0.020 Extract box with map and model: 7.760 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 52.840 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 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 0.088 20495 Z= 0.327 Angle : 0.969 21.075 27830 Z= 0.497 Chirality : 0.058 0.474 3395 Planarity : 0.005 0.095 3416 Dihedral : 14.190 120.185 8592 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.61 % Favored : 95.31 % Rotamer: Outliers : 0.09 % Allowed : 1.09 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.16), residues: 2343 helix: -3.31 (0.18), residues: 337 sheet: 0.51 (0.21), residues: 552 loop : -1.18 (0.15), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 427 HIS 0.006 0.001 HIS I 89 PHE 0.020 0.001 PHE I 98 TYR 0.029 0.002 TYR F 50 ARG 0.065 0.002 ARG F 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 272 time to evaluate : 2.061 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 outliers start: 2 outliers final: 1 residues processed: 274 average time/residue: 0.3918 time to fit residues: 154.7649 Evaluate side-chains 119 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 2.244 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1769 time to fit residues: 3.2651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 183 optimal weight: 40.0000 chunk 70 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 212 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN D 105 HIS D 398 ASN D 478 ASN J 246 GLN ** J 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 478 ASN K 550 GLN K 651 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN H 97 ASN H 98 ASN L 37 GLN ** L 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20495 Z= 0.279 Angle : 0.701 10.095 27830 Z= 0.355 Chirality : 0.047 0.385 3395 Planarity : 0.005 0.068 3416 Dihedral : 9.272 102.568 4173 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.48 % Favored : 95.39 % Rotamer: Outliers : 1.47 % Allowed : 8.24 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.17), residues: 2343 helix: -0.89 (0.27), residues: 338 sheet: 0.34 (0.20), residues: 642 loop : -0.72 (0.17), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 338 HIS 0.016 0.001 HIS C 8 PHE 0.023 0.002 PHE H 78 TYR 0.023 0.002 TYR H 33 ARG 0.008 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 129 time to evaluate : 2.186 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 outliers start: 31 outliers final: 20 residues processed: 151 average time/residue: 0.3354 time to fit residues: 78.0122 Evaluate side-chains 123 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 2.054 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1760 time to fit residues: 9.3227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 0.0770 chunk 176 optimal weight: 20.0000 chunk 144 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 212 optimal weight: 20.0000 chunk 229 optimal weight: 3.9990 chunk 189 optimal weight: 30.0000 chunk 211 optimal weight: 20.0000 chunk 72 optimal weight: 8.9990 chunk 170 optimal weight: 7.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 203 GLN ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 653 GLN J 377 ASN J 398 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN A 35AASN A 77 GLN C 37 GLN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 20495 Z= 0.333 Angle : 0.700 10.046 27830 Z= 0.351 Chirality : 0.046 0.357 3395 Planarity : 0.005 0.067 3416 Dihedral : 8.288 85.112 4173 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.33 % Allowed : 11.17 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.18), residues: 2343 helix: -0.07 (0.29), residues: 358 sheet: 0.16 (0.20), residues: 666 loop : -0.57 (0.18), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP K 628 HIS 0.011 0.001 HIS C 8 PHE 0.023 0.002 PHE H 78 TYR 0.026 0.002 TYR H 33 ARG 0.007 0.001 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 110 time to evaluate : 2.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 11 residues processed: 135 average time/residue: 0.3193 time to fit residues: 69.0919 Evaluate side-chains 103 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 2.390 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.1852 time to fit residues: 6.9388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 20.0000 chunk 160 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 142 optimal weight: 0.8980 chunk 213 optimal weight: 30.0000 chunk 226 optimal weight: 20.0000 chunk 111 optimal weight: 6.9990 chunk 202 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 HIS D 183 GLN D 478 ASN E 616 ASN ** J 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 428 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 20495 Z= 0.486 Angle : 0.846 12.979 27830 Z= 0.422 Chirality : 0.049 0.353 3395 Planarity : 0.006 0.078 3416 Dihedral : 8.735 62.688 4173 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.13 % Allowed : 13.54 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 1.01 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.18), residues: 2343 helix: 0.38 (0.29), residues: 341 sheet: -0.07 (0.20), residues: 681 loop : -0.79 (0.18), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D 45 HIS 0.008 0.002 HIS D 105 PHE 0.022 0.003 PHE B 522 TYR 0.021 0.002 TYR J 217 ARG 0.006 0.001 ARG C 9 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 94 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 20 residues processed: 133 average time/residue: 0.3280 time to fit residues: 69.4543 Evaluate side-chains 102 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 82 time to evaluate : 2.313 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2170 time to fit residues: 10.6240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 50.0000 chunk 128 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 193 optimal weight: 30.0000 chunk 156 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 203 optimal weight: 30.0000 chunk 57 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 GLN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20495 Z= 0.201 Angle : 0.626 10.130 27830 Z= 0.314 Chirality : 0.045 0.410 3395 Planarity : 0.004 0.057 3416 Dihedral : 7.880 59.913 4173 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.09 % Allowed : 14.35 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.18), residues: 2343 helix: 0.85 (0.30), residues: 341 sheet: -0.03 (0.20), residues: 669 loop : -0.60 (0.18), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 45 HIS 0.010 0.001 HIS C 8 PHE 0.014 0.001 PHE F 78 TYR 0.013 0.001 TYR A 90 ARG 0.004 0.000 ARG C 9 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 110 average time/residue: 0.3370 time to fit residues: 58.4870 Evaluate side-chains 92 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 2.254 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1951 time to fit residues: 6.9358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 7.9990 chunk 203 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 226 optimal weight: 1.9990 chunk 187 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 377 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 20495 Z= 0.444 Angle : 0.778 9.546 27830 Z= 0.386 Chirality : 0.047 0.365 3395 Planarity : 0.005 0.073 3416 Dihedral : 8.270 59.635 4173 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 1.80 % Allowed : 14.96 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.18), residues: 2343 helix: 0.71 (0.29), residues: 341 sheet: -0.19 (0.19), residues: 690 loop : -0.77 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP K 628 HIS 0.007 0.001 HIS C 8 PHE 0.023 0.002 PHE B 522 TYR 0.017 0.002 TYR D 435 ARG 0.005 0.001 ARG C 9 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 80 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 12 residues processed: 115 average time/residue: 0.3525 time to fit residues: 63.5512 Evaluate side-chains 91 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 2.481 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1995 time to fit residues: 7.0794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 190 optimal weight: 30.0000 chunk 126 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 99 ASN ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20495 Z= 0.248 Angle : 0.662 11.978 27830 Z= 0.329 Chirality : 0.046 0.402 3395 Planarity : 0.004 0.060 3416 Dihedral : 7.746 58.633 4173 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.80 % Allowed : 16.10 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.18), residues: 2343 helix: 1.24 (0.31), residues: 323 sheet: -0.16 (0.20), residues: 678 loop : -0.71 (0.18), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 45 HIS 0.006 0.001 HIS C 8 PHE 0.016 0.001 PHE F 78 TYR 0.012 0.001 TYR J 217 ARG 0.005 0.000 ARG K 542 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 2.422 Fit side-chains outliers start: 17 outliers final: 7 residues processed: 102 average time/residue: 0.3340 time to fit residues: 55.2529 Evaluate side-chains 84 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 2.436 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2092 time to fit residues: 5.7290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 153 optimal weight: 20.0000 chunk 111 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 177 optimal weight: 20.0000 chunk 205 optimal weight: 20.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 GLN ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 ASN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20495 Z= 0.359 Angle : 0.730 11.171 27830 Z= 0.361 Chirality : 0.047 0.386 3395 Planarity : 0.004 0.074 3416 Dihedral : 7.868 59.276 4173 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 0.71 % Allowed : 16.95 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.18), residues: 2343 helix: 0.92 (0.31), residues: 341 sheet: -0.32 (0.19), residues: 693 loop : -0.73 (0.18), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 45 HIS 0.006 0.001 HIS G 216 PHE 0.017 0.002 PHE G 233 TYR 0.015 0.002 TYR J 217 ARG 0.007 0.001 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 2.248 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 93 average time/residue: 0.2918 time to fit residues: 45.6139 Evaluate side-chains 84 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 2.235 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2025 time to fit residues: 5.4415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 20.0000 chunk 197 optimal weight: 10.0000 chunk 210 optimal weight: 30.0000 chunk 126 optimal weight: 0.9980 chunk 91 optimal weight: 0.0040 chunk 165 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 189 optimal weight: 40.0000 chunk 198 optimal weight: 6.9990 chunk 209 optimal weight: 20.0000 chunk 138 optimal weight: 1.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20495 Z= 0.185 Angle : 0.642 13.444 27830 Z= 0.317 Chirality : 0.045 0.423 3395 Planarity : 0.004 0.051 3416 Dihedral : 7.167 59.935 4173 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.38 % Allowed : 16.86 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.18), residues: 2343 helix: 1.24 (0.31), residues: 341 sheet: -0.04 (0.21), residues: 600 loop : -0.64 (0.18), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 45 HIS 0.004 0.001 HIS D 105 PHE 0.019 0.001 PHE H 78 TYR 0.013 0.001 TYR A 90 ARG 0.004 0.000 ARG K 542 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 2.296 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 88 average time/residue: 0.3118 time to fit residues: 45.5123 Evaluate side-chains 81 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 2.324 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2099 time to fit residues: 4.1611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 50.0000 chunk 135 optimal weight: 3.9990 chunk 105 optimal weight: 0.1980 chunk 154 optimal weight: 2.9990 chunk 233 optimal weight: 8.9990 chunk 214 optimal weight: 10.0000 chunk 185 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 147 optimal weight: 8.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 GLN ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20495 Z= 0.253 Angle : 0.653 9.596 27830 Z= 0.322 Chirality : 0.045 0.398 3395 Planarity : 0.004 0.061 3416 Dihedral : 7.089 58.992 4173 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.09 % Allowed : 17.33 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2343 helix: 1.36 (0.31), residues: 338 sheet: -0.05 (0.20), residues: 651 loop : -0.67 (0.18), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 45 HIS 0.004 0.001 HIS D 105 PHE 0.014 0.001 PHE F 78 TYR 0.020 0.001 TYR A 90 ARG 0.008 0.000 ARG E 588 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 2.240 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 82 average time/residue: 0.3302 time to fit residues: 44.5186 Evaluate side-chains 82 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 2.323 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2013 time to fit residues: 3.7749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 171 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 190 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.048229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.032860 restraints weight = 165810.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.033828 restraints weight = 92528.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.034423 restraints weight = 65261.147| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20495 Z= 0.299 Angle : 0.687 12.862 27830 Z= 0.338 Chirality : 0.046 0.387 3395 Planarity : 0.004 0.063 3416 Dihedral : 7.228 58.711 4173 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 0.19 % Allowed : 17.57 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.18), residues: 2343 helix: 1.22 (0.31), residues: 341 sheet: -0.31 (0.19), residues: 699 loop : -0.66 (0.18), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 45 HIS 0.005 0.001 HIS D 105 PHE 0.014 0.002 PHE B 522 TYR 0.017 0.001 TYR A 90 ARG 0.006 0.000 ARG E 588 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2988.68 seconds wall clock time: 56 minutes 59.46 seconds (3419.46 seconds total)