Starting phenix.real_space_refine on Thu Mar 5 21:00:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sd3_25045/03_2026/7sd3_25045.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sd3_25045/03_2026/7sd3_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 { model { file = "/net/cci-nas-00/data/ceres_data/7sd3_25045/03_2026/7sd3_25045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sd3_25045/03_2026/7sd3_25045.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sd3_25045/03_2026/7sd3_25045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sd3_25045/03_2026/7sd3_25045.map" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ARG:plan': 2, 'GLN:plan1': 1, '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: {'ARG:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 1, '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: {'ARG:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 1, '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, 'ASP:plan': 2, 'TRP:plan': 4, 'ASN:plan1': 2, 'PHE:plan': 1} 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, 'TRP:plan': 5, 'PHE:plan': 1, 'ASN:plan1': 1} 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, 'ASP:plan': 2, 'TRP:plan': 5, 'ASN:plan1': 2, 'PHE:plan': 1} 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: 8.54, per 1000 atoms: 0.34 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 - 3.00 Amino acid : True - 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=4, 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=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.6 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: 0.89 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: 4.89 Time building geometry restraints manager: 3.21 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: 0.00 - 3.21: 34269 3.21 - 6.41: 902 6.41 - 9.62: 114 9.62 - 12.83: 26 12.83 - 16.03: 10 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: 1.44 - 2.13: 13 2.13 - 2.83: 8284 2.83 - 3.52: 33355 3.52 - 4.21: 59939 4.21 - 4.90: 99503 Nonbonded interactions: 201094 Sorted by model distance: 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=" NE2 GLN E 258 " pdb=" OD1 ASN E 362 " model vdw 1.945 3.120 nonbonded pdb=" ND2 ASN A 362 " pdb=" O THR A 371 " model vdw 1.949 2.496 ... (remaining 201089 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 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 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 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: 5.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.710 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.090 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.910 ------------------------------------------------------------------------------- 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 25967 Z= 0.519 Angle : 1.326 16.031 35588 Z= 0.709 Chirality : 0.074 0.510 4201 Planarity : 0.008 0.080 4491 Dihedral : 17.094 107.487 10511 Min Nonbonded Distance : 1.443 Molprobity Statistics. All-atom Clashscore : 11.59 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.019 0.001 ARG E 502 TYR 0.024 0.003 TYR H 91 PHE 0.028 0.004 PHE E 375 TRP 0.022 0.003 TRP A 394 HIS 0.024 0.003 HIS N 189 Details of bonding type rmsd covalent geometry : bond 0.01128 (25858) covalent geometry : angle 1.27530 (35321) SS BOND : bond 0.01330 ( 46) SS BOND : angle 2.99571 ( 92) hydrogen bonds : bond 0.24445 ( 651) hydrogen bonds : angle 9.64615 ( 1735) Misc. bond : bond 0.00445 ( 4) link_BETA1-4 : bond 0.02015 ( 15) link_BETA1-4 : angle 6.94207 ( 45) link_NAG-ASN : bond 0.00962 ( 42) link_NAG-ASN : angle 4.05807 ( 126) link_NAG-SER : bond 0.01434 ( 2) link_NAG-SER : angle 4.08120 ( 4) *********************** 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 to be fit. rotamer outliers: 138 poor density : 264 time to evaluate : 0.942 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: 0.7692 (m100) REVERT: G 226 GLU cc_start: 0.6598 (mt-10) cc_final: 0.6325 (mm-30) REVERT: K 79 TYR cc_start: 0.8310 (m-10) cc_final: 0.8019 (m-10) REVERT: I 48 MET cc_start: 0.8038 (mtp) cc_final: 0.7682 (mtm) REVERT: I 95 GLU cc_start: 0.7775 (pt0) cc_final: 0.7498 (pt0) REVERT: I 206 TYR cc_start: 0.6208 (m-80) cc_final: 0.5867 (m-80) REVERT: A 69 TRP cc_start: 0.7880 (m-90) cc_final: 0.7618 (m-90) REVERT: A 125 LEU cc_start: 0.8894 (tp) cc_final: 0.8436 (tp) REVERT: A 195 ASN cc_start: 0.8439 (p0) cc_final: 0.8194 (p0) REVERT: A 241 SER cc_start: 0.8259 (OUTLIER) cc_final: 0.7932 (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: 0.7957 (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: 0.7418 (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: 0.4423 (mtp) outliers start: 138 outliers final: 47 residues processed: 382 average time/residue: 0.1842 time to fit residues: 108.0466 Evaluate side-chains 199 residues out of total 2585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 146 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN A 300 ASN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.127848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.099257 restraints weight = 557794.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.102444 restraints weight = 176803.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.105255 restraints weight = 61190.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.104542 restraints weight = 52816.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.104782 restraints weight = 37320.291| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4108 r_free = 0.4108 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4105 r_free = 0.4105 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 110 | |-----------------------------------------------------------------------------| r_final: 0.4105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25967 Z= 0.155 Angle : 0.786 14.106 35588 Z= 0.385 Chirality : 0.050 0.465 4201 Planarity : 0.005 0.072 4491 Dihedral : 11.824 101.267 4886 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 5.85 % Allowed : 13.63 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.06 % Twisted Proline : 0.62 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.97 (0.13), residues: 3209 helix: -1.74 (0.21), residues: 480 sheet: -2.79 (0.16), residues: 822 loop : -2.90 (0.12), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 83 TYR 0.029 0.002 TYR A 165 PHE 0.019 0.001 PHE G 29 TRP 0.021 0.002 TRP E 425 HIS 0.006 0.001 HIS N 189 Details of bonding type rmsd covalent geometry : bond 0.00335 (25858) covalent geometry : angle 0.74502 (35321) SS BOND : bond 0.00333 ( 46) SS BOND : angle 1.37531 ( 92) hydrogen bonds : bond 0.04720 ( 651) hydrogen bonds : angle 7.30089 ( 1735) Misc. bond : bond 0.00050 ( 4) link_BETA1-4 : bond 0.01593 ( 15) link_BETA1-4 : angle 4.51913 ( 45) link_NAG-ASN : bond 0.00488 ( 42) link_NAG-ASN : angle 3.15413 ( 126) link_NAG-SER : bond 0.00585 ( 2) link_NAG-SER : angle 2.27051 ( 4) *********************** 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 276 residues out of total 2585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 175 time to evaluate : 0.981 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: H 60 ASP cc_start: 0.7136 (t0) cc_final: 0.6925 (p0) REVERT: G 226 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6220 (mm-30) REVERT: A 125 LEU cc_start: 0.8850 (tp) cc_final: 0.8488 (tp) REVERT: A 154 THR cc_start: 0.3775 (OUTLIER) cc_final: 0.3490 (m) REVERT: A 241 SER cc_start: 0.7586 (OUTLIER) cc_final: 0.7214 (p) REVERT: A 423 ASN cc_start: 0.7261 (OUTLIER) cc_final: 0.7053 (t0) REVERT: A 424 MET cc_start: 0.6604 (ttt) cc_final: 0.6350 (ttt) REVERT: A 483 LYS cc_start: 0.8132 (pttt) cc_final: 0.7728 (ptpp) REVERT: B 599 SER cc_start: 0.9130 (OUTLIER) cc_final: 0.8694 (p) REVERT: B 653 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8048 (mp10) REVERT: B 657 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7732 (tp30) REVERT: C 294 ILE cc_start: 0.7371 (OUTLIER) cc_final: 0.7037 (pt) REVERT: C 473 MET cc_start: 0.7576 (tpp) cc_final: 0.7209 (mpp) REVERT: D 535 MET cc_start: 0.8588 (tpp) cc_final: 0.8380 (tpp) REVERT: E 69 TRP cc_start: 0.6403 (m-90) cc_final: 0.5899 (m-10) REVERT: E 264 SER cc_start: 0.7963 (m) cc_final: 0.7692 (p) REVERT: E 423 ASN cc_start: 0.5944 (OUTLIER) cc_final: 0.5674 (t0) REVERT: F 530 MET cc_start: 0.5186 (mtm) cc_final: 0.4861 (mtp) REVERT: F 543 ASN cc_start: 0.7268 (t0) cc_final: 0.6893 (m110) outliers start: 101 outliers final: 50 residues processed: 266 average time/residue: 0.1579 time to fit residues: 67.4487 Evaluate side-chains 203 residues out of total 2585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 146 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 423 ASN 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 638 TYR Chi-restraints excluded: chain B residue 653 GLN 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 364 SER 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 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 202 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 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 121 optimal weight: 5.9990 chunk 304 optimal weight: 7.9990 chunk 124 optimal weight: 30.0000 chunk 143 optimal weight: 1.9990 chunk 204 optimal weight: 0.6980 chunk 215 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 208 optimal weight: 0.6980 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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** 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 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN C 258 GLN ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN 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** F 550 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.132328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.101896 restraints weight = 645554.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.104501 restraints weight = 189539.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.107206 restraints weight = 69140.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.106339 restraints weight = 59630.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.106607 restraints weight = 43163.005| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4030 r_free = 0.4030 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 110 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4029 r_free = 0.4029 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 113 | |-----------------------------------------------------------------------------| r_final: 0.4029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 25967 Z= 0.219 Angle : 0.789 12.986 35588 Z= 0.385 Chirality : 0.051 0.477 4201 Planarity : 0.005 0.050 4491 Dihedral : 9.483 83.940 4838 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 5.08 % Allowed : 15.45 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.62 (0.14), residues: 3209 helix: -1.12 (0.23), residues: 483 sheet: -2.66 (0.16), residues: 852 loop : -2.70 (0.13), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 83 TYR 0.022 0.002 TYR H 192 PHE 0.020 0.002 PHE K 148 TRP 0.026 0.002 TRP E 425 HIS 0.008 0.001 HIS C 373 Details of bonding type rmsd covalent geometry : bond 0.00503 (25858) covalent geometry : angle 0.75358 (35321) SS BOND : bond 0.00457 ( 46) SS BOND : angle 1.37808 ( 92) hydrogen bonds : bond 0.04453 ( 651) hydrogen bonds : angle 6.72220 ( 1735) Misc. bond : bond 0.00092 ( 4) link_BETA1-4 : bond 0.01455 ( 15) link_BETA1-4 : angle 4.37035 ( 45) link_NAG-ASN : bond 0.00569 ( 42) link_NAG-ASN : angle 2.84805 ( 126) link_NAG-SER : bond 0.00912 ( 2) link_NAG-SER : angle 2.50187 ( 4) *********************** 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 230 residues out of total 2585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 150 time to evaluate : 0.949 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: H 60 ASP cc_start: 0.7217 (t0) cc_final: 0.6909 (p0) REVERT: G 226 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6267 (mm-30) REVERT: K 79 TYR cc_start: 0.8219 (m-10) cc_final: 0.7997 (m-10) REVERT: I 95 GLU cc_start: 0.7630 (pt0) cc_final: 0.7083 (tt0) REVERT: A 125 LEU cc_start: 0.8942 (tp) cc_final: 0.8396 (tp) REVERT: A 241 SER cc_start: 0.7744 (OUTLIER) cc_final: 0.7204 (p) REVERT: B 599 SER cc_start: 0.9258 (OUTLIER) cc_final: 0.8797 (p) REVERT: B 657 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7765 (tp30) REVERT: C 201 ILE cc_start: 0.9043 (tt) cc_final: 0.8815 (tt) REVERT: C 294 ILE cc_start: 0.7336 (OUTLIER) cc_final: 0.6906 (pt) REVERT: C 425 TRP cc_start: 0.5994 (p-90) cc_final: 0.5619 (p-90) REVERT: D 543 ASN cc_start: 0.8288 (t0) cc_final: 0.7958 (t0) REVERT: E 69 TRP cc_start: 0.6429 (m-90) cc_final: 0.5800 (m-10) REVERT: F 543 ASN cc_start: 0.7345 (m-40) cc_final: 0.7014 (m110) REVERT: F 653 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8019 (pm20) outliers start: 80 outliers final: 50 residues processed: 218 average time/residue: 0.1637 time to fit residues: 57.5854 Evaluate side-chains 191 residues out of total 2585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 137 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 606 THR 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 348 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 499 CYS Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 653 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 161 optimal weight: 0.6980 chunk 243 optimal weight: 8.9990 chunk 299 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 160 optimal weight: 0.6980 chunk 30 optimal weight: 10.0000 chunk 234 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** ** M 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN E 82 GLN ** E 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 426 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.133379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.102956 restraints weight = 689548.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.105833 restraints weight = 185602.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.109111 restraints weight = 64307.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.107836 restraints weight = 55656.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.108205 restraints weight = 51889.697| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4060 r_free = 0.4060 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 113 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4060 r_free = 0.4060 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 131 | |-----------------------------------------------------------------------------| r_final: 0.4060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25967 Z= 0.144 Angle : 0.707 10.845 35588 Z= 0.342 Chirality : 0.049 0.455 4201 Planarity : 0.004 0.047 4491 Dihedral : 8.114 59.315 4827 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 5.15 % Allowed : 16.44 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.14), residues: 3209 helix: -0.70 (0.24), residues: 487 sheet: -2.42 (0.17), residues: 821 loop : -2.59 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 617 TYR 0.017 0.001 TYR H 192 PHE 0.012 0.001 PHE I 122 TRP 0.015 0.001 TRP E 425 HIS 0.008 0.001 HIS M 198 Details of bonding type rmsd covalent geometry : bond 0.00322 (25858) covalent geometry : angle 0.67420 (35321) SS BOND : bond 0.00438 ( 46) SS BOND : angle 1.23022 ( 92) hydrogen bonds : bond 0.03725 ( 651) hydrogen bonds : angle 6.29606 ( 1735) Misc. bond : bond 0.00061 ( 4) link_BETA1-4 : bond 0.01260 ( 15) link_BETA1-4 : angle 4.00042 ( 45) link_NAG-ASN : bond 0.00492 ( 42) link_NAG-ASN : angle 2.59934 ( 126) link_NAG-SER : bond 0.00926 ( 2) link_NAG-SER : angle 2.21143 ( 4) *********************** 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 233 residues out of total 2585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 151 time to evaluate : 0.907 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: 0.7169 (t0) cc_final: 0.6848 (p0) REVERT: G 226 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6222 (mm-30) REVERT: I 95 GLU cc_start: 0.7567 (pt0) cc_final: 0.7010 (tt0) REVERT: A 42 VAL cc_start: 0.8694 (m) cc_final: 0.8272 (p) REVERT: A 69 TRP cc_start: 0.7708 (m-90) cc_final: 0.7423 (m-90) REVERT: A 125 LEU cc_start: 0.8881 (tp) cc_final: 0.8571 (tp) REVERT: A 255 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8760 (m) REVERT: B 599 SER cc_start: 0.9226 (OUTLIER) cc_final: 0.8818 (p) REVERT: B 605 CYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6490 (m) REVERT: B 657 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7823 (tp30) REVERT: C 294 ILE cc_start: 0.7355 (OUTLIER) cc_final: 0.7058 (pt) REVERT: C 425 TRP cc_start: 0.5953 (p-90) cc_final: 0.5567 (p-90) REVERT: E 69 TRP cc_start: 0.6433 (m-90) cc_final: 0.5778 (m-10) REVERT: E 264 SER cc_start: 0.8046 (m) cc_final: 0.7818 (p) REVERT: E 425 TRP cc_start: 0.6053 (p-90) cc_final: 0.5200 (p-90) REVERT: F 530 MET cc_start: 0.4678 (tpt) cc_final: 0.4465 (mmm) REVERT: F 535 MET cc_start: 0.7058 (mtm) cc_final: 0.6421 (tpp) REVERT: F 543 ASN cc_start: 0.7354 (m-40) cc_final: 0.7058 (m110) outliers start: 82 outliers final: 50 residues processed: 221 average time/residue: 0.1582 time to fit residues: 56.0090 Evaluate side-chains 187 residues out of total 2585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 133 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 11 VAL 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 274 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 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 605 CYS 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 50 THR 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 165 TYR 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 274 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 135 THR 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 426 GLN 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 262 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 87 optimal weight: 40.0000 chunk 275 optimal weight: 3.9990 chunk 245 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 154 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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** N 42 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN ** M 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS B 616 ASN ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 HIS D 616 ASN E 105 HIS ** E 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 552 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.130919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.101248 restraints weight = 614321.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.104245 restraints weight = 181586.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.106210 restraints weight = 62325.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.106371 restraints weight = 45824.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.106642 restraints weight = 38468.280| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4042 r_free = 0.4042 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 131 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4042 r_free = 0.4042 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 155 | |-----------------------------------------------------------------------------| r_final: 0.4042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 25967 Z= 0.213 Angle : 0.746 12.003 35588 Z= 0.362 Chirality : 0.050 0.422 4201 Planarity : 0.005 0.045 4491 Dihedral : 7.992 58.831 4817 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 5.41 % Allowed : 17.03 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.14), residues: 3209 helix: -0.64 (0.24), residues: 487 sheet: -2.41 (0.17), residues: 868 loop : -2.49 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 427 TYR 0.021 0.002 TYR K 79 PHE 0.012 0.002 PHE E 93 TRP 0.023 0.002 TRP E 425 HIS 0.009 0.001 HIS C 373 Details of bonding type rmsd covalent geometry : bond 0.00494 (25858) covalent geometry : angle 0.71443 (35321) SS BOND : bond 0.00451 ( 46) SS BOND : angle 1.26984 ( 92) hydrogen bonds : bond 0.03970 ( 651) hydrogen bonds : angle 6.28239 ( 1735) Misc. bond : bond 0.00100 ( 4) link_BETA1-4 : bond 0.01306 ( 15) link_BETA1-4 : angle 3.99777 ( 45) link_NAG-ASN : bond 0.00460 ( 42) link_NAG-ASN : angle 2.64671 ( 126) link_NAG-SER : bond 0.00802 ( 2) link_NAG-SER : angle 2.39554 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 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 233 residues out of total 2585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 144 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 213 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7718 (tppt) REVERT: G 226 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6255 (mm-30) REVERT: K 79 TYR cc_start: 0.7860 (m-10) cc_final: 0.7626 (m-10) REVERT: I 95 GLU cc_start: 0.7551 (pt0) cc_final: 0.7087 (tt0) REVERT: A 69 TRP cc_start: 0.7832 (m-90) cc_final: 0.7424 (m-90) REVERT: A 125 LEU cc_start: 0.8959 (tp) cc_final: 0.8538 (tp) REVERT: A 473 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7222 (mpp) REVERT: B 657 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7847 (tp30) REVERT: C 87 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7374 (tp30) REVERT: C 289 ASN cc_start: 0.8105 (OUTLIER) cc_final: 0.7899 (p0) REVERT: C 294 ILE cc_start: 0.7434 (OUTLIER) cc_final: 0.7037 (pt) REVERT: C 425 TRP cc_start: 0.5809 (p-90) cc_final: 0.5481 (p-90) REVERT: D 530 MET cc_start: 0.4827 (mtm) cc_final: 0.4620 (mtp) REVERT: E 69 TRP cc_start: 0.6484 (m-90) cc_final: 0.5777 (m-10) REVERT: E 425 TRP cc_start: 0.6374 (p-90) cc_final: 0.5792 (p-90) REVERT: F 543 ASN cc_start: 0.7353 (m-40) cc_final: 0.7093 (m110) outliers start: 89 outliers final: 56 residues processed: 220 average time/residue: 0.1578 time to fit residues: 56.5517 Evaluate side-chains 193 residues out of total 2585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 132 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 213 LYS Chi-restraints excluded: chain K residue 11 VAL 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 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 242 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 473 MET 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 606 THR Chi-restraints excluded: chain B residue 632 ASP 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 54 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 289 ASN 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 D residue 570 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 74 CYS Chi-restraints excluded: chain E residue 135 THR 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 264 SER 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 432 MET Chi-restraints excluded: chain E residue 499 CYS Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 605 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 112 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 253 optimal weight: 0.0040 chunk 162 optimal weight: 0.9980 chunk 302 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 123 optimal weight: 40.0000 chunk 268 optimal weight: 3.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- 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 137 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 279 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 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.131506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.101980 restraints weight = 615795.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.104730 restraints weight = 183542.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.107823 restraints weight = 64731.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.106387 restraints weight = 58808.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.106536 restraints weight = 57843.152| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4039 r_free = 0.4039 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 155 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4039 r_free = 0.4039 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 164 | |-----------------------------------------------------------------------------| r_final: 0.4039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25967 Z= 0.161 Angle : 0.709 11.580 35588 Z= 0.342 Chirality : 0.049 0.423 4201 Planarity : 0.004 0.046 4491 Dihedral : 7.750 58.405 4816 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 5.01 % Allowed : 17.68 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.14), residues: 3209 helix: -0.52 (0.24), residues: 488 sheet: -2.29 (0.17), residues: 853 loop : -2.41 (0.13), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 83 TYR 0.022 0.001 TYR M 86 PHE 0.018 0.001 PHE C 288 TRP 0.015 0.001 TRP A 337 HIS 0.007 0.001 HIS C 373 Details of bonding type rmsd covalent geometry : bond 0.00370 (25858) covalent geometry : angle 0.67787 (35321) SS BOND : bond 0.00454 ( 46) SS BOND : angle 1.23713 ( 92) hydrogen bonds : bond 0.03677 ( 651) hydrogen bonds : angle 6.12761 ( 1735) Misc. bond : bond 0.00076 ( 4) link_BETA1-4 : bond 0.01284 ( 15) link_BETA1-4 : angle 3.89381 ( 45) link_NAG-ASN : bond 0.00401 ( 42) link_NAG-ASN : angle 2.57179 ( 126) link_NAG-SER : bond 0.00767 ( 2) link_NAG-SER : angle 2.20422 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 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 to be fit. rotamer outliers: 78 poor density : 143 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 213 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7863 (tppt) REVERT: G 226 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6194 (mm-30) REVERT: K 79 TYR cc_start: 0.7913 (m-10) cc_final: 0.7708 (m-10) REVERT: A 69 TRP cc_start: 0.7784 (m-90) cc_final: 0.7496 (m-10) REVERT: A 125 LEU cc_start: 0.8928 (tp) cc_final: 0.8627 (tp) REVERT: A 473 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7030 (mpp) REVERT: B 605 CYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6625 (m) REVERT: B 614 TRP cc_start: 0.6570 (m-90) cc_final: 0.6302 (m-90) REVERT: B 657 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7757 (tp30) REVERT: C 294 ILE cc_start: 0.7406 (OUTLIER) cc_final: 0.7047 (pt) REVERT: C 425 TRP cc_start: 0.5844 (p-90) cc_final: 0.5519 (p-90) REVERT: E 69 TRP cc_start: 0.6565 (m-90) cc_final: 0.5825 (m-10) REVERT: E 264 SER cc_start: 0.8072 (OUTLIER) cc_final: 0.7797 (p) REVERT: E 423 ASN cc_start: 0.6886 (OUTLIER) cc_final: 0.6530 (m-40) REVERT: F 543 ASN cc_start: 0.7430 (m-40) cc_final: 0.7138 (m110) outliers start: 78 outliers final: 53 residues processed: 206 average time/residue: 0.1647 time to fit residues: 55.2114 Evaluate side-chains 190 residues out of total 2585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 131 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 213 LYS Chi-restraints excluded: chain K residue 11 VAL 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 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 242 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 50 THR 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 126 CYS Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 242 VAL 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 294 ILE Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 CYS Chi-restraints excluded: chain E residue 135 THR 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 242 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 264 SER 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 423 ASN Chi-restraints excluded: chain F residue 593 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 255 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 chunk 186 optimal weight: 9.9990 chunk 272 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 300 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 138 ASN ** H 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 373 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.132608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.102461 restraints weight = 601348.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.105046 restraints weight = 188924.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.107893 restraints weight = 67778.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.106896 restraints weight = 59469.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.107141 restraints weight = 42703.330| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4056 r_free = 0.4056 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 164 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4055 r_free = 0.4055 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 165 | |-----------------------------------------------------------------------------| r_final: 0.4055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 25967 Z= 0.199 Angle : 0.741 12.533 35588 Z= 0.358 Chirality : 0.050 0.411 4201 Planarity : 0.004 0.046 4491 Dihedral : 7.802 58.356 4814 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 5.44 % Allowed : 17.61 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.14), residues: 3209 helix: -0.48 (0.24), residues: 488 sheet: -2.25 (0.18), residues: 839 loop : -2.37 (0.13), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 542 TYR 0.024 0.002 TYR M 173 PHE 0.013 0.002 PHE E 93 TRP 0.018 0.002 TRP E 425 HIS 0.010 0.001 HIS C 373 Details of bonding type rmsd covalent geometry : bond 0.00461 (25858) covalent geometry : angle 0.70900 (35321) SS BOND : bond 0.00497 ( 46) SS BOND : angle 1.34535 ( 92) hydrogen bonds : bond 0.03887 ( 651) hydrogen bonds : angle 6.12040 ( 1735) Misc. bond : bond 0.00102 ( 4) link_BETA1-4 : bond 0.01345 ( 15) link_BETA1-4 : angle 4.01020 ( 45) link_NAG-ASN : bond 0.00457 ( 42) link_NAG-ASN : angle 2.62915 ( 126) link_NAG-SER : bond 0.00471 ( 2) link_NAG-SER : angle 2.36720 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 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 227 residues out of total 2585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 137 time to evaluate : 0.997 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: G 213 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7756 (tppt) REVERT: G 226 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6063 (mm-30) REVERT: I 95 GLU cc_start: 0.7560 (pt0) cc_final: 0.7055 (tt0) REVERT: A 69 TRP cc_start: 0.7847 (m-90) cc_final: 0.7505 (m-10) REVERT: A 125 LEU cc_start: 0.8913 (tp) cc_final: 0.8528 (tp) REVERT: A 473 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.7084 (mpp) REVERT: B 605 CYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6689 (m) REVERT: B 657 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7805 (tp30) REVERT: C 425 TRP cc_start: 0.5836 (p-90) cc_final: 0.5461 (p-90) REVERT: E 69 TRP cc_start: 0.6533 (m-90) cc_final: 0.5774 (m-10) REVERT: F 543 ASN cc_start: 0.7474 (m-40) cc_final: 0.7143 (m110) outliers start: 90 outliers final: 63 residues processed: 213 average time/residue: 0.1520 time to fit residues: 53.0758 Evaluate side-chains 193 residues out of total 2585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 127 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 213 LYS Chi-restraints excluded: chain K residue 11 VAL 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 11 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 632 ASP 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 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 126 CYS Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 CYS Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 274 SER 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 368 LEU Chi-restraints excluded: chain E residue 369 GLU Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 593 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 281 optimal weight: 1.9990 chunk 123 optimal weight: 0.2980 chunk 196 optimal weight: 0.9990 chunk 109 optimal weight: 9.9990 chunk 250 optimal weight: 0.9980 chunk 271 optimal weight: 1.9990 chunk 289 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 152 optimal weight: 0.9980 chunk 252 optimal weight: 5.9990 chunk 68 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN B 540 GLN C 114 GLN C 262 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.133074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.098188 restraints weight = 651270.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.099875 restraints weight = 169998.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.102824 restraints weight = 67733.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.101960 restraints weight = 55222.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.103742 restraints weight = 43810.318| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3990 r_free = 0.3990 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 165 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3990 r_free = 0.3990 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 168 | |-----------------------------------------------------------------------------| r_final: 0.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25967 Z= 0.115 Angle : 0.677 10.753 35588 Z= 0.324 Chirality : 0.048 0.408 4201 Planarity : 0.004 0.046 4491 Dihedral : 7.358 58.400 4814 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 4.42 % Allowed : 18.78 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.14), residues: 3209 helix: -0.23 (0.24), residues: 490 sheet: -1.97 (0.18), residues: 825 loop : -2.29 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 326 TYR 0.019 0.001 TYR M 173 PHE 0.016 0.001 PHE E 360 TRP 0.037 0.001 TRP E 425 HIS 0.007 0.001 HIS I 172 Details of bonding type rmsd covalent geometry : bond 0.00252 (25858) covalent geometry : angle 0.64644 (35321) SS BOND : bond 0.00426 ( 46) SS BOND : angle 1.19652 ( 92) hydrogen bonds : bond 0.03313 ( 651) hydrogen bonds : angle 5.83442 ( 1735) Misc. bond : bond 0.00047 ( 4) link_BETA1-4 : bond 0.01321 ( 15) link_BETA1-4 : angle 3.79684 ( 45) link_NAG-ASN : bond 0.00373 ( 42) link_NAG-ASN : angle 2.41962 ( 126) link_NAG-SER : bond 0.01211 ( 2) link_NAG-SER : angle 2.47078 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 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 210 residues out of total 2585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 148 time to evaluate : 0.789 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: G 213 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.7926 (tppt) REVERT: G 226 GLU cc_start: 0.6482 (mt-10) cc_final: 0.5778 (mm-30) REVERT: I 95 GLU cc_start: 0.7689 (pt0) cc_final: 0.7014 (tt0) REVERT: A 69 TRP cc_start: 0.7774 (m-90) cc_final: 0.7446 (m-10) REVERT: B 605 CYS cc_start: 0.7013 (OUTLIER) cc_final: 0.6426 (m) REVERT: B 657 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7654 (tp30) REVERT: C 352 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.6820 (p90) REVERT: C 360 PHE cc_start: 0.7097 (m-80) cc_final: 0.6811 (m-80) REVERT: C 425 TRP cc_start: 0.5614 (p-90) cc_final: 0.5092 (p-90) REVERT: E 69 TRP cc_start: 0.6597 (m-90) cc_final: 0.5817 (m-10) REVERT: E 264 SER cc_start: 0.8060 (OUTLIER) cc_final: 0.7843 (p) REVERT: E 369 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7134 (pt0) REVERT: E 498 ARG cc_start: 0.8053 (pmt-80) cc_final: 0.7687 (pmt-80) REVERT: F 535 MET cc_start: 0.7100 (mtm) cc_final: 0.6575 (tpp) REVERT: F 542 ARG cc_start: 0.3959 (tpt170) cc_final: 0.3584 (ttt90) REVERT: F 543 ASN cc_start: 0.7309 (m-40) cc_final: 0.6957 (m110) REVERT: F 601 LYS cc_start: 0.8629 (mtpp) cc_final: 0.8334 (ptpp) outliers start: 62 outliers final: 45 residues processed: 198 average time/residue: 0.1569 time to fit residues: 50.5036 Evaluate side-chains 181 residues out of total 2585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 131 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 213 LYS Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain M residue 206 THR Chi-restraints excluded: chain I residue 11 VAL 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 242 VAL Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 74 CYS 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 322 ILE Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 CYS Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 369 GLU Chi-restraints excluded: chain E residue 499 CYS Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 593 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 75 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.125958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.100394 restraints weight = 648273.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.103714 restraints weight = 176626.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.103962 restraints weight = 55813.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.104426 restraints weight = 51011.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.105117 restraints weight = 39045.695| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4117 r_free = 0.4117 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 168 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4116 r_free = 0.4116 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 182 | |-----------------------------------------------------------------------------| r_final: 0.4116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 25967 Z= 0.265 Angle : 0.797 13.101 35588 Z= 0.387 Chirality : 0.051 0.406 4201 Planarity : 0.005 0.044 4491 Dihedral : 7.918 58.917 4814 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 4.49 % Allowed : 19.11 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.14), residues: 3209 helix: -0.29 (0.24), residues: 471 sheet: -2.21 (0.17), residues: 863 loop : -2.34 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 427 TYR 0.023 0.002 TYR H 192 PHE 0.020 0.002 PHE E 93 TRP 0.025 0.002 TRP E 425 HIS 0.013 0.002 HIS C 373 Details of bonding type rmsd covalent geometry : bond 0.00620 (25858) covalent geometry : angle 0.76631 (35321) SS BOND : bond 0.00607 ( 46) SS BOND : angle 1.55098 ( 92) hydrogen bonds : bond 0.04122 ( 651) hydrogen bonds : angle 6.15155 ( 1735) Misc. bond : bond 0.00128 ( 4) link_BETA1-4 : bond 0.01284 ( 15) link_BETA1-4 : angle 4.03295 ( 45) link_NAG-ASN : bond 0.00536 ( 42) link_NAG-ASN : angle 2.64626 ( 126) link_NAG-SER : bond 0.01114 ( 2) link_NAG-SER : angle 2.71658 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 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 190 residues out of total 2585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 126 time to evaluate : 1.041 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: G 213 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7686 (tppt) REVERT: I 95 GLU cc_start: 0.7384 (pt0) cc_final: 0.6953 (tt0) REVERT: A 69 TRP cc_start: 0.7920 (m-90) cc_final: 0.7684 (m-10) REVERT: A 473 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.6839 (mpp) REVERT: B 657 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7761 (tp30) REVERT: C 326 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6453 (mtp85) REVERT: C 425 TRP cc_start: 0.5924 (p-90) cc_final: 0.5666 (p-90) REVERT: D 654 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7517 (tm-30) REVERT: E 498 ARG cc_start: 0.7850 (pmt-80) cc_final: 0.7551 (pmt-80) REVERT: F 530 MET cc_start: 0.4505 (mmm) cc_final: 0.4113 (mmm) REVERT: F 543 ASN cc_start: 0.7469 (m-40) cc_final: 0.7140 (m110) outliers start: 64 outliers final: 55 residues processed: 181 average time/residue: 0.1681 time to fit residues: 49.6070 Evaluate side-chains 177 residues out of total 2585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 119 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 213 LYS Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 211 ASN Chi-restraints excluded: chain M residue 206 THR Chi-restraints excluded: chain I residue 11 VAL 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 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 326 ARG Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 CYS Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 499 CYS Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 606 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 64 optimal weight: 0.0570 chunk 224 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 278 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 218 optimal weight: 2.9990 chunk 246 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.132365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.097828 restraints weight = 636901.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.099003 restraints weight = 163952.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.102573 restraints weight = 69987.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.101744 restraints weight = 52631.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.102006 restraints weight = 43431.591| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3966 r_free = 0.3966 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 182 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3966 r_free = 0.3966 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 173 | |-----------------------------------------------------------------------------| r_final: 0.3966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25967 Z= 0.126 Angle : 0.692 10.441 35588 Z= 0.331 Chirality : 0.048 0.394 4201 Planarity : 0.004 0.043 4491 Dihedral : 7.417 58.676 4814 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 4.20 % Allowed : 19.55 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.15), residues: 3209 helix: -0.03 (0.25), residues: 475 sheet: -1.98 (0.18), residues: 828 loop : -2.26 (0.14), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 273 TYR 0.017 0.001 TYR M 173 PHE 0.012 0.001 PHE E 360 TRP 0.023 0.001 TRP A 425 HIS 0.006 0.001 HIS I 172 Details of bonding type rmsd covalent geometry : bond 0.00285 (25858) covalent geometry : angle 0.66162 (35321) SS BOND : bond 0.00416 ( 46) SS BOND : angle 1.27946 ( 92) hydrogen bonds : bond 0.03421 ( 651) hydrogen bonds : angle 5.84428 ( 1735) Misc. bond : bond 0.00053 ( 4) link_BETA1-4 : bond 0.01297 ( 15) link_BETA1-4 : angle 3.84102 ( 45) link_NAG-ASN : bond 0.00375 ( 42) link_NAG-ASN : angle 2.40022 ( 126) link_NAG-SER : bond 0.00971 ( 2) link_NAG-SER : angle 2.52845 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 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 195 residues out of total 2585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 139 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 213 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.7960 (tppt) REVERT: G 226 GLU cc_start: 0.6570 (mt-10) cc_final: 0.5830 (mm-30) REVERT: I 95 GLU cc_start: 0.7640 (pt0) cc_final: 0.7001 (tt0) REVERT: A 69 TRP cc_start: 0.7839 (m-90) cc_final: 0.7516 (m-10) REVERT: B 605 CYS cc_start: 0.6915 (OUTLIER) cc_final: 0.6391 (m) REVERT: B 657 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7590 (tp30) REVERT: C 326 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6506 (mtm180) REVERT: C 360 PHE cc_start: 0.7354 (m-80) cc_final: 0.7101 (m-80) REVERT: C 425 TRP cc_start: 0.5600 (p-90) cc_final: 0.5354 (p-90) REVERT: E 264 SER cc_start: 0.8119 (OUTLIER) cc_final: 0.7885 (p) REVERT: E 498 ARG cc_start: 0.8069 (pmt-80) cc_final: 0.7633 (pmt-80) REVERT: F 535 MET cc_start: 0.7045 (mtm) cc_final: 0.6343 (tpp) REVERT: F 542 ARG cc_start: 0.4050 (tpt170) cc_final: 0.3649 (ttt90) REVERT: F 543 ASN cc_start: 0.7373 (m-40) cc_final: 0.7006 (m110) REVERT: F 601 LYS cc_start: 0.8625 (mtpp) cc_final: 0.8352 (ptpp) outliers start: 56 outliers final: 49 residues processed: 184 average time/residue: 0.1606 time to fit residues: 47.8736 Evaluate side-chains 187 residues out of total 2585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 134 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 122 PHE Chi-restraints excluded: chain G residue 213 LYS Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain M residue 206 THR Chi-restraints excluded: chain I residue 11 VAL 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 201 ILE Chi-restraints excluded: chain A residue 202 THR 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 555 LEU Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 241 SER 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 326 ARG Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 499 CYS Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 606 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 307 optimal weight: 50.0000 chunk 195 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 242 optimal weight: 6.9990 chunk 162 optimal weight: 0.9990 chunk 297 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 60 optimal weight: 20.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 ASN ** E 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.125502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.099594 restraints weight = 665578.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.102923 restraints weight = 176976.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.103195 restraints weight = 55770.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.103640 restraints weight = 50888.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.103753 restraints weight = 38816.161| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4089 r_free = 0.4089 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 173 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4089 r_free = 0.4089 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 148 | |-----------------------------------------------------------------------------| r_final: 0.4089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 25967 Z= 0.247 Angle : 0.785 13.081 35588 Z= 0.380 Chirality : 0.051 0.396 4201 Planarity : 0.005 0.043 4491 Dihedral : 7.916 59.383 4814 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 4.49 % Allowed : 19.36 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.14), residues: 3209 helix: -0.26 (0.24), residues: 470 sheet: -2.15 (0.17), residues: 884 loop : -2.27 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 170 TYR 0.023 0.002 TYR H 192 PHE 0.019 0.002 PHE E 93 TRP 0.020 0.002 TRP F 571 HIS 0.012 0.002 HIS C 373 Details of bonding type rmsd covalent geometry : bond 0.00576 (25858) covalent geometry : angle 0.75444 (35321) SS BOND : bond 0.00551 ( 46) SS BOND : angle 1.50556 ( 92) hydrogen bonds : bond 0.04071 ( 651) hydrogen bonds : angle 6.13291 ( 1735) Misc. bond : bond 0.00129 ( 4) link_BETA1-4 : bond 0.01305 ( 15) link_BETA1-4 : angle 4.04729 ( 45) link_NAG-ASN : bond 0.00502 ( 42) link_NAG-ASN : angle 2.63419 ( 126) link_NAG-SER : bond 0.01145 ( 2) link_NAG-SER : angle 2.50528 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4239.23 seconds wall clock time: 74 minutes 22.37 seconds (4462.37 seconds total)