Starting phenix.real_space_refine on Fri Aug 9 07:03:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sd3_25045/08_2024/7sd3_25045.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sd3_25045/08_2024/7sd3_25045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sd3_25045/08_2024/7sd3_25045.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sd3_25045/08_2024/7sd3_25045.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sd3_25045/08_2024/7sd3_25045.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sd3_25045/08_2024/7sd3_25045.cif" } resolution = 3.67 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= 0.001 sd= 0.040 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 140 5.16 5 C 15822 2.51 5 N 4324 2.21 5 O 4970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H ARG 18": "NH1" <-> "NH2" Residue "H ARG 77": "NH1" <-> "NH2" Residue "H ARG 142": "NH1" <-> "NH2" Residue "H ARG 142": "NH1" <-> "NH2" Residue "H GLU 161": "OE1" <-> "OE2" Residue "H GLU 187": "OE1" <-> "OE2" Residue "H GLU 195": "OE1" <-> "OE2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G ARG 43": "NH1" <-> "NH2" Residue "G ARG 66": "NH1" <-> "NH2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G ARG 94": "NH1" <-> "NH2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N ARG 77": "NH1" <-> "NH2" Residue "N GLU 123": "OE1" <-> "OE2" Residue "N ARG 142": "NH1" <-> "NH2" Residue "N ARG 142": "NH1" <-> "NH2" Residue "N TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 38": "NH1" <-> "NH2" Residue "K ARG 66": "NH1" <-> "NH2" Residue "K ARG 73": "NH1" <-> "NH2" Residue "K ARG 73": "NH1" <-> "NH2" Residue "K ARG 94": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 77": "NH1" <-> "NH2" Residue "M PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 142": "NH1" <-> "NH2" Residue "M ARG 142": "NH1" <-> "NH2" Residue "I ARG 38": "NH1" <-> "NH2" Residue "I ARG 66": "NH1" <-> "NH2" Residue "I ARG 73": "NH1" <-> "NH2" Residue "I ARG 73": "NH1" <-> "NH2" Residue "I ARG 94": "NH1" <-> "NH2" Residue "I GLU 226": "OE1" <-> "OE2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B GLU 560": "OE1" <-> "OE2" Residue "C PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C GLU 275": "OE1" <-> "OE2" Residue "C PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 557": "NH1" <-> "NH2" Residue "D GLU 560": "OE1" <-> "OE2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 158": "NH1" <-> "NH2" Residue "E GLU 275": "OE1" <-> "OE2" Residue "E PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 557": "NH1" <-> "NH2" Residue "F GLU 560": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25256 Number of models: 1 Model: "" Number of chains: 27 Chain: "H" Number of atoms: 1733 Number of conformers: 3 Conformer: "B" Number of residues, atoms: 214, 1638 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 202} Conformer: "C" Number of residues, atoms: 212, 1551 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 2 Unresolved chain link angles: 30 Unresolved chain link dihedrals: 60 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 1558 Conformer: "A" Number of residues, atoms: 214, 1630 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 202} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1558 Chain: "G" Number of atoms: 1702 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1622 Classifications: {'peptide': 220} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 220, 1622 Classifications: {'peptide': 220} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 1567 Chain: "N" Number of atoms: 1746 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 214, 1630 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 214, 1638 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} bond proxies already assigned to first conformer: 1542 Conformer: "C" Number of residues, atoms: 212, 1538 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200} Chain breaks: 2 Unresolved chain link angles: 36 Unresolved chain link dihedrals: 72 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 1542 Chain: "K" Number of atoms: 1725 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1612 Classifications: {'peptide': 220} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 220, 1612 Classifications: {'peptide': 220} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 1517 Chain: "M" Number of atoms: 1746 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 214, 1630 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 214, 1638 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} bond proxies already assigned to first conformer: 1542 Conformer: "C" Number of residues, atoms: 212, 1538 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200} Chain breaks: 2 Unresolved chain link angles: 36 Unresolved chain link dihedrals: 72 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 1542 Chain: "I" Number of atoms: 1725 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1612 Classifications: {'peptide': 220} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 220, 1612 Classifications: {'peptide': 220} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 1517 Chain: "A" Number of atoms: 3448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3448 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1236 Classifications: {'peptide': 163} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 160} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 3452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3452 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1236 Classifications: {'peptide': 163} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 160} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 69 Chain: "E" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3458 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1227 Classifications: {'peptide': 163} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 160} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 78 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Residues with excluded nonbonded symmetry interactions: 20 residue: pdb=" N AASP H 70 " occ=0.57 ... (14 atoms not shown) pdb=" OD2BASP H 70 " occ=0.43 residue: pdb=" N AARG H 142 " occ=0.70 ... (20 atoms not shown) pdb=" NH2BARG H 142 " occ=0.30 residue: pdb=" N AILE G 67 " occ=0.85 ... (14 atoms not shown) pdb=" CD1BILE G 67 " occ=0.15 residue: pdb=" N AGLU G 150 " occ=0.72 ... (16 atoms not shown) pdb=" OE2BGLU G 150 " occ=0.28 residue: pdb=" N AVAL G 152 " occ=0.65 ... (12 atoms not shown) pdb=" CG2BVAL G 152 " occ=0.35 residue: pdb=" N ATHR G 205 " occ=0.60 ... (12 atoms not shown) pdb=" CG2BTHR G 205 " occ=0.40 residue: pdb=" N AASP N 70 " occ=0.57 ... (14 atoms not shown) pdb=" OD2BASP N 70 " occ=0.43 residue: pdb=" N AARG N 142 " occ=0.70 ... (20 atoms not shown) pdb=" NH2BARG N 142 " occ=0.30 residue: pdb=" N AILE K 67 " occ=0.85 ... (14 atoms not shown) pdb=" CD1BILE K 67 " occ=0.15 residue: pdb=" N AARG K 73 " occ=0.67 ... (20 atoms not shown) pdb=" NH2BARG K 73 " occ=0.33 residue: pdb=" N AGLU K 150 " occ=0.72 ... (16 atoms not shown) pdb=" OE2BGLU K 150 " occ=0.28 residue: pdb=" N AVAL K 152 " occ=0.65 ... (12 atoms not shown) pdb=" CG2BVAL K 152 " occ=0.35 ... (remaining 8 not shown) Time building chain proxies: 20.59, per 1000 atoms: 0.82 Number of scatterers: 25256 At special positions: 0 Unit cell: (148.32, 131.84, 187.46, 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 140 16.00 O 4970 8.00 N 4324 7.00 C 15822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG ACYS H 134 " - pdb=" SG ACYS H 194 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG ACYS G 92 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG BCYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 142 " - pdb=" SG ACYS G 208 " distance=2.05 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG ACYS N 134 " - pdb=" SG ACYS N 194 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG ACYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG BCYS K 92 " distance=2.03 Simple disulfide: pdb=" SG ACYS K 142 " - pdb=" SG ACYS K 208 " distance=2.03 Simple disulfide: pdb=" SG BCYS K 142 " - pdb=" SG BCYS K 208 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.02 Simple disulfide: pdb=" SG ACYS M 134 " - pdb=" SG ACYS M 194 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG ACYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG BCYS I 92 " distance=2.03 Simple disulfide: pdb=" SG ACYS I 142 " - pdb=" SG ACYS I 208 " distance=2.03 Simple disulfide: pdb=" SG BCYS I 142 " - pdb=" SG BCYS I 208 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.00 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 149 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 330 " distance=2.00 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 443 " distance=2.01 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 416 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.01 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.01 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 149 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 330 " distance=2.00 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 443 " distance=2.02 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 416 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.01 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.00 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 149 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 330 " distance=2.00 Simple disulfide: pdb=" SG CYS E 377 " - pdb=" SG CYS E 443 " distance=2.02 Simple disulfide: pdb=" SG CYS E 384 " - pdb=" SG CYS E 416 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.01 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=3, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG L 1 " - " NAG L 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG A 601 " - " ASN A 152 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 331 " " NAG A 605 " - " ASN A 446 " " NAG A 606 " - " ASN A 391 " " NAG A 607 " - " ASN A 385 " " NAG A 608 " - " ASN A 88 " " NAG A 609 " - " ASN A 148 " " NAG B 701 " - " ASN B 625 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 601 " - " ASN C 152 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 331 " " NAG C 605 " - " ASN C 446 " " NAG C 606 " - " ASN C 391 " " NAG C 607 " - " ASN C 385 " " NAG C 608 " - " ASN C 88 " " NAG C 609 " - " ASN C 148 " " NAG D 701 " - " ASN D 625 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E 601 " - " ASN E 152 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 301 " " NAG E 604 " - " ASN E 331 " " NAG E 605 " - " ASN E 446 " " NAG E 606 " - " ASN E 391 " " NAG E 607 " - " ASN E 385 " " NAG E 608 " - " ASN E 88 " " NAG E 609 " - " ASN E 148 " " NAG F 701 " - " ASN F 625 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG L 1 " - " ASN A 234 " " NAG O 1 " - " ASN A 354 " " NAG Q 1 " - " ASN C 234 " " NAG R 1 " - " ASN C 354 " " NAG T 1 " - " ASN E 234 " " NAG U 1 " - " ASN E 354 " NAG-SER " NAG J 1 " - " SER A 445 " " NAG P 1 " - " SER C 445 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.06 Conformation dependent library (CDL) restraints added in 7.5 seconds 6418 Ramachandran restraints generated. 3209 Oldfield, 0 Emsley, 3209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5992 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 62 sheets defined 16.3% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.77 Creating SS restraints... Processing helix chain 'H' and resid 28 through 31 removed outlier: 3.835A pdb=" N ASN H 31 " --> pdb=" O VAL H 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 31' Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 182 through 187 Processing helix chain 'N' and resid 28 through 31 removed outlier: 4.081A pdb=" N ASN N 31 " --> pdb=" O VAL N 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 31' Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.008A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 126 Processing helix chain 'N' and resid 182 through 187 Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.525A pdb=" N ASN M 31 " --> pdb=" O VAL M 28 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS M 32 " --> pdb=" O GLY M 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 28 through 32' Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.718A pdb=" N PHE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 183 through 187 Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.713A pdb=" N THR I 87 " --> pdb=" O PRO I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 165 No H-bonds generated for 'chain 'I' and resid 163 through 165' Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.571A pdb=" N LYS A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.767A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 347 Processing helix chain 'A' and resid 366 through 372 removed outlier: 3.780A pdb=" N VAL A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 479 removed outlier: 4.081A pdb=" N TRP A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 539 Processing helix chain 'B' and resid 543 through 550 Processing helix chain 'B' and resid 552 through 558 Processing helix chain 'B' and resid 570 through 595 removed outlier: 3.747A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLN B 590 " --> pdb=" O TYR B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 652 removed outlier: 4.151A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 673 through 684 removed outlier: 3.943A pdb=" N ASN B 677 " --> pdb=" O PHE B 673 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE B 682 " --> pdb=" O TRP B 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.572A pdb=" N LYS C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.768A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 347 Processing helix chain 'C' and resid 367 through 372 removed outlier: 3.654A pdb=" N THR C 371 " --> pdb=" O ASP C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 479 removed outlier: 4.081A pdb=" N TRP C 477 " --> pdb=" O MET C 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 539 Processing helix chain 'D' and resid 543 through 550 Processing helix chain 'D' and resid 552 through 558 Processing helix chain 'D' and resid 570 through 595 removed outlier: 3.747A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLN D 590 " --> pdb=" O TYR D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 652 removed outlier: 4.152A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER D 649 " --> pdb=" O LEU D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 675 through 684 Processing helix chain 'E' and resid 99 through 117 removed outlier: 3.571A pdb=" N LYS E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.767A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 347 Processing helix chain 'E' and resid 473 through 479 removed outlier: 4.082A pdb=" N TRP E 477 " --> pdb=" O MET E 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 539 Processing helix chain 'F' and resid 543 through 550 Processing helix chain 'F' and resid 552 through 558 Processing helix chain 'F' and resid 570 through 595 removed outlier: 3.747A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLN F 590 " --> pdb=" O TYR F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 652 removed outlier: 4.152A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER F 649 " --> pdb=" O LEU F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 662 removed outlier: 3.907A pdb=" N ALA F 662 " --> pdb=" O GLN F 658 " (cutoff:3.500A) Processing helix chain 'F' and resid 674 through 684 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'H' and resid 45 through 49 removed outlier: 6.376A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL H 85 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR H 102 " --> pdb=" O TYR H 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 62 through 67 removed outlier: 3.645A pdb=" N SER H 67 " --> pdb=" O AASP H 70 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N AASP H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 114 through 118 removed outlier: 3.578A pdb=" N ASN H 137 " --> pdb=" O SER H 114 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER H 177 " --> pdb=" O CYS H 134 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N THR H 172 " --> pdb=" O GLN H 166 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN H 166 " --> pdb=" O THR H 172 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER H 174 " --> pdb=" O THR H 164 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN H 160 " --> pdb=" O THR H 178 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 145 through 150 Processing sheet with id=AA6, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'G' and resid 27 through 28 removed outlier: 3.546A pdb=" N GLY G 27 " --> pdb=" O THR K 57 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN K 58 " --> pdb=" O GLY K 50 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY K 50 " --> pdb=" O ASN K 58 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA K 88 " --> pdb=" O VAL K 109 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 46 through 51 removed outlier: 6.997A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLY G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR G 107 " --> pdb=" O TYR G 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 138 through 141 removed outlier: 3.635A pdb=" N VAL G 193 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU G 140 " --> pdb=" O VAL G 191 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL G 191 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU G 187 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS G 145 " --> pdb=" O LEU G 187 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 138 through 141 removed outlier: 3.635A pdb=" N VAL G 193 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU G 140 " --> pdb=" O VAL G 191 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL G 191 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER G 186 " --> pdb=" O ALA G 176 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ALA G 176 " --> pdb=" O SER G 186 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER G 188 " --> pdb=" O PHE G 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 154 through 157 removed outlier: 3.894A pdb=" N TYR G 206 " --> pdb=" O VAL G 225 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AB4, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.501A pdb=" N GLN N 11 " --> pdb=" O LYS N 103 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU N 105 " --> pdb=" O GLN N 11 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 44 through 48 removed outlier: 6.711A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL N 85 " --> pdb=" O GLN N 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 133 through 137 removed outlier: 3.592A pdb=" N CYS N 134 " --> pdb=" O SER N 177 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER N 177 " --> pdb=" O CYS N 134 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER N 162 " --> pdb=" O SER N 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 144 through 145 Processing sheet with id=AB8, first strand: chain 'N' and resid 191 through 192 Processing sheet with id=AB9, first strand: chain 'K' and resid 3 through 5 Processing sheet with id=AC1, first strand: chain 'K' and resid 17 through 20 Processing sheet with id=AC2, first strand: chain 'K' and resid 93 through 94 removed outlier: 3.620A pdb=" N HIS K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 122 through 123 removed outlier: 3.651A pdb=" N SER K 189 " --> pdb=" O CYS K 142 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP K 146 " --> pdb=" O TYR K 185 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N TYR K 185 " --> pdb=" O ASP K 146 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 122 through 123 removed outlier: 3.651A pdb=" N SER K 189 " --> pdb=" O CYS K 142 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP K 146 " --> pdb=" O TYR K 185 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N TYR K 185 " --> pdb=" O ASP K 146 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER K 186 " --> pdb=" O VAL K 177 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL K 177 " --> pdb=" O SER K 186 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 154 through 157 removed outlier: 4.650A pdb=" N TYR K 206 " --> pdb=" O VAL K 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 4 through 5 Processing sheet with id=AC7, first strand: chain 'M' and resid 19 through 21 removed outlier: 3.633A pdb=" N AASP M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 44 through 48 removed outlier: 6.394A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL M 85 " --> pdb=" O GLN M 38 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 129 through 130 removed outlier: 3.631A pdb=" N LEU M 181 " --> pdb=" O ALA M 130 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 134 through 139 removed outlier: 3.540A pdb=" N SER M 177 " --> pdb=" O CYS M 134 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR M 173 " --> pdb=" O ASN M 138 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 144 through 146 removed outlier: 3.539A pdb=" N LYS M 145 " --> pdb=" O THR M 197 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 153 through 154 removed outlier: 3.798A pdb=" N VAL M 150 " --> pdb=" O ALA M 153 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS M 149 " --> pdb=" O ALA M 193 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA M 193 " --> pdb=" O LYS M 149 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 3 through 6 removed outlier: 3.763A pdb=" N VAL I 18 " --> pdb=" O LEU I 82 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA I 78 " --> pdb=" O CYS I 22 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 12 removed outlier: 7.177A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'I' and resid 45 through 51 removed outlier: 6.216A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLY I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ARG I 94 " --> pdb=" O ALA I 101 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 120 through 123 Processing sheet with id=AD8, first strand: chain 'I' and resid 153 through 157 Processing sheet with id=AD9, first strand: chain 'A' and resid 492 through 497 removed outlier: 4.771A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS B 604 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.871A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AE3, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AE4, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AE5, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.833A pdb=" N LEU A 260 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 272 through 273 removed outlier: 3.693A pdb=" N VAL A 286 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 450 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 441 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 445 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS A 329 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ALA A 328 " --> pdb=" O CYS A 416 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 419 " --> pdb=" O PHE A 381 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE A 381 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AE8, first strand: chain 'A' and resid 421 through 423 Processing sheet with id=AE9, first strand: chain 'C' and resid 492 through 497 removed outlier: 3.656A pdb=" N VAL C 36 " --> pdb=" O VAL D 608 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.871A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AF3, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AF4, first strand: chain 'C' and resid 173 through 174 Processing sheet with id=AF5, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.832A pdb=" N LEU C 260 " --> pdb=" O THR C 448 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 272 through 273 removed outlier: 3.693A pdb=" N VAL C 286 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU C 450 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 441 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 445 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS C 329 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA C 328 " --> pdb=" O CYS C 416 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C 419 " --> pdb=" O PHE C 381 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE C 381 " --> pdb=" O LYS C 419 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AF8, first strand: chain 'C' and resid 421 through 423 Processing sheet with id=AF9, first strand: chain 'E' and resid 492 through 497 removed outlier: 5.872A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.871A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 91 through 93 Processing sheet with id=AG3, first strand: chain 'E' and resid 130 through 133 Processing sheet with id=AG4, first strand: chain 'E' and resid 173 through 174 Processing sheet with id=AG5, first strand: chain 'E' and resid 259 through 261 removed outlier: 4.175A pdb=" N GLY E 449 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 272 through 273 removed outlier: 3.694A pdb=" N VAL E 286 " --> pdb=" O LEU E 450 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 450 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE E 441 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER E 445 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS E 329 " --> pdb=" O THR E 297 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA E 328 " --> pdb=" O CYS E 416 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS E 419 " --> pdb=" O PHE E 381 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE E 381 " --> pdb=" O LYS E 419 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AG8, first strand: chain 'E' and resid 421 through 423 659 hydrogen bonds defined for protein. 1735 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: 9.03 Time building geometry restraints manager: 12.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 5645 1.33 - 1.47: 8728 1.47 - 1.61: 11309 1.61 - 1.74: 3 1.74 - 1.88: 173 Bond restraints: 25858 Sorted by residual: bond pdb=" C1 BMA P 3 " pdb=" C2 BMA P 3 " ideal model delta sigma weight residual 1.519 1.605 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C1 BMA J 3 " pdb=" C2 BMA J 3 " ideal model delta sigma weight residual 1.519 1.605 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C1 BMA S 3 " pdb=" C2 BMA S 3 " ideal model delta sigma weight residual 1.519 1.604 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C ALA E 361 " pdb=" O ALA E 361 " ideal model delta sigma weight residual 1.233 1.188 0.045 1.09e-02 8.42e+03 1.71e+01 bond pdb=" CA SER C 264 " pdb=" CB SER C 264 " ideal model delta sigma weight residual 1.527 1.478 0.049 1.30e-02 5.92e+03 1.44e+01 ... (remaining 25853 not shown) Histogram of bond angle deviations from ideal: 97.82 - 105.60: 597 105.60 - 113.39: 14944 113.39 - 121.17: 12107 121.17 - 128.96: 7446 128.96 - 136.74: 227 Bond angle restraints: 35321 Sorted by residual: angle pdb=" C ALA A 361 " pdb=" N ASN A 362 " pdb=" CA ASN A 362 " ideal model delta sigma weight residual 120.82 132.89 -12.07 1.47e+00 4.63e-01 6.74e+01 angle pdb=" CA GLN D 653 " pdb=" CB GLN D 653 " pdb=" CG GLN D 653 " ideal model delta sigma weight residual 114.10 129.92 -15.82 2.00e+00 2.50e-01 6.25e+01 angle pdb=" CA GLN F 653 " pdb=" CB GLN F 653 " pdb=" CG GLN F 653 " ideal model delta sigma weight residual 114.10 129.91 -15.81 2.00e+00 2.50e-01 6.25e+01 angle pdb=" CA GLN B 653 " pdb=" CB GLN B 653 " pdb=" CG GLN B 653 " ideal model delta sigma weight residual 114.10 129.90 -15.80 2.00e+00 2.50e-01 6.24e+01 angle pdb=" O ALA A 361 " pdb=" C ALA A 361 " pdb=" N ASN A 362 " ideal model delta sigma weight residual 122.65 131.87 -9.22 1.23e+00 6.61e-01 5.62e+01 ... (remaining 35316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 15116 21.50 - 42.99: 1154 42.99 - 64.49: 277 64.49 - 85.99: 65 85.99 - 107.49: 29 Dihedral angle restraints: 16641 sinusoidal: 7245 harmonic: 9396 Sorted by residual: dihedral pdb=" CB CYS E 377 " pdb=" SG CYS E 377 " pdb=" SG CYS E 443 " pdb=" CB CYS E 443 " ideal model delta sinusoidal sigma weight residual -86.00 -148.82 62.82 1 1.00e+01 1.00e-02 5.21e+01 dihedral pdb=" CB CYS C 377 " pdb=" SG CYS C 377 " pdb=" SG CYS C 443 " pdb=" CB CYS C 443 " ideal model delta sinusoidal sigma weight residual -86.00 -148.81 62.81 1 1.00e+01 1.00e-02 5.21e+01 dihedral pdb=" CB CYS A 377 " pdb=" SG CYS A 377 " pdb=" SG CYS A 443 " pdb=" CB CYS A 443 " ideal model delta sinusoidal sigma weight residual -86.00 -148.80 62.80 1 1.00e+01 1.00e-02 5.21e+01 ... (remaining 16638 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 3674 0.102 - 0.204: 451 0.204 - 0.306: 56 0.306 - 0.408: 14 0.408 - 0.510: 6 Chirality restraints: 4201 Sorted by residual: chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 9.75e+00 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 9.59e+00 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 9.56e+00 ... (remaining 4198 not shown) Planarity restraints: 4533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 661 " 0.036 2.00e-02 2.50e+03 7.38e-02 5.45e+01 pdb=" C LEU D 661 " -0.128 2.00e-02 2.50e+03 pdb=" O LEU D 661 " 0.049 2.00e-02 2.50e+03 pdb=" N ALA D 662 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 260 " 0.035 2.00e-02 2.50e+03 7.26e-02 5.28e+01 pdb=" C LEU A 260 " -0.126 2.00e-02 2.50e+03 pdb=" O LEU A 260 " 0.049 2.00e-02 2.50e+03 pdb=" N LEU A 261 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 366 " -0.033 2.00e-02 2.50e+03 6.79e-02 4.61e+01 pdb=" C GLY C 366 " 0.117 2.00e-02 2.50e+03 pdb=" O GLY C 366 " -0.045 2.00e-02 2.50e+03 pdb=" N ASP C 367 " -0.040 2.00e-02 2.50e+03 ... (remaining 4530 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 14 2.12 - 2.81: 7791 2.81 - 3.51: 33295 3.51 - 4.20: 60086 4.20 - 4.90: 99913 Nonbonded interactions: 201099 Sorted by model distance: nonbonded pdb=" ND2 ASN A 362 " pdb=" CA THR A 371 " model vdw 1.424 3.550 nonbonded pdb=" OE1 GLU A 156 " pdb=" O GLY A 310 " model vdw 1.443 3.040 nonbonded pdb=" OE1 GLU C 156 " pdb=" O GLY C 310 " model vdw 1.519 3.040 nonbonded pdb=" ND2 ASN E 362 " pdb=" O THR E 371 " model vdw 1.588 3.120 nonbonded pdb=" ND2 ASN A 362 " pdb=" C THR A 371 " model vdw 1.925 3.350 ... (remaining 201094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 153 or (resid 154 and (name N or name CA or nam \ e C or name O or name CB )) or resid 155 through 161 or (resid 162 and (name N o \ r name CA or name C or name O or name CB )) or resid 163 through 259 or (resid 2 \ 60 and (name N or name CA or name C or name O or name CB )) or resid 261 through \ 368 or (resid 369 and (name N or name CA or name C or name O or name CB )) or r \ esid 370 through 444 or (resid 445 and (name N or name CA or name C or name O or \ name CB )) or resid 446 through 504 or resid 601 through 609)) selection = (chain 'C' and (resid 31 through 259 or (resid 260 and (name N or name CA or nam \ e C or name O or name CB )) or resid 261 through 444 or (resid 445 and (name N o \ r name CA or name C or name O or name CB )) or resid 446 through 447 or (resid 4 \ 48 and (name N or name CA or name C or name O or name CB )) or resid 449 through \ 497 or (resid 498 and (name N or name CA or name C or name O or name CB )) or r \ esid 499 through 501 or (resid 502 and (name N or name CA or name C or name O or \ name CB )) or resid 503 through 504 or resid 601 through 609)) selection = (chain 'E' and (resid 31 through 153 or (resid 154 and (name N or name CA or nam \ e C or name O or name CB )) or resid 155 through 161 or (resid 162 and (name N o \ r name CA or name C or name O or name CB )) or resid 163 through 368 or (resid 3 \ 69 and (name N or name CA or name C or name O or name CB )) or resid 370 through \ 447 or (resid 448 and (name N or name CA or name C or name O or name CB )) or r \ esid 449 through 497 or (resid 498 and (name N or name CA or name C or name O or \ name CB )) or resid 499 through 501 or (resid 502 and (name N or name CA or nam \ e C or name O or name CB )) or resid 503 through 504 or resid 601 through 609)) } ncs_group { reference = (chain 'B' and (resid 522 through 677 or (resid 678 through 684 and (name N or n \ ame CA or name C or name O or name CB )) or resid 701 through 703)) selection = (chain 'D' and (resid 522 through 663 or (resid 664 through 684 and (name N or n \ ame CA or name C or name O or name CB )) or resid 701 through 703)) selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 1 through 9 or resid 11 through 16 or resid 18 through 29 \ or resid 31 through 42 or resid 44 through 61 or resid 63 through 66 or resid 68 \ through 72 or resid 74 through 80 or resid 82 through 82A or resid 82C or resid \ 84 through 91 or resid 93 or resid 95 through 99 or (resid 100 through 100B and \ (name N or name CA or name C or name O )) or resid 100C through 141 or resid 14 \ 3 through 149 or resid 151 or resid 153 through 167 or resid 169 through 185 or \ resid 187 or resid 189 through 203 or resid 206 through 207 or resid 209 through \ 227)) selection = (chain 'I' and (resid 1 through 9 or resid 11 through 16 or resid 18 through 29 \ or resid 31 through 42 or resid 44 through 61 or resid 63 through 66 or resid 68 \ through 72 or resid 74 through 80 or resid 82 through 82A or resid 82C or resid \ 84 through 91 or resid 93 or resid 95 through 141 or resid 143 through 149 or r \ esid 151 or resid 153 through 167 or resid 169 through 185 or resid 187 or resid \ 189 through 203 or resid 206 through 207 or resid 209 through 227)) selection = (chain 'K' and (resid 1 through 9 or resid 11 through 16 or resid 18 through 29 \ or resid 31 through 42 or resid 44 through 61 or resid 63 through 66 or resid 68 \ through 72 or resid 74 through 80 or resid 82 through 82A or resid 82C or resid \ 84 through 91 or resid 93 or resid 95 through 141 or resid 143 through 149 or r \ esid 151 or resid 153 through 167 or resid 169 through 185 or resid 187 or resid \ 189 through 203 or resid 206 through 207 or resid 209 through 227)) } ncs_group { reference = (chain 'H' and (resid 1 through 21 or resid 23 or resid 25 through 27 or resid 2 \ 8 through 31 or resid 33 through 44 or resid 46 through 53 or resid 55 through 6 \ 2 or resid 64 through 66 or resid 68 through 69 or resid 71 through 99 or resid \ 101 through 122 or resid 124 through 128 or resid 130 through 133 or resid 135 t \ hrough 141 or resid 143 through 145 or resid 147 through 151 or resid 153 throug \ h 175 or resid 177 through 189 or resid 191 through 193 or resid 195 through 196 \ or resid 198 through 202 or resid 204 through 213)) selection = (chain 'M' and (resid 1 through 21 or resid 23 or resid 25 through 27 or resid 2 \ 8 through 31 or resid 33 through 44 or resid 46 through 53 or resid 55 through 6 \ 2 or resid 64 through 66 or resid 68 through 69 or resid 71 through 99 or resid \ 101 through 122 or resid 124 through 128 or resid 130 through 133 or resid 135 t \ hrough 141 or resid 143 through 145 or resid 147 through 151 or resid 153 throug \ h 175 or resid 177 through 189 or resid 191 through 193 or resid 195 through 196 \ or resid 198 through 202 or resid 204 through 213)) selection = (chain 'N' and (resid 1 through 21 or resid 23 or resid 25 through 27 or resid 2 \ 8 through 31 or resid 33 through 44 or resid 46 through 53 or resid 55 through 6 \ 2 or resid 64 through 66 or resid 68 through 69 or resid 71 through 99 or resid \ 101 through 122 or resid 124 through 128 or resid 130 through 133 or resid 135 t \ hrough 141 or resid 143 through 145 or resid 147 through 151 or resid 153 throug \ h 175 or resid 177 through 189 or resid 191 through 193 or resid 195 through 196 \ or resid 198 through 202 or resid 204 through 213)) } ncs_group { reference = chain 'J' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'L' selection = chain 'Q' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.11 max=1.00 mean=0.98 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: 4.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.420 Check model and map are aligned: 0.170 Set scattering table: 0.260 Process input model: 82.250 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 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 : 0.011 0.095 25858 Z= 0.741 Angle : 1.275 16.031 35321 Z= 0.698 Chirality : 0.074 0.510 4201 Planarity : 0.008 0.080 4491 Dihedral : 17.094 107.487 10511 Min Nonbonded Distance : 1.424 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.86 % Favored : 90.08 % Rotamer: Outliers : 7.23 % Allowed : 9.46 % Favored : 83.30 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.06 % Twisted Proline : 2.48 % 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: -4.66 (0.12), residues: 3209 helix: -3.23 (0.16), residues: 461 sheet: -3.03 (0.16), residues: 803 loop : -3.21 (0.12), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 394 HIS 0.024 0.003 HIS N 189 PHE 0.028 0.004 PHE E 375 TYR 0.024 0.003 TYR H 91 ARG 0.019 0.001 ARG E 502 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6418 Ramachandran restraints generated. 3209 Oldfield, 0 Emsley, 3209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6418 Ramachandran restraints generated. 3209 Oldfield, 0 Emsley, 3209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 264 time to evaluate : 2.978 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: G 36 TRP cc_start: 0.7942 (m100) cc_final: 0.7575 (m100) REVERT: G 226 GLU cc_start: 0.6598 (mt-10) cc_final: 0.6324 (mm-30) REVERT: K 79 TYR cc_start: 0.8310 (m-10) cc_final: 0.8018 (m-10) REVERT: I 48 MET cc_start: 0.8038 (mtp) cc_final: 0.7681 (mtm) REVERT: I 95 GLU cc_start: 0.7775 (pt0) cc_final: 0.7501 (pt0) REVERT: I 206 TYR cc_start: 0.6208 (m-80) cc_final: 0.5866 (m-80) REVERT: A 69 TRP cc_start: 0.7881 (m-90) cc_final: 0.7620 (m-90) REVERT: A 125 LEU cc_start: 0.8894 (tp) cc_final: 0.8434 (tp) REVERT: A 195 ASN cc_start: 0.8439 (p0) cc_final: 0.8195 (p0) REVERT: A 241 SER cc_start: 0.8259 (OUTLIER) cc_final: 0.7931 (p) REVERT: B 599 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8725 (p) REVERT: B 626 MET cc_start: 0.7573 (ttm) cc_final: 0.6873 (ttm) REVERT: B 647 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7958 (tm-30) REVERT: C 447 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7638 (mt) REVERT: D 601 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8106 (mtpp) REVERT: D 661 LEU cc_start: 0.7687 (tp) cc_final: 0.7482 (tp) REVERT: E 69 TRP cc_start: 0.6385 (m-90) cc_final: 0.5919 (m-10) REVERT: E 255 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8371 (p) REVERT: E 492 LEU cc_start: 0.9336 (tp) cc_final: 0.9002 (tp) REVERT: F 530 MET cc_start: 0.4633 (mtm) cc_final: 0.4424 (mtp) outliers start: 138 outliers final: 47 residues processed: 382 average time/residue: 0.3971 time to fit residues: 232.1222 Evaluate side-chains 201 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 148 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 554 ASN Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 653 GLN Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain E residue 499 CYS Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 653 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 0.7980 chunk 234 optimal weight: 0.8980 chunk 129 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 157 optimal weight: 0.8980 chunk 125 optimal weight: 20.0000 chunk 242 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 chunk 180 optimal weight: 0.9980 chunk 280 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 27 GLN H 37 GLN ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 GLN G 216 ASN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 100 GLN B N 152 ASN A N 158 ASN K 64 GLN K 179 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN A M 152 ASN A I 3 GLN I 6 GLN I 58 ASN I 82AASN I 179 GLN A 82 GLN A 246 GLN ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN A 300 ASN ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS A 423 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN C 300 ASN C 302 ASN C 373 HIS C 423 ASN D 550 GLN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN E 258 GLN E 262 ASN ** E 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 ASN E 300 ASN ** E 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN ** E 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25858 Z= 0.215 Angle : 0.744 11.415 35321 Z= 0.375 Chirality : 0.050 0.469 4201 Planarity : 0.005 0.071 4491 Dihedral : 11.610 100.903 4886 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 5.70 % Allowed : 13.55 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.06 % Twisted Proline : 0.62 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.13), residues: 3209 helix: -1.71 (0.21), residues: 480 sheet: -2.76 (0.16), residues: 822 loop : -2.88 (0.12), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 425 HIS 0.006 0.001 HIS N 189 PHE 0.020 0.001 PHE G 29 TYR 0.025 0.002 TYR A 165 ARG 0.009 0.001 ARG E 498 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6418 Ramachandran restraints generated. 3209 Oldfield, 0 Emsley, 3209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6418 Ramachandran restraints generated. 3209 Oldfield, 0 Emsley, 3209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 183 time to evaluate : 2.719 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: H 60 ASP cc_start: 0.7390 (t0) cc_final: 0.7027 (p0) REVERT: G 13 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6768 (mmm160) REVERT: G 206 TYR cc_start: 0.6703 (m-80) cc_final: 0.6414 (m-80) REVERT: G 226 GLU cc_start: 0.6569 (mt-10) cc_final: 0.5856 (mm-30) REVERT: I 48 MET cc_start: 0.7986 (mtp) cc_final: 0.7691 (mtm) REVERT: I 95 GLU cc_start: 0.7907 (pt0) cc_final: 0.7645 (pt0) REVERT: A 69 TRP cc_start: 0.7791 (m-90) cc_final: 0.7523 (m-90) REVERT: A 125 LEU cc_start: 0.8812 (tp) cc_final: 0.8513 (tp) REVERT: A 241 SER cc_start: 0.7864 (OUTLIER) cc_final: 0.7500 (p) REVERT: A 473 MET cc_start: 0.8016 (mmm) cc_final: 0.7802 (mmm) REVERT: A 483 LYS cc_start: 0.8207 (pttt) cc_final: 0.7989 (ptpp) REVERT: B 599 SER cc_start: 0.9070 (OUTLIER) cc_final: 0.8776 (p) REVERT: B 605 CYS cc_start: 0.6909 (OUTLIER) cc_final: 0.6601 (m) REVERT: B 647 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8356 (tm-30) REVERT: B 657 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7635 (tp30) REVERT: C 294 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.7312 (pt) REVERT: C 473 MET cc_start: 0.7806 (tpp) cc_final: 0.7453 (mpp) REVERT: D 535 MET cc_start: 0.8928 (tpp) cc_final: 0.8686 (tpp) REVERT: E 69 TRP cc_start: 0.6376 (m-90) cc_final: 0.5759 (m-10) REVERT: E 264 SER cc_start: 0.7909 (m) cc_final: 0.7709 (p) REVERT: E 423 ASN cc_start: 0.5850 (OUTLIER) cc_final: 0.5621 (t0) REVERT: F 530 MET cc_start: 0.4505 (mtm) cc_final: 0.4173 (mtp) REVERT: F 543 ASN cc_start: 0.7144 (t0) cc_final: 0.6676 (m110) outliers start: 97 outliers final: 48 residues processed: 269 average time/residue: 0.3679 time to fit residues: 157.5104 Evaluate side-chains 198 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 144 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain N residue 210 ASN Chi-restraints excluded: chain M residue 206 THR Chi-restraints excluded: chain I residue 146 ASP Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 352 PHE Chi-restraints excluded: chain E residue 423 ASN Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 3.9990 chunk 87 optimal weight: 40.0000 chunk 233 optimal weight: 6.9990 chunk 191 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 281 optimal weight: 0.9980 chunk 303 optimal weight: 5.9990 chunk 250 optimal weight: 3.9990 chunk 278 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 225 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100 GLN B ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 147 GLN K 6 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 423 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 GLN D 656 ASN E 82 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN ** E 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 25858 Z= 0.300 Angle : 0.731 11.718 35321 Z= 0.366 Chirality : 0.051 0.466 4201 Planarity : 0.005 0.050 4491 Dihedral : 9.292 59.519 4833 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 4.93 % Allowed : 15.56 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.14), residues: 3209 helix: -1.07 (0.23), residues: 486 sheet: -2.60 (0.16), residues: 856 loop : -2.70 (0.13), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 394 HIS 0.008 0.001 HIS C 85 PHE 0.019 0.002 PHE K 148 TYR 0.032 0.002 TYR A 165 ARG 0.012 0.001 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6418 Ramachandran restraints generated. 3209 Oldfield, 0 Emsley, 3209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6418 Ramachandran restraints generated. 3209 Oldfield, 0 Emsley, 3209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 144 time to evaluate : 2.786 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: H 60 ASP cc_start: 0.7416 (t0) cc_final: 0.7013 (p0) REVERT: G 226 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6093 (mm-30) REVERT: K 79 TYR cc_start: 0.8380 (m-10) cc_final: 0.8153 (m-10) REVERT: I 48 MET cc_start: 0.7983 (mtp) cc_final: 0.7659 (mtm) REVERT: I 95 GLU cc_start: 0.7949 (pt0) cc_final: 0.7644 (pt0) REVERT: A 69 TRP cc_start: 0.7819 (m-90) cc_final: 0.7476 (m-10) REVERT: A 125 LEU cc_start: 0.8894 (tp) cc_final: 0.8405 (tp) REVERT: A 241 SER cc_start: 0.8094 (OUTLIER) cc_final: 0.7577 (p) REVERT: B 599 SER cc_start: 0.9231 (OUTLIER) cc_final: 0.8939 (p) REVERT: B 657 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7669 (tp30) REVERT: C 201 ILE cc_start: 0.9127 (tt) cc_final: 0.8849 (tt) REVERT: C 294 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7343 (pt) REVERT: D 535 MET cc_start: 0.8939 (tpp) cc_final: 0.8710 (tpp) REVERT: D 543 ASN cc_start: 0.8255 (t0) cc_final: 0.7846 (t0) REVERT: E 69 TRP cc_start: 0.6317 (m-90) cc_final: 0.5638 (m-10) REVERT: E 264 SER cc_start: 0.8005 (m) cc_final: 0.7643 (p) REVERT: F 543 ASN cc_start: 0.7176 (m-40) cc_final: 0.6748 (m110) outliers start: 77 outliers final: 45 residues processed: 209 average time/residue: 0.3452 time to fit residues: 117.0167 Evaluate side-chains 184 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 136 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 211 ASN Chi-restraints excluded: chain M residue 206 THR Chi-restraints excluded: chain I residue 146 ASP Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 352 PHE Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain E residue 432 MET Chi-restraints excluded: chain E residue 499 CYS Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 605 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 0.6980 chunk 211 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 282 optimal weight: 3.9990 chunk 298 optimal weight: 0.6980 chunk 147 optimal weight: 0.0970 chunk 267 optimal weight: 0.6980 chunk 80 optimal weight: 8.9990 overall best weight: 1.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN D 616 ASN ** E 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 373 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 550 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25858 Z= 0.195 Angle : 0.659 10.021 35321 Z= 0.328 Chirality : 0.049 0.447 4201 Planarity : 0.004 0.048 4491 Dihedral : 8.040 59.595 4825 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 4.71 % Allowed : 16.51 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.14), residues: 3209 helix: -0.65 (0.24), residues: 483 sheet: -2.35 (0.17), residues: 837 loop : -2.58 (0.13), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 425 HIS 0.006 0.001 HIS N 189 PHE 0.011 0.001 PHE I 122 TYR 0.019 0.001 TYR A 165 ARG 0.006 0.000 ARG G 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6418 Ramachandran restraints generated. 3209 Oldfield, 0 Emsley, 3209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6418 Ramachandran restraints generated. 3209 Oldfield, 0 Emsley, 3209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 153 time to evaluate : 2.756 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: H 60 ASP cc_start: 0.7437 (t0) cc_final: 0.7005 (p0) REVERT: G 226 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6062 (mm-30) REVERT: K 79 TYR cc_start: 0.8275 (m-10) cc_final: 0.8066 (m-10) REVERT: I 48 MET cc_start: 0.7913 (mtp) cc_final: 0.7623 (mtm) REVERT: I 95 GLU cc_start: 0.7882 (pt0) cc_final: 0.7554 (pt0) REVERT: A 42 VAL cc_start: 0.8705 (m) cc_final: 0.8267 (p) REVERT: A 69 TRP cc_start: 0.7763 (m-90) cc_final: 0.7425 (m-10) REVERT: A 125 LEU cc_start: 0.8827 (tp) cc_final: 0.8545 (tp) REVERT: A 255 VAL cc_start: 0.9168 (OUTLIER) cc_final: 0.8934 (m) REVERT: B 599 SER cc_start: 0.9216 (OUTLIER) cc_final: 0.8902 (p) REVERT: B 657 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7679 (tp30) REVERT: C 294 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7406 (pt) REVERT: D 624 ASP cc_start: 0.8070 (m-30) cc_final: 0.7860 (t0) REVERT: D 648 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: E 69 TRP cc_start: 0.6418 (m-90) cc_final: 0.5676 (m-10) REVERT: F 535 MET cc_start: 0.7681 (mtm) cc_final: 0.7004 (tpp) REVERT: F 543 ASN cc_start: 0.7155 (m-40) cc_final: 0.6745 (m110) outliers start: 71 outliers final: 45 residues processed: 214 average time/residue: 0.3695 time to fit residues: 127.8981 Evaluate side-chains 179 residues out of total 2585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 130 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 211 ASN Chi-restraints excluded: chain M residue 206 THR Chi-restraints excluded: chain I residue 207 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 432 MET Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 605 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 222 optimal weight: 2.9990 chunk 123 optimal weight: 40.0000 chunk 254 optimal weight: 6.9990 chunk 206 optimal weight: 0.8980 chunk 0 optimal weight: 40.0000 chunk 152 optimal weight: 2.9990 chunk 268 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: