Starting phenix.real_space_refine on Fri Feb 23 06:33:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v22_21025/02_2024/6v22_21025_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v22_21025/02_2024/6v22_21025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v22_21025/02_2024/6v22_21025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v22_21025/02_2024/6v22_21025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v22_21025/02_2024/6v22_21025_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v22_21025/02_2024/6v22_21025_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.319 sd= 0.838 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: 8 Type Number sf(0) Gaussians Ca 8 9.91 5 K 4 8.98 5 P 40 5.49 5 Mg 4 5.21 5 S 244 5.16 5 C 24256 2.51 5 N 5748 2.21 5 O 6700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 17": "NH1" <-> "NH2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "A PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 368": "NH1" <-> "NH2" Residue "A ASP 432": "OD1" <-> "OD2" Residue "A ASP 437": "OD1" <-> "OD2" Residue "A TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 482": "OD1" <-> "OD2" Residue "A GLU 520": "OE1" <-> "OE2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 817": "OD1" <-> "OD2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A ASP 896": "OD1" <-> "OD2" Residue "A ASP 931": "OD1" <-> "OD2" Residue "A ASP 984": "OD1" <-> "OD2" Residue "A PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 992": "OD1" <-> "OD2" Residue "A GLU 1040": "OE1" <-> "OE2" Residue "A ASP 1047": "OD1" <-> "OD2" Residue "E GLU 2012": "OE1" <-> "OE2" Residue "E ASP 2015": "OD1" <-> "OD2" Residue "E ASP 2046": "OD1" <-> "OD2" Residue "E GLU 2064": "OE1" <-> "OE2" Residue "E TYR 2088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 2097": "NH1" <-> "NH2" Residue "E ASP 2158": "OD1" <-> "OD2" Residue "E ARG 2163": "NH1" <-> "NH2" Residue "E ASP 2166": "OD1" <-> "OD2" Residue "E GLU 2167": "OE1" <-> "OE2" Residue "E PHE 2174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 2202": "OE1" <-> "OE2" Residue "B ARG 17": "NH1" <-> "NH2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 368": "NH1" <-> "NH2" Residue "B ASP 432": "OD1" <-> "OD2" Residue "B ASP 437": "OD1" <-> "OD2" Residue "B TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 482": "OD1" <-> "OD2" Residue "B GLU 520": "OE1" <-> "OE2" Residue "B GLU 591": "OE1" <-> "OE2" Residue "B PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 817": "OD1" <-> "OD2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B ASP 896": "OD1" <-> "OD2" Residue "B ASP 931": "OD1" <-> "OD2" Residue "B ASP 984": "OD1" <-> "OD2" Residue "B PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 992": "OD1" <-> "OD2" Residue "B GLU 1040": "OE1" <-> "OE2" Residue "B ASP 1047": "OD1" <-> "OD2" Residue "F GLU 2012": "OE1" <-> "OE2" Residue "F ASP 2015": "OD1" <-> "OD2" Residue "F ASP 2046": "OD1" <-> "OD2" Residue "F GLU 2064": "OE1" <-> "OE2" Residue "F TYR 2088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 2097": "NH1" <-> "NH2" Residue "F ASP 2158": "OD1" <-> "OD2" Residue "F ARG 2163": "NH1" <-> "NH2" Residue "F ASP 2166": "OD1" <-> "OD2" Residue "F GLU 2167": "OE1" <-> "OE2" Residue "F PHE 2174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 2202": "OE1" <-> "OE2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "C PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 368": "NH1" <-> "NH2" Residue "C ASP 432": "OD1" <-> "OD2" Residue "C ASP 437": "OD1" <-> "OD2" Residue "C TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 482": "OD1" <-> "OD2" Residue "C GLU 520": "OE1" <-> "OE2" Residue "C GLU 591": "OE1" <-> "OE2" Residue "C PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 817": "OD1" <-> "OD2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C ASP 896": "OD1" <-> "OD2" Residue "C ASP 931": "OD1" <-> "OD2" Residue "C ASP 984": "OD1" <-> "OD2" Residue "C PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 992": "OD1" <-> "OD2" Residue "C GLU 1040": "OE1" <-> "OE2" Residue "C ASP 1047": "OD1" <-> "OD2" Residue "G GLU 2012": "OE1" <-> "OE2" Residue "G ASP 2015": "OD1" <-> "OD2" Residue "G ASP 2046": "OD1" <-> "OD2" Residue "G GLU 2064": "OE1" <-> "OE2" Residue "G TYR 2088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 2097": "NH1" <-> "NH2" Residue "G ASP 2158": "OD1" <-> "OD2" Residue "G ARG 2163": "NH1" <-> "NH2" Residue "G ASP 2166": "OD1" <-> "OD2" Residue "G GLU 2167": "OE1" <-> "OE2" Residue "G PHE 2174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 2202": "OE1" <-> "OE2" Residue "D ARG 17": "NH1" <-> "NH2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "D PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 368": "NH1" <-> "NH2" Residue "D ASP 432": "OD1" <-> "OD2" Residue "D ASP 437": "OD1" <-> "OD2" Residue "D TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 482": "OD1" <-> "OD2" Residue "D GLU 520": "OE1" <-> "OE2" Residue "D GLU 591": "OE1" <-> "OE2" Residue "D PHE 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 817": "OD1" <-> "OD2" Residue "D GLU 819": "OE1" <-> "OE2" Residue "D ASP 896": "OD1" <-> "OD2" Residue "D ASP 931": "OD1" <-> "OD2" Residue "D ASP 984": "OD1" <-> "OD2" Residue "D PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 992": "OD1" <-> "OD2" Residue "D GLU 1040": "OE1" <-> "OE2" Residue "D ASP 1047": "OD1" <-> "OD2" Residue "H GLU 2012": "OE1" <-> "OE2" Residue "H ASP 2015": "OD1" <-> "OD2" Residue "H ASP 2046": "OD1" <-> "OD2" Residue "H GLU 2064": "OE1" <-> "OE2" Residue "H TYR 2088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 2097": "NH1" <-> "NH2" Residue "H ASP 2158": "OD1" <-> "OD2" Residue "H ARG 2163": "NH1" <-> "NH2" Residue "H ASP 2166": "OD1" <-> "OD2" Residue "H GLU 2167": "OE1" <-> "OE2" Residue "H PHE 2174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 2202": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 37004 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 7137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 896, 7137 Classifications: {'peptide': 896} Link IDs: {'PTRANS': 27, 'TRANS': 868} Chain breaks: 4 Chain: "E" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1586 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 8, 'TRANS': 190} Chain: "B" Number of atoms: 7137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 896, 7137 Classifications: {'peptide': 896} Link IDs: {'PTRANS': 27, 'TRANS': 868} Chain breaks: 4 Chain: "F" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1586 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 8, 'TRANS': 190} Chain: "C" Number of atoms: 7137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 896, 7137 Classifications: {'peptide': 896} Link IDs: {'PTRANS': 27, 'TRANS': 868} Chain breaks: 4 Chain: "G" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1586 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 8, 'TRANS': 190} Chain: "D" Number of atoms: 7137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 896, 7137 Classifications: {'peptide': 896} Link IDs: {'PTRANS': 27, 'TRANS': 868} Chain breaks: 4 Chain: "H" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1586 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 8, 'TRANS': 190} Chain: "A" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 419 Unusual residues: {' K': 4, ' CA': 2, ' MG': 1, 'CLR': 4, 'POV': 11} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-3': 4, 'POV:plan-2': 3, 'POV:plan-1': 6} Unresolved non-hydrogen planarities: 46 Chain: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 112 Unusual residues: {'NAG': 2, 'POV': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 415 Unusual residues: {' CA': 2, ' MG': 1, 'CLR': 4, 'POV': 11} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-3': 4, 'POV:plan-2': 3, 'POV:plan-1': 6} Unresolved non-hydrogen planarities: 46 Chain: "F" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 112 Unusual residues: {'NAG': 2, 'POV': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 415 Unusual residues: {' CA': 2, ' MG': 1, 'CLR': 4, 'POV': 11} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-3': 4, 'POV:plan-2': 3, 'POV:plan-1': 6} Unresolved non-hydrogen planarities: 46 Chain: "G" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 112 Unusual residues: {'NAG': 2, 'POV': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 415 Unusual residues: {' CA': 2, ' MG': 1, 'CLR': 4, 'POV': 11} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-3': 4, 'POV:plan-2': 3, 'POV:plan-1': 6} Unresolved non-hydrogen planarities: 46 Chain: "H" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 112 Unusual residues: {'NAG': 2, 'POV': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 19.14, per 1000 atoms: 0.52 Number of scatterers: 37004 At special positions: 0 Unit cell: (144.56, 144.56, 160.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 8 19.99 K 4 19.00 S 244 16.00 P 40 15.00 Mg 4 11.99 O 6700 8.00 N 5748 7.00 C 24256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS E2054 " - pdb=" SG CYS E2148 " distance=2.03 Simple disulfide: pdb=" SG CYS E2068 " - pdb=" SG CYS E2119 " distance=2.03 Simple disulfide: pdb=" SG CYS E2072 " - pdb=" SG CYS E2076 " distance=2.02 Simple disulfide: pdb=" SG CYS E2084 " - pdb=" SG CYS E2113 " distance=2.03 Simple disulfide: pdb=" SG CYS F2054 " - pdb=" SG CYS F2148 " distance=2.03 Simple disulfide: pdb=" SG CYS F2068 " - pdb=" SG CYS F2119 " distance=2.03 Simple disulfide: pdb=" SG CYS F2072 " - pdb=" SG CYS F2076 " distance=2.02 Simple disulfide: pdb=" SG CYS F2084 " - pdb=" SG CYS F2113 " distance=2.03 Simple disulfide: pdb=" SG CYS G2054 " - pdb=" SG CYS G2148 " distance=2.03 Simple disulfide: pdb=" SG CYS G2068 " - pdb=" SG CYS G2119 " distance=2.03 Simple disulfide: pdb=" SG CYS G2072 " - pdb=" SG CYS G2076 " distance=2.02 Simple disulfide: pdb=" SG CYS G2084 " - pdb=" SG CYS G2113 " distance=2.03 Simple disulfide: pdb=" SG CYS H2054 " - pdb=" SG CYS H2148 " distance=2.03 Simple disulfide: pdb=" SG CYS H2068 " - pdb=" SG CYS H2119 " distance=2.03 Simple disulfide: pdb=" SG CYS H2072 " - pdb=" SG CYS H2076 " distance=2.02 Simple disulfide: pdb=" SG CYS H2084 " - pdb=" SG CYS H2113 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=16, symmetry=0 Links applied NAG-ASN " NAG E2305 " - " ASN E2053 " " NAG E2306 " - " ASN E2090 " " NAG F2305 " - " ASN F2053 " " NAG F2306 " - " ASN F2090 " " NAG G2305 " - " ASN G2053 " " NAG G2306 " - " ASN G2090 " " NAG H2305 " - " ASN H2053 " " NAG H2306 " - " ASN H2090 " Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.82 Conformation dependent library (CDL) restraints added in 6.6 seconds 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8312 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 168 helices and 24 sheets defined 46.5% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.55 Creating SS restraints... Processing helix chain 'A' and resid 22 through 46 removed outlier: 3.722A pdb=" N LEU A 26 " --> pdb=" O TRP A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 110 through 135 removed outlier: 4.358A pdb=" N SER A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 170 Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 181 through 199 removed outlier: 3.801A pdb=" N ASP A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) Proline residue: A 191 - end of helix removed outlier: 3.883A pdb=" N PHE A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 222 removed outlier: 3.581A pdb=" N LEU A 214 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER A 218 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 220 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 221 " --> pdb=" O SER A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 258 Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 298 through 325 removed outlier: 4.986A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 385 through 393 Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 433 through 450 Processing helix chain 'A' and resid 464 through 470 removed outlier: 3.718A pdb=" N LEU A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 499 Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.864A pdb=" N GLU A 530 " --> pdb=" O LYS A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 550 through 560 Processing helix chain 'A' and resid 605 through 608 Processing helix chain 'A' and resid 700 through 702 No H-bonds generated for 'chain 'A' and resid 700 through 702' Processing helix chain 'A' and resid 707 through 712 Processing helix chain 'A' and resid 734 through 742 removed outlier: 4.783A pdb=" N MET A 739 " --> pdb=" O ASN A 736 " (cutoff:3.500A) Proline residue: A 740 - end of helix Processing helix chain 'A' and resid 760 through 770 removed outlier: 5.022A pdb=" N GLU A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU A 770 " --> pdb=" O GLU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 791 Processing helix chain 'A' and resid 818 through 829 Processing helix chain 'A' and resid 885 through 890 removed outlier: 3.917A pdb=" N GLN A 889 " --> pdb=" O THR A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 905 No H-bonds generated for 'chain 'A' and resid 903 through 905' Processing helix chain 'A' and resid 907 through 910 No H-bonds generated for 'chain 'A' and resid 907 through 910' Processing helix chain 'A' and resid 917 through 929 removed outlier: 4.178A pdb=" N SER A 922 " --> pdb=" O VAL A 919 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET A 924 " --> pdb=" O ASP A 921 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A 925 " --> pdb=" O SER A 922 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 929 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 941 Processing helix chain 'A' and resid 947 through 955 Processing helix chain 'A' and resid 966 through 973 removed outlier: 3.806A pdb=" N ARG A 972 " --> pdb=" O THR A 968 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 991 removed outlier: 3.620A pdb=" N GLY A 991 " --> pdb=" O ALA A 988 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 988 through 991' Processing helix chain 'A' and resid 996 through 1006 Processing helix chain 'E' and resid 2012 through 2038 removed outlier: 3.950A pdb=" N PHE E2037 " --> pdb=" O PHE E2033 " (cutoff:3.500A) Processing helix chain 'E' and resid 2040 through 2048 Processing helix chain 'E' and resid 2104 through 2109 Processing helix chain 'E' and resid 2123 through 2139 Processing helix chain 'E' and resid 2167 through 2203 removed outlier: 3.991A pdb=" N CYS E2173 " --> pdb=" O LEU E2170 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU E2175 " --> pdb=" O HIS E2172 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TRP E2176 " --> pdb=" O CYS E2173 " (cutoff:3.500A) Proline residue: E2177 - end of helix removed outlier: 3.545A pdb=" N VAL E2183 " --> pdb=" O THR E2180 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL E2189 " --> pdb=" O LEU E2186 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR E2191 " --> pdb=" O VAL E2188 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS E2193 " --> pdb=" O LEU E2190 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU E2197 " --> pdb=" O ALA E2194 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 46 removed outlier: 3.722A pdb=" N LEU B 26 " --> pdb=" O TRP B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 105 Processing helix chain 'B' and resid 110 through 135 removed outlier: 4.358A pdb=" N SER B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 170 Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 181 through 199 removed outlier: 3.801A pdb=" N ASP B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) Proline residue: B 191 - end of helix removed outlier: 3.883A pdb=" N PHE B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 222 removed outlier: 3.581A pdb=" N LEU B 214 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER B 218 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 220 " --> pdb=" O PHE B 217 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 221 " --> pdb=" O SER B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 258 Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'B' and resid 274 through 285 Processing helix chain 'B' and resid 298 through 325 removed outlier: 4.986A pdb=" N ALA B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 385 through 393 Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 433 through 450 Processing helix chain 'B' and resid 464 through 470 removed outlier: 3.718A pdb=" N LEU B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 499 Processing helix chain 'B' and resid 503 through 510 Processing helix chain 'B' and resid 524 through 532 removed outlier: 3.864A pdb=" N GLU B 530 " --> pdb=" O LYS B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 550 through 560 Processing helix chain 'B' and resid 605 through 608 Processing helix chain 'B' and resid 700 through 702 No H-bonds generated for 'chain 'B' and resid 700 through 702' Processing helix chain 'B' and resid 707 through 712 Processing helix chain 'B' and resid 734 through 742 removed outlier: 4.784A pdb=" N MET B 739 " --> pdb=" O ASN B 736 " (cutoff:3.500A) Proline residue: B 740 - end of helix Processing helix chain 'B' and resid 760 through 770 removed outlier: 5.022A pdb=" N GLU B 768 " --> pdb=" O LYS B 764 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU B 770 " --> pdb=" O GLU B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 791 Processing helix chain 'B' and resid 818 through 829 Processing helix chain 'B' and resid 885 through 890 removed outlier: 3.917A pdb=" N GLN B 889 " --> pdb=" O THR B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 905 No H-bonds generated for 'chain 'B' and resid 903 through 905' Processing helix chain 'B' and resid 907 through 910 No H-bonds generated for 'chain 'B' and resid 907 through 910' Processing helix chain 'B' and resid 917 through 929 removed outlier: 4.178A pdb=" N SER B 922 " --> pdb=" O VAL B 919 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET B 924 " --> pdb=" O ASP B 921 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 925 " --> pdb=" O SER B 922 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE B 929 " --> pdb=" O ALA B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 941 Processing helix chain 'B' and resid 947 through 955 Processing helix chain 'B' and resid 966 through 973 removed outlier: 3.806A pdb=" N ARG B 972 " --> pdb=" O THR B 968 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP B 973 " --> pdb=" O LEU B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 991 removed outlier: 3.620A pdb=" N GLY B 991 " --> pdb=" O ALA B 988 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 988 through 991' Processing helix chain 'B' and resid 996 through 1006 Processing helix chain 'F' and resid 2012 through 2038 removed outlier: 3.950A pdb=" N PHE F2037 " --> pdb=" O PHE F2033 " (cutoff:3.500A) Processing helix chain 'F' and resid 2040 through 2048 Processing helix chain 'F' and resid 2104 through 2109 Processing helix chain 'F' and resid 2123 through 2139 Processing helix chain 'F' and resid 2167 through 2203 removed outlier: 3.990A pdb=" N CYS F2173 " --> pdb=" O LEU F2170 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU F2175 " --> pdb=" O HIS F2172 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TRP F2176 " --> pdb=" O CYS F2173 " (cutoff:3.500A) Proline residue: F2177 - end of helix removed outlier: 3.546A pdb=" N VAL F2183 " --> pdb=" O THR F2180 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL F2189 " --> pdb=" O LEU F2186 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR F2191 " --> pdb=" O VAL F2188 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS F2193 " --> pdb=" O LEU F2190 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU F2197 " --> pdb=" O ALA F2194 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 46 removed outlier: 3.722A pdb=" N LEU C 26 " --> pdb=" O TRP C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 105 Processing helix chain 'C' and resid 110 through 135 removed outlier: 4.358A pdb=" N SER C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 170 Processing helix chain 'C' and resid 174 through 178 Processing helix chain 'C' and resid 181 through 199 removed outlier: 3.801A pdb=" N ASP C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) Proline residue: C 191 - end of helix removed outlier: 3.883A pdb=" N PHE C 194 " --> pdb=" O VAL C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 222 removed outlier: 3.581A pdb=" N LEU C 214 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER C 218 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 220 " --> pdb=" O PHE C 217 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 221 " --> pdb=" O SER C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 258 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 274 through 285 Processing helix chain 'C' and resid 298 through 325 removed outlier: 4.987A pdb=" N ALA C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 385 through 393 Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 433 through 450 Processing helix chain 'C' and resid 464 through 470 removed outlier: 3.718A pdb=" N LEU C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU C 470 " --> pdb=" O LYS C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 499 Processing helix chain 'C' and resid 503 through 510 Processing helix chain 'C' and resid 524 through 532 removed outlier: 3.864A pdb=" N GLU C 530 " --> pdb=" O LYS C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 545 No H-bonds generated for 'chain 'C' and resid 543 through 545' Processing helix chain 'C' and resid 550 through 560 Processing helix chain 'C' and resid 605 through 608 Processing helix chain 'C' and resid 700 through 702 No H-bonds generated for 'chain 'C' and resid 700 through 702' Processing helix chain 'C' and resid 707 through 712 Processing helix chain 'C' and resid 734 through 742 removed outlier: 4.784A pdb=" N MET C 739 " --> pdb=" O ASN C 736 " (cutoff:3.500A) Proline residue: C 740 - end of helix Processing helix chain 'C' and resid 760 through 770 removed outlier: 5.022A pdb=" N GLU C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR C 769 " --> pdb=" O ARG C 765 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU C 770 " --> pdb=" O GLU C 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 786 through 791 Processing helix chain 'C' and resid 818 through 829 Processing helix chain 'C' and resid 885 through 890 removed outlier: 3.917A pdb=" N GLN C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 905 No H-bonds generated for 'chain 'C' and resid 903 through 905' Processing helix chain 'C' and resid 907 through 910 No H-bonds generated for 'chain 'C' and resid 907 through 910' Processing helix chain 'C' and resid 917 through 929 removed outlier: 4.177A pdb=" N SER C 922 " --> pdb=" O VAL C 919 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET C 924 " --> pdb=" O ASP C 921 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER C 925 " --> pdb=" O SER C 922 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE C 929 " --> pdb=" O ALA C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 932 through 941 Processing helix chain 'C' and resid 947 through 955 Processing helix chain 'C' and resid 966 through 973 removed outlier: 3.805A pdb=" N ARG C 972 " --> pdb=" O THR C 968 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP C 973 " --> pdb=" O LEU C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 991 removed outlier: 3.619A pdb=" N GLY C 991 " --> pdb=" O ALA C 988 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 988 through 991' Processing helix chain 'C' and resid 996 through 1006 Processing helix chain 'G' and resid 2012 through 2038 removed outlier: 3.951A pdb=" N PHE G2037 " --> pdb=" O PHE G2033 " (cutoff:3.500A) Processing helix chain 'G' and resid 2040 through 2048 Processing helix chain 'G' and resid 2104 through 2109 Processing helix chain 'G' and resid 2123 through 2139 Processing helix chain 'G' and resid 2167 through 2203 removed outlier: 3.991A pdb=" N CYS G2173 " --> pdb=" O LEU G2170 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU G2175 " --> pdb=" O HIS G2172 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TRP G2176 " --> pdb=" O CYS G2173 " (cutoff:3.500A) Proline residue: G2177 - end of helix removed outlier: 3.546A pdb=" N VAL G2183 " --> pdb=" O THR G2180 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL G2189 " --> pdb=" O LEU G2186 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR G2191 " --> pdb=" O VAL G2188 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS G2193 " --> pdb=" O LEU G2190 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU G2197 " --> pdb=" O ALA G2194 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 46 removed outlier: 3.722A pdb=" N LEU D 26 " --> pdb=" O TRP D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 105 Processing helix chain 'D' and resid 110 through 135 removed outlier: 4.358A pdb=" N SER D 135 " --> pdb=" O PHE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 170 Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 181 through 199 removed outlier: 3.801A pdb=" N ASP D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) Proline residue: D 191 - end of helix removed outlier: 3.883A pdb=" N PHE D 194 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 222 removed outlier: 3.581A pdb=" N LEU D 214 " --> pdb=" O ALA D 211 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER D 218 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE D 220 " --> pdb=" O PHE D 217 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU D 221 " --> pdb=" O SER D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 258 Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 274 through 285 Processing helix chain 'D' and resid 298 through 325 removed outlier: 4.986A pdb=" N ALA D 313 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 353 through 363 Processing helix chain 'D' and resid 385 through 393 Processing helix chain 'D' and resid 408 through 413 Processing helix chain 'D' and resid 433 through 450 Processing helix chain 'D' and resid 464 through 470 removed outlier: 3.718A pdb=" N LEU D 469 " --> pdb=" O ASN D 465 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 499 Processing helix chain 'D' and resid 503 through 510 Processing helix chain 'D' and resid 524 through 532 removed outlier: 3.864A pdb=" N GLU D 530 " --> pdb=" O LYS D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 545 No H-bonds generated for 'chain 'D' and resid 543 through 545' Processing helix chain 'D' and resid 550 through 560 Processing helix chain 'D' and resid 605 through 608 Processing helix chain 'D' and resid 700 through 702 No H-bonds generated for 'chain 'D' and resid 700 through 702' Processing helix chain 'D' and resid 707 through 712 Processing helix chain 'D' and resid 734 through 742 removed outlier: 4.784A pdb=" N MET D 739 " --> pdb=" O ASN D 736 " (cutoff:3.500A) Proline residue: D 740 - end of helix Processing helix chain 'D' and resid 760 through 770 removed outlier: 5.022A pdb=" N GLU D 768 " --> pdb=" O LYS D 764 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR D 769 " --> pdb=" O ARG D 765 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU D 770 " --> pdb=" O GLU D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 791 Processing helix chain 'D' and resid 818 through 829 Processing helix chain 'D' and resid 885 through 890 removed outlier: 3.917A pdb=" N GLN D 889 " --> pdb=" O THR D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 903 through 905 No H-bonds generated for 'chain 'D' and resid 903 through 905' Processing helix chain 'D' and resid 907 through 910 No H-bonds generated for 'chain 'D' and resid 907 through 910' Processing helix chain 'D' and resid 917 through 929 removed outlier: 4.178A pdb=" N SER D 922 " --> pdb=" O VAL D 919 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET D 924 " --> pdb=" O ASP D 921 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER D 925 " --> pdb=" O SER D 922 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE D 929 " --> pdb=" O ALA D 926 " (cutoff:3.500A) Processing helix chain 'D' and resid 932 through 941 Processing helix chain 'D' and resid 947 through 955 Processing helix chain 'D' and resid 966 through 973 removed outlier: 3.806A pdb=" N ARG D 972 " --> pdb=" O THR D 968 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP D 973 " --> pdb=" O LEU D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 988 through 991 removed outlier: 3.620A pdb=" N GLY D 991 " --> pdb=" O ALA D 988 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 988 through 991' Processing helix chain 'D' and resid 996 through 1006 Processing helix chain 'H' and resid 2012 through 2038 removed outlier: 3.950A pdb=" N PHE H2037 " --> pdb=" O PHE H2033 " (cutoff:3.500A) Processing helix chain 'H' and resid 2040 through 2048 Processing helix chain 'H' and resid 2104 through 2109 Processing helix chain 'H' and resid 2123 through 2139 Processing helix chain 'H' and resid 2167 through 2203 removed outlier: 3.990A pdb=" N CYS H2173 " --> pdb=" O LEU H2170 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU H2175 " --> pdb=" O HIS H2172 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TRP H2176 " --> pdb=" O CYS H2173 " (cutoff:3.500A) Proline residue: H2177 - end of helix removed outlier: 3.546A pdb=" N VAL H2183 " --> pdb=" O THR H2180 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL H2189 " --> pdb=" O LEU H2186 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR H2191 " --> pdb=" O VAL H2188 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS H2193 " --> pdb=" O LEU H2190 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU H2197 " --> pdb=" O ALA H2194 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 139 through 141 Processing sheet with id= B, first strand: chain 'A' and resid 482 through 485 removed outlier: 6.218A pdb=" N CYS A 422 " --> pdb=" O ILE A 457 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLN A 459 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE A 424 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA A 421 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLU A 374 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL A 347 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL A 376 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N GLY A 349 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU A 378 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS A 379 " --> pdb=" O TYR A 401 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 535 through 540 removed outlier: 3.708A pdb=" N ALA A 567 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE A 598 " --> pdb=" O MET A 565 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N MET A 565 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 914 through 916 removed outlier: 7.803A pdb=" N PHE A 915 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR A 880 " --> pdb=" O PHE A 915 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N GLU A 881 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ILE A 802 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 976 through 981 Processing sheet with id= F, first strand: chain 'E' and resid 2146 through 2150 removed outlier: 6.871A pdb=" N TYR E2088 " --> pdb=" O LEU E2057 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL E2059 " --> pdb=" O GLN E2086 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN E2086 " --> pdb=" O VAL E2059 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL E2087 " --> pdb=" O LEU E2100 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 139 through 141 Processing sheet with id= H, first strand: chain 'B' and resid 482 through 485 removed outlier: 6.218A pdb=" N CYS B 422 " --> pdb=" O ILE B 457 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLN B 459 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE B 424 " --> pdb=" O GLN B 459 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA B 421 " --> pdb=" O HIS B 344 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU B 374 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL B 347 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL B 376 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N GLY B 349 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU B 378 " --> pdb=" O GLY B 349 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS B 379 " --> pdb=" O TYR B 401 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 535 through 540 removed outlier: 3.709A pdb=" N ALA B 567 " --> pdb=" O PHE B 596 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE B 598 " --> pdb=" O MET B 565 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N MET B 565 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 914 through 916 removed outlier: 7.803A pdb=" N PHE B 915 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR B 880 " --> pdb=" O PHE B 915 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N CYS B 800 " --> pdb=" O ILE B 879 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N GLU B 881 " --> pdb=" O CYS B 800 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE B 802 " --> pdb=" O GLU B 881 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 976 through 981 Processing sheet with id= L, first strand: chain 'F' and resid 2146 through 2150 removed outlier: 6.871A pdb=" N TYR F2088 " --> pdb=" O LEU F2057 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL F2059 " --> pdb=" O GLN F2086 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN F2086 " --> pdb=" O VAL F2059 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL F2087 " --> pdb=" O LEU F2100 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 139 through 141 Processing sheet with id= N, first strand: chain 'C' and resid 482 through 485 removed outlier: 6.218A pdb=" N CYS C 422 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLN C 459 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE C 424 " --> pdb=" O GLN C 459 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA C 421 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU C 374 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL C 347 " --> pdb=" O GLU C 374 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL C 376 " --> pdb=" O VAL C 347 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N GLY C 349 " --> pdb=" O VAL C 376 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU C 378 " --> pdb=" O GLY C 349 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS C 379 " --> pdb=" O TYR C 401 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 535 through 540 removed outlier: 3.708A pdb=" N ALA C 567 " --> pdb=" O PHE C 596 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE C 598 " --> pdb=" O MET C 565 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N MET C 565 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 914 through 916 removed outlier: 7.802A pdb=" N PHE C 915 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR C 880 " --> pdb=" O PHE C 915 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS C 800 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N GLU C 881 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE C 802 " --> pdb=" O GLU C 881 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 976 through 981 Processing sheet with id= R, first strand: chain 'G' and resid 2146 through 2150 removed outlier: 6.870A pdb=" N TYR G2088 " --> pdb=" O LEU G2057 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL G2059 " --> pdb=" O GLN G2086 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN G2086 " --> pdb=" O VAL G2059 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL G2087 " --> pdb=" O LEU G2100 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 139 through 141 Processing sheet with id= T, first strand: chain 'D' and resid 482 through 485 removed outlier: 6.218A pdb=" N CYS D 422 " --> pdb=" O ILE D 457 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLN D 459 " --> pdb=" O CYS D 422 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE D 424 " --> pdb=" O GLN D 459 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA D 421 " --> pdb=" O HIS D 344 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU D 374 " --> pdb=" O ILE D 345 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL D 347 " --> pdb=" O GLU D 374 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL D 376 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N GLY D 349 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU D 378 " --> pdb=" O GLY D 349 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS D 379 " --> pdb=" O TYR D 401 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 535 through 540 removed outlier: 3.709A pdb=" N ALA D 567 " --> pdb=" O PHE D 596 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE D 598 " --> pdb=" O MET D 565 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N MET D 565 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 914 through 916 removed outlier: 7.803A pdb=" N PHE D 915 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR D 880 " --> pdb=" O PHE D 915 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N CYS D 800 " --> pdb=" O ILE D 879 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N GLU D 881 " --> pdb=" O CYS D 800 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE D 802 " --> pdb=" O GLU D 881 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 976 through 981 Processing sheet with id= X, first strand: chain 'H' and resid 2146 through 2150 removed outlier: 6.871A pdb=" N TYR H2088 " --> pdb=" O LEU H2057 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL H2059 " --> pdb=" O GLN H2086 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN H2086 " --> pdb=" O VAL H2059 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL H2087 " --> pdb=" O LEU H2100 " (cutoff:3.500A) 1448 hydrogen bonds defined for protein. 3756 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: 13.13 Time building geometry restraints manager: 14.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 5724 1.30 - 1.43: 10050 1.43 - 1.56: 21312 1.56 - 1.69: 342 1.69 - 1.81: 360 Bond restraints: 37788 Sorted by residual: bond pdb=" C5 CLR A1113 " pdb=" C6 CLR A1113 " ideal model delta sigma weight residual 1.332 1.571 -0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C5 CLR C1118 " pdb=" C6 CLR C1118 " ideal model delta sigma weight residual 1.332 1.571 -0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C5 CLR B1118 " pdb=" C6 CLR B1118 " ideal model delta sigma weight residual 1.332 1.571 -0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C5 CLR D1118 " pdb=" C6 CLR D1118 " ideal model delta sigma weight residual 1.332 1.571 -0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C5 CLR A1111 " pdb=" C6 CLR A1111 " ideal model delta sigma weight residual 1.332 1.569 -0.237 2.00e-02 2.50e+03 1.40e+02 ... (remaining 37783 not shown) Histogram of bond angle deviations from ideal: 98.74 - 105.84: 760 105.84 - 112.94: 21153 112.94 - 120.03: 13577 120.03 - 127.13: 15225 127.13 - 134.23: 417 Bond angle restraints: 51132 Sorted by residual: angle pdb=" O13 POV C1105 " pdb=" P POV C1105 " pdb=" O14 POV C1105 " ideal model delta sigma weight residual 121.11 100.61 20.50 3.00e+00 1.11e-01 4.67e+01 angle pdb=" O13 POV A1122 " pdb=" P POV A1122 " pdb=" O14 POV A1122 " ideal model delta sigma weight residual 121.11 100.61 20.50 3.00e+00 1.11e-01 4.67e+01 angle pdb=" O13 POV D1105 " pdb=" P POV D1105 " pdb=" O14 POV D1105 " ideal model delta sigma weight residual 121.11 100.64 20.47 3.00e+00 1.11e-01 4.66e+01 angle pdb=" O13 POV B1105 " pdb=" P POV B1105 " pdb=" O14 POV B1105 " ideal model delta sigma weight residual 121.11 100.65 20.46 3.00e+00 1.11e-01 4.65e+01 angle pdb=" O13 POV E2301 " pdb=" P POV E2301 " pdb=" O14 POV E2301 " ideal model delta sigma weight residual 121.11 100.70 20.41 3.00e+00 1.11e-01 4.63e+01 ... (remaining 51127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.89: 22372 33.89 - 67.77: 956 67.77 - 101.66: 88 101.66 - 135.54: 16 135.54 - 169.43: 16 Dihedral angle restraints: 23448 sinusoidal: 10624 harmonic: 12824 Sorted by residual: dihedral pdb=" CB CYS G2054 " pdb=" SG CYS G2054 " pdb=" SG CYS G2148 " pdb=" CB CYS G2148 " ideal model delta sinusoidal sigma weight residual -86.00 -158.77 72.77 1 1.00e+01 1.00e-02 6.76e+01 dihedral pdb=" CB CYS F2054 " pdb=" SG CYS F2054 " pdb=" SG CYS F2148 " pdb=" CB CYS F2148 " ideal model delta sinusoidal sigma weight residual -86.00 -158.73 72.73 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" CB CYS H2054 " pdb=" SG CYS H2054 " pdb=" SG CYS H2148 " pdb=" CB CYS H2148 " ideal model delta sinusoidal sigma weight residual -86.00 -158.73 72.73 1 1.00e+01 1.00e-02 6.75e+01 ... (remaining 23445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4744 0.069 - 0.138: 855 0.138 - 0.207: 105 0.207 - 0.276: 12 0.276 - 0.345: 40 Chirality restraints: 5756 Sorted by residual: chirality pdb=" C13 CLR B1117 " pdb=" C12 CLR B1117 " pdb=" C14 CLR B1117 " pdb=" C17 CLR B1117 " both_signs ideal model delta sigma weight residual False -2.93 -2.59 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C13 CLR D1117 " pdb=" C12 CLR D1117 " pdb=" C14 CLR D1117 " pdb=" C17 CLR D1117 " both_signs ideal model delta sigma weight residual False -2.93 -2.59 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C13 CLR C1117 " pdb=" C12 CLR C1117 " pdb=" C14 CLR C1117 " pdb=" C17 CLR C1117 " both_signs ideal model delta sigma weight residual False -2.93 -2.59 -0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 5753 not shown) Planarity restraints: 6204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV B1111 " 0.154 2.00e-02 2.50e+03 3.41e-01 1.16e+03 pdb=" C29 POV B1111 " -0.452 2.00e-02 2.50e+03 pdb="C210 POV B1111 " 0.459 2.00e-02 2.50e+03 pdb="C211 POV B1111 " -0.160 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D1111 " -0.154 2.00e-02 2.50e+03 3.41e-01 1.16e+03 pdb=" C29 POV D1111 " 0.452 2.00e-02 2.50e+03 pdb="C210 POV D1111 " -0.459 2.00e-02 2.50e+03 pdb="C211 POV D1111 " 0.160 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C1111 " -0.153 2.00e-02 2.50e+03 3.41e-01 1.16e+03 pdb=" C29 POV C1111 " 0.452 2.00e-02 2.50e+03 pdb="C210 POV C1111 " -0.459 2.00e-02 2.50e+03 pdb="C211 POV C1111 " 0.160 2.00e-02 2.50e+03 ... (remaining 6201 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.83: 11982 2.83 - 3.41: 38303 3.41 - 3.99: 68513 3.99 - 4.56: 97737 4.56 - 5.14: 143818 Nonbonded interactions: 360353 Sorted by model distance: nonbonded pdb=" O ARG A 938 " pdb=" OG1 THR A 942 " model vdw 2.257 2.440 nonbonded pdb=" O ARG D 938 " pdb=" OG1 THR D 942 " model vdw 2.257 2.440 nonbonded pdb=" O ARG B 938 " pdb=" OG1 THR B 942 " model vdw 2.257 2.440 nonbonded pdb=" O ARG C 938 " pdb=" OG1 THR C 942 " model vdw 2.258 2.440 nonbonded pdb=" OE2 GLU B 399 " pdb="MG MG B1106 " model vdw 2.277 2.170 ... (remaining 360348 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 1056 or (resid 1104 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C3 \ or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name \ C37 or name C38 or name O11 or name O12 or name O13 or name O14 or name O21 or n \ ame O22 or name O31 or name O32 or name P )) or resid 1105 or (resid 1109 and (n \ ame C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name C38)))) selection = (chain 'B' and (resid 16 through 1056 or (resid 1104 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C3 \ or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name \ C37 or name C38 or name O11 or name O12 or name O13 or name O14 or name O21 or n \ ame O22 or name O31 or name O32 or name P )) or (resid 1105 and (name C31 or nam \ e C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or \ name C39 or name O31 or name O32 or name C310 or name C311)) or (resid 1109 and \ (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38)))) selection = (chain 'C' and (resid 16 through 1056 or (resid 1104 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C3 \ or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name \ C37 or name C38 or name O11 or name O12 or name O13 or name O14 or name O21 or n \ ame O22 or name O31 or name O32 or name P )) or (resid 1105 and (name C31 or nam \ e C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or \ name C39 or name O31 or name O32 or name C310 or name C311)) or (resid 1109 and \ (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38)))) selection = (chain 'D' and (resid 16 through 1056 or (resid 1104 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C3 \ or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name \ C37 or name C38 or name O11 or name O12 or name O13 or name O14 or name O21 or n \ ame O22 or name O31 or name O32 or name P )) or (resid 1105 and (name C31 or nam \ e C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or \ name C39 or name O31 or name O32 or name C310 or name C311)) or (resid 1109 and \ (name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38)))) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.280 Check model and map are aligned: 0.520 Set scattering table: 0.300 Process input model: 96.180 Find NCS groups from input model: 2.820 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 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 : 0.014 0.239 37788 Z= 0.883 Angle : 1.410 20.498 51132 Z= 0.576 Chirality : 0.060 0.345 5756 Planarity : 0.019 0.341 6196 Dihedral : 18.515 169.427 15088 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.21 % Allowed : 8.01 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.10), residues: 4332 helix: -2.75 (0.07), residues: 2148 sheet: -1.61 (0.22), residues: 516 loop : -2.08 (0.13), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 767 HIS 0.006 0.001 HIS C 771 PHE 0.023 0.002 PHE G2070 TYR 0.015 0.002 TYR D 48 ARG 0.007 0.001 ARG D 786 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 345 time to evaluate : 4.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 604 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8250 (mt-10) REVERT: A 691 MET cc_start: 0.9120 (mmt) cc_final: 0.8858 (mmt) REVERT: A 1053 MET cc_start: 0.8385 (mtp) cc_final: 0.8182 (mtm) REVERT: E 2015 ASP cc_start: 0.8586 (t0) cc_final: 0.8356 (t0) REVERT: E 2112 LYS cc_start: 0.9108 (mtmt) cc_final: 0.8846 (ttmt) REVERT: E 2163 ARG cc_start: 0.7802 (mtt-85) cc_final: 0.7435 (mtt-85) REVERT: E 2168 ILE cc_start: 0.9261 (tt) cc_final: 0.8945 (tt) REVERT: B 691 MET cc_start: 0.9133 (mmt) cc_final: 0.8870 (mmt) REVERT: B 1053 MET cc_start: 0.8352 (mtp) cc_final: 0.8142 (mtm) REVERT: F 2015 ASP cc_start: 0.8582 (t0) cc_final: 0.8377 (t0) REVERT: F 2019 ARG cc_start: 0.8100 (mtt-85) cc_final: 0.7829 (mtt90) REVERT: F 2112 LYS cc_start: 0.9103 (mtmt) cc_final: 0.8845 (ttmt) REVERT: F 2163 ARG cc_start: 0.7796 (mtt-85) cc_final: 0.7419 (mtt-85) REVERT: F 2166 ASP cc_start: 0.7935 (t0) cc_final: 0.7710 (t0) REVERT: F 2168 ILE cc_start: 0.9257 (tt) cc_final: 0.8924 (tt) REVERT: C 691 MET cc_start: 0.9110 (mmt) cc_final: 0.8839 (mmt) REVERT: C 1053 MET cc_start: 0.8339 (mtp) cc_final: 0.8137 (mtm) REVERT: G 2019 ARG cc_start: 0.8081 (mtt-85) cc_final: 0.7820 (mtt90) REVERT: G 2112 LYS cc_start: 0.9109 (mtmt) cc_final: 0.8851 (ttmt) REVERT: G 2163 ARG cc_start: 0.7827 (mtt-85) cc_final: 0.7441 (mtt-85) REVERT: G 2168 ILE cc_start: 0.9248 (tt) cc_final: 0.8925 (tt) REVERT: D 691 MET cc_start: 0.9134 (mmt) cc_final: 0.8873 (mmt) REVERT: D 1053 MET cc_start: 0.8365 (mtp) cc_final: 0.8147 (mtm) REVERT: H 2015 ASP cc_start: 0.8592 (t0) cc_final: 0.8386 (t0) REVERT: H 2019 ARG cc_start: 0.8103 (mtt-85) cc_final: 0.7832 (mtt90) REVERT: H 2112 LYS cc_start: 0.9102 (mtmt) cc_final: 0.8845 (ttmt) REVERT: H 2163 ARG cc_start: 0.7798 (mtt-85) cc_final: 0.7416 (mtt-85) REVERT: H 2166 ASP cc_start: 0.7936 (t0) cc_final: 0.7711 (t0) REVERT: H 2168 ILE cc_start: 0.9256 (tt) cc_final: 0.8924 (tt) outliers start: 8 outliers final: 0 residues processed: 353 average time/residue: 0.5963 time to fit residues: 321.2802 Evaluate side-chains 246 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 4.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 4.9990 chunk 327 optimal weight: 7.9990 chunk 181 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 220 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 338 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 392 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 143 ASN A 200 ASN ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 ASN A 534 ASN A 793 ASN A 884 ASN E2095 ASN E2144 GLN B 142 GLN B 143 ASN B 200 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 ASN B 534 ASN B 793 ASN B 884 ASN B1054 GLN F2095 ASN F2144 GLN C 142 GLN C 143 ASN C 200 ASN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 ASN C 534 ASN C 793 ASN C 884 ASN C1054 GLN G2095 ASN G2144 GLN D 142 GLN D 143 ASN D 200 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN ** D 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 ASN D 534 ASN D 793 ASN D 884 ASN D1054 GLN H2095 ASN H2144 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 37788 Z= 0.276 Angle : 0.542 8.724 51132 Z= 0.281 Chirality : 0.041 0.154 5756 Planarity : 0.004 0.046 6196 Dihedral : 16.188 146.553 7036 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.81 % Allowed : 11.11 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.12), residues: 4332 helix: -0.64 (0.10), residues: 2128 sheet: -1.28 (0.22), residues: 524 loop : -1.41 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 263 HIS 0.003 0.001 HIS A 254 PHE 0.017 0.001 PHE C 120 TYR 0.012 0.001 TYR E2136 ARG 0.003 0.000 ARG G2155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 259 time to evaluate : 4.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 604 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8323 (mt-10) REVERT: A 691 MET cc_start: 0.9084 (mmt) cc_final: 0.8717 (mmt) REVERT: E 2015 ASP cc_start: 0.8632 (t0) cc_final: 0.8364 (t0) REVERT: E 2019 ARG cc_start: 0.8107 (mtt-85) cc_final: 0.7503 (mtt90) REVERT: E 2163 ARG cc_start: 0.7706 (mtt-85) cc_final: 0.7360 (mtt-85) REVERT: E 2166 ASP cc_start: 0.8368 (t0) cc_final: 0.8099 (t0) REVERT: E 2168 ILE cc_start: 0.9245 (tt) cc_final: 0.9035 (tt) REVERT: B 691 MET cc_start: 0.9076 (mmt) cc_final: 0.8690 (mmt) REVERT: F 2015 ASP cc_start: 0.8631 (t0) cc_final: 0.8374 (t0) REVERT: F 2019 ARG cc_start: 0.8105 (mtt-85) cc_final: 0.7512 (mtt90) REVERT: F 2112 LYS cc_start: 0.9120 (mtmt) cc_final: 0.8851 (ttmt) REVERT: F 2163 ARG cc_start: 0.7754 (mtt-85) cc_final: 0.7410 (mtt-85) REVERT: F 2166 ASP cc_start: 0.8110 (t0) cc_final: 0.7905 (t0) REVERT: F 2168 ILE cc_start: 0.9302 (tt) cc_final: 0.9007 (tt) REVERT: C 691 MET cc_start: 0.9067 (mmt) cc_final: 0.8679 (mmt) REVERT: G 2112 LYS cc_start: 0.9115 (mtmt) cc_final: 0.8845 (ttmt) REVERT: G 2163 ARG cc_start: 0.7732 (mtt-85) cc_final: 0.7386 (mtt-85) REVERT: G 2166 ASP cc_start: 0.8360 (t0) cc_final: 0.8070 (t0) REVERT: G 2168 ILE cc_start: 0.9228 (tt) cc_final: 0.9015 (tt) REVERT: D 691 MET cc_start: 0.9073 (mmt) cc_final: 0.8688 (mmt) REVERT: H 2015 ASP cc_start: 0.8636 (t0) cc_final: 0.8377 (t0) REVERT: H 2019 ARG cc_start: 0.8105 (mtt-85) cc_final: 0.7508 (mtt90) REVERT: H 2112 LYS cc_start: 0.9119 (mtmt) cc_final: 0.8850 (ttmt) REVERT: H 2163 ARG cc_start: 0.7752 (mtt-85) cc_final: 0.7411 (mtt-85) REVERT: H 2166 ASP cc_start: 0.8114 (t0) cc_final: 0.7906 (t0) REVERT: H 2168 ILE cc_start: 0.9302 (tt) cc_final: 0.9007 (tt) outliers start: 70 outliers final: 28 residues processed: 307 average time/residue: 0.4950 time to fit residues: 249.1316 Evaluate side-chains 264 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 236 time to evaluate : 4.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain E residue 2146 PHE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain F residue 2146 PHE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain G residue 2146 PHE Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain H residue 2146 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 326 optimal weight: 0.9990 chunk 267 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 393 optimal weight: 2.9990 chunk 424 optimal weight: 3.9990 chunk 350 optimal weight: 0.6980 chunk 389 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 315 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 465 ASN B 465 ASN C 465 ASN D 267 GLN D 465 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 37788 Z= 0.158 Angle : 0.450 7.768 51132 Z= 0.233 Chirality : 0.039 0.149 5756 Planarity : 0.003 0.032 6196 Dihedral : 14.450 131.403 7036 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.63 % Allowed : 12.01 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.12), residues: 4332 helix: 0.10 (0.11), residues: 2136 sheet: -0.90 (0.23), residues: 524 loop : -1.08 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F2176 HIS 0.004 0.001 HIS B 254 PHE 0.014 0.001 PHE C 120 TYR 0.007 0.001 TYR A 48 ARG 0.002 0.000 ARG B 368 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 276 time to evaluate : 4.150 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: A 604 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8324 (mt-10) REVERT: A 691 MET cc_start: 0.9157 (mmt) cc_final: 0.8836 (mmt) REVERT: A 799 MET cc_start: 0.9327 (tpp) cc_final: 0.9123 (tpp) REVERT: E 2015 ASP cc_start: 0.8624 (t0) cc_final: 0.8347 (t0) REVERT: E 2019 ARG cc_start: 0.8110 (mtt-85) cc_final: 0.7499 (mtt90) REVERT: E 2163 ARG cc_start: 0.7703 (mtt-85) cc_final: 0.7379 (mtt-85) REVERT: E 2166 ASP cc_start: 0.8402 (t0) cc_final: 0.8104 (t0) REVERT: E 2168 ILE cc_start: 0.9251 (tt) cc_final: 0.9033 (tt) REVERT: B 691 MET cc_start: 0.9154 (mmt) cc_final: 0.8829 (mmt) REVERT: B 799 MET cc_start: 0.9328 (tpp) cc_final: 0.9125 (tpp) REVERT: F 2015 ASP cc_start: 0.8620 (t0) cc_final: 0.8350 (t0) REVERT: F 2019 ARG cc_start: 0.8098 (mtt-85) cc_final: 0.7498 (mtt90) REVERT: F 2112 LYS cc_start: 0.9133 (mtmt) cc_final: 0.8876 (ttmt) REVERT: F 2163 ARG cc_start: 0.7745 (mtt-85) cc_final: 0.7407 (mtt-85) REVERT: F 2168 ILE cc_start: 0.9279 (tt) cc_final: 0.8989 (tt) REVERT: C 691 MET cc_start: 0.9151 (mmt) cc_final: 0.8823 (mmt) REVERT: C 799 MET cc_start: 0.9328 (tpp) cc_final: 0.9117 (tpp) REVERT: G 2112 LYS cc_start: 0.9132 (mtmt) cc_final: 0.8876 (ttmt) REVERT: G 2163 ARG cc_start: 0.7716 (mtt-85) cc_final: 0.7389 (mtt-85) REVERT: G 2166 ASP cc_start: 0.8379 (t0) cc_final: 0.8081 (t0) REVERT: G 2168 ILE cc_start: 0.9223 (tt) cc_final: 0.9006 (tt) REVERT: D 691 MET cc_start: 0.9156 (mmt) cc_final: 0.8830 (mmt) REVERT: D 799 MET cc_start: 0.9326 (tpp) cc_final: 0.9123 (tpp) REVERT: H 2015 ASP cc_start: 0.8630 (t0) cc_final: 0.8355 (t0) REVERT: H 2019 ARG cc_start: 0.8103 (mtt-85) cc_final: 0.7500 (mtt90) REVERT: H 2112 LYS cc_start: 0.9133 (mtmt) cc_final: 0.8877 (ttmt) REVERT: H 2163 ARG cc_start: 0.7745 (mtt-85) cc_final: 0.7409 (mtt-85) REVERT: H 2168 ILE cc_start: 0.9279 (tt) cc_final: 0.8990 (tt) outliers start: 63 outliers final: 44 residues processed: 327 average time/residue: 0.5113 time to fit residues: 271.8162 Evaluate side-chains 288 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 244 time to evaluate : 4.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain E residue 2146 PHE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 830 MET Chi-restraints excluded: chain B residue 931 ASP Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain F residue 2146 PHE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain C residue 931 ASP Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain G residue 2146 PHE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 815 LEU Chi-restraints excluded: chain D residue 830 MET Chi-restraints excluded: chain D residue 931 ASP Chi-restraints excluded: chain D residue 998 ASP Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain H residue 2146 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 8.9990 chunk 295 optimal weight: 6.9990 chunk 203 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 263 optimal weight: 0.9990 chunk 394 optimal weight: 2.9990 chunk 417 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 373 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 HIS E2091 ASN E2124 GLN E2165 HIS ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 HIS F2124 GLN F2165 HIS ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 HIS C 267 GLN C1008 ASN G2165 HIS ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 HIS H2091 ASN H2165 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 37788 Z= 0.273 Angle : 0.500 6.730 51132 Z= 0.258 Chirality : 0.041 0.150 5756 Planarity : 0.003 0.031 6196 Dihedral : 14.161 106.174 7036 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.22 % Allowed : 13.40 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.13), residues: 4332 helix: 0.45 (0.11), residues: 2124 sheet: -0.88 (0.23), residues: 540 loop : -0.78 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 263 HIS 0.003 0.001 HIS H2165 PHE 0.018 0.001 PHE C 120 TYR 0.010 0.001 TYR B 130 ARG 0.002 0.000 ARG A 368 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 265 time to evaluate : 4.346 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: A 691 MET cc_start: 0.9137 (mmt) cc_final: 0.8809 (mmt) REVERT: E 2015 ASP cc_start: 0.8679 (t0) cc_final: 0.8342 (t0) REVERT: E 2019 ARG cc_start: 0.8152 (mtt-85) cc_final: 0.7518 (mtt90) REVERT: E 2138 LYS cc_start: 0.8846 (mmmt) cc_final: 0.8348 (mtpt) REVERT: E 2163 ARG cc_start: 0.7749 (mtt-85) cc_final: 0.7393 (mtt-85) REVERT: E 2166 ASP cc_start: 0.8398 (t0) cc_final: 0.8099 (t0) REVERT: E 2168 ILE cc_start: 0.9311 (tt) cc_final: 0.9056 (tt) REVERT: E 2202 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7947 (tm-30) REVERT: B 691 MET cc_start: 0.9141 (mmt) cc_final: 0.8817 (mmt) REVERT: F 2015 ASP cc_start: 0.8683 (t0) cc_final: 0.8371 (t0) REVERT: F 2112 LYS cc_start: 0.9093 (mtmt) cc_final: 0.8841 (ttmt) REVERT: F 2138 LYS cc_start: 0.8846 (mmmt) cc_final: 0.8349 (mtpt) REVERT: F 2163 ARG cc_start: 0.7734 (mtt-85) cc_final: 0.7376 (mtt-85) REVERT: C 691 MET cc_start: 0.9133 (mmt) cc_final: 0.8810 (mmt) REVERT: G 2112 LYS cc_start: 0.9092 (mtmt) cc_final: 0.8840 (ttmt) REVERT: G 2138 LYS cc_start: 0.8837 (mmmt) cc_final: 0.8347 (mtpt) REVERT: G 2163 ARG cc_start: 0.7725 (mtt-85) cc_final: 0.7363 (mtt-85) REVERT: G 2166 ASP cc_start: 0.8381 (t0) cc_final: 0.8114 (t0) REVERT: G 2168 ILE cc_start: 0.9298 (tt) cc_final: 0.9050 (tt) REVERT: D 691 MET cc_start: 0.9140 (mmt) cc_final: 0.8817 (mmt) REVERT: H 2015 ASP cc_start: 0.8692 (t0) cc_final: 0.8378 (t0) REVERT: H 2112 LYS cc_start: 0.9096 (mtmt) cc_final: 0.8844 (ttmt) REVERT: H 2138 LYS cc_start: 0.8846 (mmmt) cc_final: 0.8348 (mtpt) REVERT: H 2163 ARG cc_start: 0.7738 (mtt-85) cc_final: 0.7382 (mtt-85) outliers start: 86 outliers final: 63 residues processed: 339 average time/residue: 0.5146 time to fit residues: 283.5991 Evaluate side-chains 307 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 244 time to evaluate : 4.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain E residue 2039 TRP Chi-restraints excluded: chain E residue 2146 PHE Chi-restraints excluded: chain E residue 2157 ASP Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 830 MET Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 931 ASP Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain F residue 2039 TRP Chi-restraints excluded: chain F residue 2146 PHE Chi-restraints excluded: chain F residue 2157 ASP Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 931 ASP Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain G residue 2039 TRP Chi-restraints excluded: chain G residue 2146 PHE Chi-restraints excluded: chain G residue 2157 ASP Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 815 LEU Chi-restraints excluded: chain D residue 830 MET Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 931 ASP Chi-restraints excluded: chain D residue 998 ASP Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain H residue 2039 TRP Chi-restraints excluded: chain H residue 2146 PHE Chi-restraints excluded: chain H residue 2157 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 1.9990 chunk 237 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 310 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 356 optimal weight: 0.9980 chunk 288 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 213 optimal weight: 0.9980 chunk 374 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN A1008 ASN E2091 ASN B 216 GLN B1008 ASN C 216 GLN C 267 GLN G2124 GLN D 216 GLN D1008 ASN H2091 ASN H2124 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 37788 Z= 0.146 Angle : 0.445 6.824 51132 Z= 0.228 Chirality : 0.039 0.151 5756 Planarity : 0.003 0.031 6196 Dihedral : 13.376 95.730 7036 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.25 % Allowed : 13.84 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.13), residues: 4332 helix: 0.78 (0.11), residues: 2124 sheet: -0.76 (0.23), residues: 532 loop : -0.64 (0.16), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G2176 HIS 0.003 0.000 HIS B 771 PHE 0.013 0.001 PHE C 120 TYR 0.006 0.001 TYR D 130 ARG 0.002 0.000 ARG G2155 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 263 time to evaluate : 4.434 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: A 148 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.6869 (t80) REVERT: A 691 MET cc_start: 0.9170 (mmt) cc_final: 0.8860 (mmt) REVERT: E 2015 ASP cc_start: 0.8664 (t0) cc_final: 0.8368 (t0) REVERT: E 2131 MET cc_start: 0.8346 (mmm) cc_final: 0.7881 (mmm) REVERT: E 2138 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8450 (mtpt) REVERT: E 2163 ARG cc_start: 0.7753 (mtt-85) cc_final: 0.7403 (mtt-85) REVERT: E 2166 ASP cc_start: 0.8409 (t0) cc_final: 0.8173 (t0) REVERT: E 2168 ILE cc_start: 0.9286 (tt) cc_final: 0.9038 (tt) REVERT: B 691 MET cc_start: 0.9174 (mmt) cc_final: 0.8867 (mmt) REVERT: F 2015 ASP cc_start: 0.8656 (t0) cc_final: 0.8358 (t0) REVERT: F 2112 LYS cc_start: 0.9094 (mtmt) cc_final: 0.8843 (ttmt) REVERT: F 2131 MET cc_start: 0.8341 (mmm) cc_final: 0.7882 (mmm) REVERT: F 2138 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8450 (mtpt) REVERT: F 2163 ARG cc_start: 0.7731 (mtt-85) cc_final: 0.7393 (mtt-85) REVERT: C 610 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.8025 (t80) REVERT: C 691 MET cc_start: 0.9166 (mmt) cc_final: 0.8858 (mmt) REVERT: G 2112 LYS cc_start: 0.9093 (mtmt) cc_final: 0.8843 (ttmt) REVERT: G 2131 MET cc_start: 0.8336 (mmm) cc_final: 0.7882 (mmm) REVERT: G 2138 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8463 (mtpt) REVERT: G 2163 ARG cc_start: 0.7750 (mtt-85) cc_final: 0.7400 (mtt-85) REVERT: G 2166 ASP cc_start: 0.8398 (t0) cc_final: 0.8159 (t0) REVERT: G 2168 ILE cc_start: 0.9281 (tt) cc_final: 0.9028 (tt) REVERT: D 691 MET cc_start: 0.9174 (mmt) cc_final: 0.8868 (mmt) REVERT: H 2015 ASP cc_start: 0.8664 (t0) cc_final: 0.8364 (t0) REVERT: H 2112 LYS cc_start: 0.9098 (mtmt) cc_final: 0.8848 (ttmt) REVERT: H 2131 MET cc_start: 0.8338 (mmm) cc_final: 0.7871 (mmm) REVERT: H 2138 LYS cc_start: 0.8805 (mmmt) cc_final: 0.8450 (mtpt) REVERT: H 2163 ARG cc_start: 0.7734 (mtt-85) cc_final: 0.7398 (mtt-85) outliers start: 87 outliers final: 62 residues processed: 334 average time/residue: 0.4997 time to fit residues: 274.2868 Evaluate side-chains 314 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 250 time to evaluate : 4.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain E residue 2146 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 830 MET Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 931 ASP Chi-restraints excluded: chain B residue 987 PHE Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain F residue 2008 TYR Chi-restraints excluded: chain F residue 2146 PHE Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 610 PHE Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 931 ASP Chi-restraints excluded: chain C residue 987 PHE Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain G residue 2146 PHE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 815 LEU Chi-restraints excluded: chain D residue 830 MET Chi-restraints excluded: chain D residue 879 ILE Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 931 ASP Chi-restraints excluded: chain D residue 987 PHE Chi-restraints excluded: chain D residue 998 ASP Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain H residue 2008 TYR Chi-restraints excluded: chain H residue 2146 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 4.9990 chunk 376 optimal weight: 9.9990 chunk 82 optimal weight: 0.2980 chunk 245 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 417 optimal weight: 10.0000 chunk 346 optimal weight: 0.8980 chunk 193 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 219 optimal weight: 0.8980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN B 216 GLN B 267 GLN C 216 GLN D 216 GLN H2091 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 37788 Z= 0.226 Angle : 0.471 7.266 51132 Z= 0.244 Chirality : 0.040 0.215 5756 Planarity : 0.003 0.031 6196 Dihedral : 13.260 92.378 7036 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.48 % Allowed : 14.75 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.13), residues: 4332 helix: 0.83 (0.11), residues: 2144 sheet: -0.78 (0.23), residues: 540 loop : -0.50 (0.16), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 263 HIS 0.003 0.001 HIS C 254 PHE 0.016 0.001 PHE C 120 TYR 0.056 0.001 TYR G2008 ARG 0.002 0.000 ARG F2121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 252 time to evaluate : 4.131 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: A 148 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.6898 (t80) REVERT: A 610 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8084 (t80) REVERT: A 691 MET cc_start: 0.9147 (mmt) cc_final: 0.8819 (mmt) REVERT: E 2015 ASP cc_start: 0.8648 (t0) cc_final: 0.8338 (t0) REVERT: E 2131 MET cc_start: 0.8322 (mmm) cc_final: 0.7896 (mmm) REVERT: E 2138 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8500 (mtpt) REVERT: E 2157 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8322 (p0) REVERT: E 2166 ASP cc_start: 0.8356 (t0) cc_final: 0.8124 (t0) REVERT: E 2168 ILE cc_start: 0.9316 (tt) cc_final: 0.9060 (tt) REVERT: B 610 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8078 (t80) REVERT: B 691 MET cc_start: 0.9151 (mmt) cc_final: 0.8825 (mmt) REVERT: F 2015 ASP cc_start: 0.8671 (t0) cc_final: 0.8368 (t0) REVERT: F 2112 LYS cc_start: 0.9093 (mtmt) cc_final: 0.8810 (ttmt) REVERT: F 2131 MET cc_start: 0.8331 (mmm) cc_final: 0.7906 (mmm) REVERT: F 2138 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8500 (mtpt) REVERT: F 2157 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8344 (p0) REVERT: F 2166 ASP cc_start: 0.8421 (t0) cc_final: 0.7971 (p0) REVERT: C 610 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8075 (t80) REVERT: C 691 MET cc_start: 0.9143 (mmt) cc_final: 0.8819 (mmt) REVERT: G 2112 LYS cc_start: 0.9094 (mtmt) cc_final: 0.8843 (ttmt) REVERT: G 2131 MET cc_start: 0.8327 (mmm) cc_final: 0.7903 (mmm) REVERT: G 2138 LYS cc_start: 0.8793 (mmmt) cc_final: 0.8499 (mtpt) REVERT: G 2157 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8342 (p0) REVERT: G 2166 ASP cc_start: 0.8316 (t0) cc_final: 0.8091 (t0) REVERT: G 2168 ILE cc_start: 0.9314 (tt) cc_final: 0.9053 (tt) REVERT: D 148 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.6872 (t80) REVERT: D 610 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8079 (t80) REVERT: D 691 MET cc_start: 0.9151 (mmt) cc_final: 0.8824 (mmt) REVERT: H 2015 ASP cc_start: 0.8680 (t0) cc_final: 0.8374 (t0) REVERT: H 2112 LYS cc_start: 0.9097 (mtmt) cc_final: 0.8813 (ttmt) REVERT: H 2131 MET cc_start: 0.8326 (mmm) cc_final: 0.7904 (mmm) REVERT: H 2138 LYS cc_start: 0.8805 (mmmt) cc_final: 0.8500 (mtpt) REVERT: H 2157 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8324 (p0) REVERT: H 2166 ASP cc_start: 0.8421 (t0) cc_final: 0.7971 (p0) outliers start: 96 outliers final: 63 residues processed: 332 average time/residue: 0.4940 time to fit residues: 271.3432 Evaluate side-chains 314 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 241 time to evaluate : 4.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain E residue 2039 TRP Chi-restraints excluded: chain E residue 2146 PHE Chi-restraints excluded: chain E residue 2157 ASP Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 610 PHE Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 830 MET Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 931 ASP Chi-restraints excluded: chain B residue 987 PHE Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain F residue 2008 TYR Chi-restraints excluded: chain F residue 2039 TRP Chi-restraints excluded: chain F residue 2146 PHE Chi-restraints excluded: chain F residue 2157 ASP Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 610 PHE Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 931 ASP Chi-restraints excluded: chain C residue 987 PHE Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain G residue 2039 TRP Chi-restraints excluded: chain G residue 2146 PHE Chi-restraints excluded: chain G residue 2157 ASP Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 148 PHE Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 815 LEU Chi-restraints excluded: chain D residue 830 MET Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 931 ASP Chi-restraints excluded: chain D residue 987 PHE Chi-restraints excluded: chain D residue 998 ASP Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain H residue 2008 TYR Chi-restraints excluded: chain H residue 2039 TRP Chi-restraints excluded: chain H residue 2146 PHE Chi-restraints excluded: chain H residue 2157 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 238 optimal weight: 0.5980 chunk 305 optimal weight: 0.8980 chunk 236 optimal weight: 1.9990 chunk 351 optimal weight: 4.9990 chunk 233 optimal weight: 0.0170 chunk 416 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 chunk 253 optimal weight: 3.9990 chunk 192 optimal weight: 0.6980 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 GLN H2091 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 37788 Z= 0.129 Angle : 0.425 6.261 51132 Z= 0.220 Chirality : 0.039 0.188 5756 Planarity : 0.003 0.031 6196 Dihedral : 12.636 86.041 7036 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.83 % Allowed : 15.75 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.13), residues: 4332 helix: 1.08 (0.12), residues: 2140 sheet: -0.69 (0.23), residues: 540 loop : -0.36 (0.16), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E2176 HIS 0.003 0.000 HIS C 771 PHE 0.012 0.001 PHE A 120 TYR 0.005 0.001 TYR E2088 ARG 0.002 0.000 ARG F2155 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 301 time to evaluate : 3.988 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: A 610 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.8061 (t80) REVERT: A 691 MET cc_start: 0.9171 (mmt) cc_final: 0.8852 (mmt) REVERT: E 2015 ASP cc_start: 0.8639 (t0) cc_final: 0.8330 (t0) REVERT: E 2155 ARG cc_start: 0.8762 (mpp80) cc_final: 0.8104 (mpt-90) REVERT: E 2166 ASP cc_start: 0.8278 (t0) cc_final: 0.8058 (t0) REVERT: E 2168 ILE cc_start: 0.9287 (tt) cc_final: 0.9036 (tt) REVERT: B 610 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.8054 (t80) REVERT: B 691 MET cc_start: 0.9181 (mmt) cc_final: 0.8868 (mmt) REVERT: F 2015 ASP cc_start: 0.8665 (t0) cc_final: 0.8361 (t0) REVERT: F 2112 LYS cc_start: 0.9102 (mtmt) cc_final: 0.8822 (ttmt) REVERT: F 2155 ARG cc_start: 0.8764 (mpp80) cc_final: 0.8102 (mpt-90) REVERT: F 2166 ASP cc_start: 0.8246 (t0) cc_final: 0.7991 (p0) REVERT: C 610 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8056 (t80) REVERT: C 691 MET cc_start: 0.9171 (mmt) cc_final: 0.8861 (mmt) REVERT: G 2112 LYS cc_start: 0.9103 (mtmt) cc_final: 0.8855 (ttpt) REVERT: G 2155 ARG cc_start: 0.8757 (mpp80) cc_final: 0.8002 (mpt-90) REVERT: G 2166 ASP cc_start: 0.8298 (t0) cc_final: 0.8082 (t0) REVERT: G 2168 ILE cc_start: 0.9266 (tt) cc_final: 0.9016 (tt) REVERT: G 2200 LYS cc_start: 0.7999 (mttt) cc_final: 0.7717 (mttp) REVERT: D 610 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.8056 (t80) REVERT: D 691 MET cc_start: 0.9180 (mmt) cc_final: 0.8867 (mmt) REVERT: H 2015 ASP cc_start: 0.8673 (t0) cc_final: 0.8363 (t0) REVERT: H 2112 LYS cc_start: 0.9104 (mtmt) cc_final: 0.8825 (ttmt) REVERT: H 2155 ARG cc_start: 0.8758 (mpp80) cc_final: 0.8105 (mpt-90) REVERT: H 2166 ASP cc_start: 0.8248 (t0) cc_final: 0.7989 (p0) outliers start: 71 outliers final: 51 residues processed: 355 average time/residue: 0.4903 time to fit residues: 285.2051 Evaluate side-chains 333 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 278 time to evaluate : 4.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain E residue 2039 TRP Chi-restraints excluded: chain E residue 2146 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 610 PHE Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 818 LYS Chi-restraints excluded: chain B residue 830 MET Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 931 ASP Chi-restraints excluded: chain B residue 987 PHE Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain F residue 2008 TYR Chi-restraints excluded: chain F residue 2039 TRP Chi-restraints excluded: chain F residue 2146 PHE Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 610 PHE Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 818 LYS Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 931 ASP Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain G residue 2039 TRP Chi-restraints excluded: chain G residue 2146 PHE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 815 LEU Chi-restraints excluded: chain D residue 818 LYS Chi-restraints excluded: chain D residue 830 MET Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 931 ASP Chi-restraints excluded: chain D residue 987 PHE Chi-restraints excluded: chain D residue 998 ASP Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain H residue 2008 TYR Chi-restraints excluded: chain H residue 2039 TRP Chi-restraints excluded: chain H residue 2146 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 0.8980 chunk 166 optimal weight: 6.9990 chunk 248 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 264 optimal weight: 2.9990 chunk 283 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 327 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 ASN A1054 GLN B 216 GLN B 957 ASN C 216 GLN C 957 ASN G2091 ASN D 216 GLN D 957 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 37788 Z= 0.265 Angle : 0.497 11.838 51132 Z= 0.254 Chirality : 0.041 0.168 5756 Planarity : 0.003 0.031 6196 Dihedral : 12.976 88.215 7036 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.43 % Allowed : 15.68 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.13), residues: 4332 helix: 0.96 (0.11), residues: 2140 sheet: -0.74 (0.24), residues: 528 loop : -0.30 (0.16), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 263 HIS 0.004 0.001 HIS A 771 PHE 0.017 0.001 PHE C 120 TYR 0.010 0.001 TYR B 130 ARG 0.005 0.000 ARG C 368 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 263 time to evaluate : 4.129 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: A 513 MET cc_start: 0.8322 (mmm) cc_final: 0.7760 (mmm) REVERT: A 610 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8112 (t80) REVERT: A 691 MET cc_start: 0.9167 (mmt) cc_final: 0.8855 (mmt) REVERT: E 2015 ASP cc_start: 0.8657 (t0) cc_final: 0.8346 (t0) REVERT: E 2155 ARG cc_start: 0.8752 (mpp80) cc_final: 0.8019 (mpt-90) REVERT: E 2166 ASP cc_start: 0.8313 (t0) cc_final: 0.8100 (t0) REVERT: E 2168 ILE cc_start: 0.9310 (tt) cc_final: 0.9036 (tt) REVERT: E 2200 LYS cc_start: 0.7999 (mttt) cc_final: 0.7708 (mttp) REVERT: B 513 MET cc_start: 0.8345 (mmm) cc_final: 0.7744 (mmm) REVERT: B 610 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8106 (t80) REVERT: B 691 MET cc_start: 0.9175 (mmt) cc_final: 0.8870 (mmt) REVERT: F 2015 ASP cc_start: 0.8662 (t0) cc_final: 0.8353 (t0) REVERT: F 2112 LYS cc_start: 0.9093 (mtmt) cc_final: 0.8840 (ttpt) REVERT: F 2155 ARG cc_start: 0.8753 (mpp80) cc_final: 0.8017 (mpt-90) REVERT: F 2200 LYS cc_start: 0.8042 (mttt) cc_final: 0.7763 (mttp) REVERT: C 513 MET cc_start: 0.8320 (mmm) cc_final: 0.7759 (mmm) REVERT: C 610 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.8111 (t80) REVERT: C 691 MET cc_start: 0.9147 (mmt) cc_final: 0.8815 (mmt) REVERT: G 2112 LYS cc_start: 0.9093 (mtmt) cc_final: 0.8840 (ttpt) REVERT: G 2153 HIS cc_start: 0.7753 (t-90) cc_final: 0.7372 (t-90) REVERT: G 2155 ARG cc_start: 0.8788 (mpp80) cc_final: 0.8018 (mpt-90) REVERT: G 2166 ASP cc_start: 0.8300 (t0) cc_final: 0.8096 (t0) REVERT: G 2168 ILE cc_start: 0.9319 (tt) cc_final: 0.9057 (tt) REVERT: G 2200 LYS cc_start: 0.7970 (mttt) cc_final: 0.7678 (mttp) REVERT: D 513 MET cc_start: 0.8337 (mmm) cc_final: 0.7758 (mmm) REVERT: D 610 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.8107 (t80) REVERT: D 691 MET cc_start: 0.9176 (mmt) cc_final: 0.8869 (mmt) REVERT: H 2015 ASP cc_start: 0.8667 (t0) cc_final: 0.8355 (t0) REVERT: H 2112 LYS cc_start: 0.9093 (mtmt) cc_final: 0.8842 (ttpt) REVERT: H 2155 ARG cc_start: 0.8748 (mpp80) cc_final: 0.8019 (mpt-90) REVERT: H 2200 LYS cc_start: 0.8044 (mttt) cc_final: 0.7763 (mttp) outliers start: 94 outliers final: 74 residues processed: 332 average time/residue: 0.5473 time to fit residues: 303.4884 Evaluate side-chains 334 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 256 time to evaluate : 4.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 987 PHE Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain E residue 2039 TRP Chi-restraints excluded: chain E residue 2146 PHE Chi-restraints excluded: chain E residue 2157 ASP Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 610 PHE Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 818 LYS Chi-restraints excluded: chain B residue 830 MET Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 931 ASP Chi-restraints excluded: chain B residue 957 ASN Chi-restraints excluded: chain B residue 987 PHE Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain F residue 2008 TYR Chi-restraints excluded: chain F residue 2039 TRP Chi-restraints excluded: chain F residue 2146 PHE Chi-restraints excluded: chain F residue 2157 ASP Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 610 PHE Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain C residue 818 LYS Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 931 ASP Chi-restraints excluded: chain C residue 957 ASN Chi-restraints excluded: chain C residue 987 PHE Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain G residue 2008 TYR Chi-restraints excluded: chain G residue 2039 TRP Chi-restraints excluded: chain G residue 2146 PHE Chi-restraints excluded: chain G residue 2157 ASP Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 815 LEU Chi-restraints excluded: chain D residue 818 LYS Chi-restraints excluded: chain D residue 830 MET Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 931 ASP Chi-restraints excluded: chain D residue 957 ASN Chi-restraints excluded: chain D residue 987 PHE Chi-restraints excluded: chain D residue 998 ASP Chi-restraints excluded: chain D residue 1004 LEU Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain H residue 2008 TYR Chi-restraints excluded: chain H residue 2039 TRP Chi-restraints excluded: chain H residue 2146 PHE Chi-restraints excluded: chain H residue 2157 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 0.9980 chunk 398 optimal weight: 1.9990 chunk 363 optimal weight: 1.9990 chunk 388 optimal weight: 0.9980 chunk 233 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 304 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 350 optimal weight: 0.6980 chunk 366 optimal weight: 0.1980 chunk 386 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 ASN B 216 GLN B 957 ASN C 216 GLN C 957 ASN G2091 ASN D 216 GLN D 957 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 37788 Z= 0.140 Angle : 0.455 12.183 51132 Z= 0.230 Chirality : 0.039 0.170 5756 Planarity : 0.003 0.032 6196 Dihedral : 12.544 88.009 7036 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.55 % Allowed : 16.45 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.13), residues: 4332 helix: 1.13 (0.12), residues: 2132 sheet: -0.67 (0.23), residues: 528 loop : -0.22 (0.16), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E2176 HIS 0.003 0.000 HIS C 771 PHE 0.012 0.001 PHE A 120 TYR 0.005 0.001 TYR C 130 ARG 0.003 0.000 ARG C 368 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 295 time to evaluate : 4.400 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: A 610 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8082 (t80) REVERT: A 691 MET cc_start: 0.9174 (mmt) cc_final: 0.8890 (mmt) REVERT: A 799 MET cc_start: 0.9327 (tpp) cc_final: 0.9053 (tpp) REVERT: E 2015 ASP cc_start: 0.8608 (t0) cc_final: 0.8310 (t0) REVERT: E 2155 ARG cc_start: 0.8774 (mpp80) cc_final: 0.8125 (mpt-90) REVERT: E 2163 ARG cc_start: 0.7764 (mtt-85) cc_final: 0.7434 (mtt-85) REVERT: E 2166 ASP cc_start: 0.8242 (t0) cc_final: 0.8034 (t0) REVERT: E 2168 ILE cc_start: 0.9313 (tt) cc_final: 0.9054 (tt) REVERT: E 2200 LYS cc_start: 0.7986 (mttt) cc_final: 0.7707 (mttp) REVERT: B 513 MET cc_start: 0.8222 (mmm) cc_final: 0.7661 (mmm) REVERT: B 610 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.8076 (t80) REVERT: B 691 MET cc_start: 0.9182 (mmt) cc_final: 0.8902 (mmt) REVERT: B 799 MET cc_start: 0.9326 (tpp) cc_final: 0.9058 (tpp) REVERT: F 2015 ASP cc_start: 0.8635 (t0) cc_final: 0.8321 (t0) REVERT: F 2112 LYS cc_start: 0.9102 (mtmt) cc_final: 0.8854 (ttpt) REVERT: F 2155 ARG cc_start: 0.8778 (mpp80) cc_final: 0.8125 (mpt-90) REVERT: F 2166 ASP cc_start: 0.8287 (t0) cc_final: 0.8001 (p0) REVERT: F 2200 LYS cc_start: 0.8016 (mttt) cc_final: 0.7766 (mttm) REVERT: C 610 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.8028 (t80) REVERT: C 691 MET cc_start: 0.9173 (mmt) cc_final: 0.8872 (mmt) REVERT: C 799 MET cc_start: 0.9330 (tpp) cc_final: 0.9055 (tpp) REVERT: G 2112 LYS cc_start: 0.9103 (mtmt) cc_final: 0.8854 (ttpt) REVERT: G 2153 HIS cc_start: 0.7806 (t-90) cc_final: 0.7437 (t-90) REVERT: G 2155 ARG cc_start: 0.8760 (mpp80) cc_final: 0.7992 (mpt-90) REVERT: G 2163 ARG cc_start: 0.7753 (mtt-85) cc_final: 0.7423 (mtt-85) REVERT: G 2166 ASP cc_start: 0.8227 (t0) cc_final: 0.8020 (t0) REVERT: G 2168 ILE cc_start: 0.9299 (tt) cc_final: 0.9042 (tt) REVERT: G 2200 LYS cc_start: 0.7967 (mttt) cc_final: 0.7682 (mttp) REVERT: D 610 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.8077 (t80) REVERT: D 691 MET cc_start: 0.9182 (mmt) cc_final: 0.8902 (mmt) REVERT: D 799 MET cc_start: 0.9328 (tpp) cc_final: 0.9055 (tpp) REVERT: H 2015 ASP cc_start: 0.8644 (t0) cc_final: 0.8326 (t0) REVERT: H 2112 LYS cc_start: 0.9103 (mtmt) cc_final: 0.8856 (ttpt) REVERT: H 2155 ARG cc_start: 0.8774 (mpp80) cc_final: 0.8085 (mpt-90) REVERT: H 2166 ASP cc_start: 0.8288 (t0) cc_final: 0.8001 (p0) REVERT: H 2200 LYS cc_start: 0.8019 (mttt) cc_final: 0.7767 (mttm) outliers start: 60 outliers final: 53 residues processed: 337 average time/residue: 0.4990 time to fit residues: 274.7120 Evaluate side-chains 337 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 280 time to evaluate : 3.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain E residue 2039 TRP Chi-restraints excluded: chain E residue 2146 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 610 PHE Chi-restraints excluded: chain B residue 818 LYS Chi-restraints excluded: chain B residue 830 MET Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 931 ASP Chi-restraints excluded: chain B residue 957 ASN Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain F residue 2008 TYR Chi-restraints excluded: chain F residue 2039 TRP Chi-restraints excluded: chain F residue 2146 PHE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 610 PHE Chi-restraints excluded: chain C residue 818 LYS Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 931 ASP Chi-restraints excluded: chain C residue 957 ASN Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain G residue 2039 TRP Chi-restraints excluded: chain G residue 2146 PHE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 818 LYS Chi-restraints excluded: chain D residue 830 MET Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 931 ASP Chi-restraints excluded: chain D residue 957 ASN Chi-restraints excluded: chain D residue 998 ASP Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain H residue 2008 TYR Chi-restraints excluded: chain H residue 2039 TRP Chi-restraints excluded: chain H residue 2146 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 5.9990 chunk 410 optimal weight: 0.3980 chunk 250 optimal weight: 0.3980 chunk 194 optimal weight: 4.9990 chunk 285 optimal weight: 1.9990 chunk 430 optimal weight: 0.9980 chunk 396 optimal weight: 0.9990 chunk 342 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 264 optimal weight: 0.6980 chunk 210 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 ASN B 957 ASN C 957 ASN D 957 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 37788 Z= 0.129 Angle : 0.440 12.103 51132 Z= 0.224 Chirality : 0.039 0.164 5756 Planarity : 0.003 0.032 6196 Dihedral : 12.149 85.752 7036 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.65 % Allowed : 16.53 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.13), residues: 4332 helix: 1.20 (0.12), residues: 2140 sheet: -0.63 (0.23), residues: 528 loop : -0.14 (0.17), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E2176 HIS 0.003 0.000 HIS C 771 PHE 0.012 0.001 PHE A 120 TYR 0.006 0.001 TYR C 130 ARG 0.002 0.000 ARG C 368 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8664 Ramachandran restraints generated. 4332 Oldfield, 0 Emsley, 4332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 292 time to evaluate : 4.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.8026 (t80) REVERT: A 691 MET cc_start: 0.9181 (mmt) cc_final: 0.8876 (mmt) REVERT: A 799 MET cc_start: 0.9319 (tpp) cc_final: 0.9054 (tpp) REVERT: E 2015 ASP cc_start: 0.8604 (t0) cc_final: 0.8306 (t0) REVERT: E 2131 MET cc_start: 0.8341 (mmp) cc_final: 0.7860 (mmm) REVERT: E 2155 ARG cc_start: 0.8726 (mpp80) cc_final: 0.8075 (mpt-90) REVERT: E 2168 ILE cc_start: 0.9350 (tt) cc_final: 0.9105 (tt) REVERT: E 2200 LYS cc_start: 0.7981 (mttt) cc_final: 0.7736 (mttm) REVERT: B 610 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.8020 (t80) REVERT: B 691 MET cc_start: 0.9188 (mmt) cc_final: 0.8893 (mmt) REVERT: B 799 MET cc_start: 0.9319 (tpp) cc_final: 0.9057 (tpp) REVERT: F 2015 ASP cc_start: 0.8594 (t0) cc_final: 0.8296 (t0) REVERT: F 2112 LYS cc_start: 0.9091 (mtmt) cc_final: 0.8837 (ttpt) REVERT: F 2131 MET cc_start: 0.8339 (mmp) cc_final: 0.7853 (mmm) REVERT: F 2155 ARG cc_start: 0.8728 (mpp80) cc_final: 0.8076 (mpt-90) REVERT: F 2166 ASP cc_start: 0.8270 (t0) cc_final: 0.7942 (p0) REVERT: F 2200 LYS cc_start: 0.7984 (mttt) cc_final: 0.7724 (mttm) REVERT: C 610 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.8026 (t80) REVERT: C 691 MET cc_start: 0.9171 (mmt) cc_final: 0.8871 (mmt) REVERT: C 799 MET cc_start: 0.9322 (tpp) cc_final: 0.9055 (tpp) REVERT: G 2112 LYS cc_start: 0.9102 (mtmt) cc_final: 0.8854 (ttpt) REVERT: G 2131 MET cc_start: 0.8331 (mmp) cc_final: 0.7850 (mmm) REVERT: G 2153 HIS cc_start: 0.7802 (t-90) cc_final: 0.7430 (t-90) REVERT: G 2155 ARG cc_start: 0.8761 (mpp80) cc_final: 0.7992 (mpt-90) REVERT: G 2163 ARG cc_start: 0.7765 (mtt-85) cc_final: 0.7421 (mtt-85) REVERT: G 2168 ILE cc_start: 0.9343 (tt) cc_final: 0.9098 (tt) REVERT: G 2200 LYS cc_start: 0.8042 (mttt) cc_final: 0.7754 (mttp) REVERT: D 610 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.8021 (t80) REVERT: D 691 MET cc_start: 0.9188 (mmt) cc_final: 0.8892 (mmt) REVERT: D 799 MET cc_start: 0.9319 (tpp) cc_final: 0.9056 (tpp) REVERT: H 2015 ASP cc_start: 0.8605 (t0) cc_final: 0.8300 (t0) REVERT: H 2112 LYS cc_start: 0.9094 (mtmt) cc_final: 0.8839 (ttpt) REVERT: H 2131 MET cc_start: 0.8334 (mmp) cc_final: 0.7851 (mmm) REVERT: H 2155 ARG cc_start: 0.8744 (mpp80) cc_final: 0.8118 (mpt-90) REVERT: H 2166 ASP cc_start: 0.8270 (t0) cc_final: 0.7942 (p0) REVERT: H 2200 LYS cc_start: 0.7987 (mttt) cc_final: 0.7726 (mttm) outliers start: 64 outliers final: 59 residues processed: 342 average time/residue: 0.5092 time to fit residues: 284.2702 Evaluate side-chains 343 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 280 time to evaluate : 3.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 610 PHE Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 931 ASP Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain E residue 2039 TRP Chi-restraints excluded: chain E residue 2146 PHE Chi-restraints excluded: chain E residue 2157 ASP Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 610 PHE Chi-restraints excluded: chain B residue 818 LYS Chi-restraints excluded: chain B residue 830 MET Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 931 ASP Chi-restraints excluded: chain B residue 957 ASN Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain F residue 2008 TYR Chi-restraints excluded: chain F residue 2039 TRP Chi-restraints excluded: chain F residue 2146 PHE Chi-restraints excluded: chain F residue 2157 ASP Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 605 VAL Chi-restraints excluded: chain C residue 610 PHE Chi-restraints excluded: chain C residue 818 LYS Chi-restraints excluded: chain C residue 830 MET Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 931 ASP Chi-restraints excluded: chain C residue 957 ASN Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain G residue 2039 TRP Chi-restraints excluded: chain G residue 2146 PHE Chi-restraints excluded: chain G residue 2157 ASP Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 610 PHE Chi-restraints excluded: chain D residue 818 LYS Chi-restraints excluded: chain D residue 830 MET Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 931 ASP Chi-restraints excluded: chain D residue 957 ASN Chi-restraints excluded: chain D residue 998 ASP Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain H residue 2008 TYR Chi-restraints excluded: chain H residue 2039 TRP Chi-restraints excluded: chain H residue 2146 PHE Chi-restraints excluded: chain H residue 2157 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 0.7980 chunk 365 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 316 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 343 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 352 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN A 957 ASN E2091 ASN B 216 GLN B 957 ASN F2091 ASN C 957 ASN G2091 ASN D 216 GLN D 957 ASN H2091 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.091156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.067560 restraints weight = 85545.943| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.71 r_work: 0.2807 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37788 Z= 0.175 Angle : 0.458 11.680 51132 Z= 0.235 Chirality : 0.039 0.160 5756 Planarity : 0.003 0.032 6196 Dihedral : 11.999 87.067 7036 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.04 % Allowed : 16.50 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.13), residues: 4332 helix: 1.20 (0.12), residues: 2136 sheet: -0.64 (0.23), residues: 528 loop : -0.09 (0.17), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 275 HIS 0.003 0.000 HIS C 771 PHE 0.014 0.001 PHE A 120 TYR 0.008 0.001 TYR C 130 ARG 0.005 0.000 ARG G2077 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7177.55 seconds wall clock time: 133 minutes 51.21 seconds (8031.21 seconds total)