Starting phenix.real_space_refine (version: dev) on Fri Apr 8 20:34:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v22_21025/04_2022/6v22_21025_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v22_21025/04_2022/6v22_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_21025/04_2022/6v22_21025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v22_21025/04_2022/6v22_21025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v22_21025/04_2022/6v22_21025_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v22_21025/04_2022/6v22_21025_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4553/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: {'POV': 11, ' K': 4, ' MG': 1, ' CA': 2, 'CLR': 4} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 229 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: {'POV': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 96 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: {'POV': 11, ' MG': 1, ' CA': 2, 'CLR': 4} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 229 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: {'POV': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 96 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: {'POV': 11, ' MG': 1, ' CA': 2, 'CLR': 4} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 229 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: {'POV': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 96 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: {'POV': 11, ' MG': 1, ' CA': 2, 'CLR': 4} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 229 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: {'POV': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 96 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: 20.80, per 1000 atoms: 0.56 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: 17.14 Conformation dependent library (CDL) restraints added in 6.2 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: 4.73 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: 14.79 Time building geometry restraints manager: 17.96 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=" C2 NAG E2305 " pdb=" C1 NAG E2305 " pdb=" O5 NAG E2305 " ideal model delta sigma weight residual 109.64 115.25 -5.61 5.38e-01 3.45e+00 1.09e+02 angle pdb=" C2 NAG F2305 " pdb=" C1 NAG F2305 " pdb=" O5 NAG F2305 " ideal model delta sigma weight residual 109.64 115.22 -5.58 5.38e-01 3.45e+00 1.07e+02 angle pdb=" C2 NAG H2305 " pdb=" C1 NAG H2305 " pdb=" O5 NAG H2305 " ideal model delta sigma weight residual 109.64 115.22 -5.58 5.38e-01 3.45e+00 1.07e+02 angle pdb=" C2 NAG G2305 " pdb=" C1 NAG G2305 " pdb=" O5 NAG G2305 " ideal model delta sigma weight residual 109.64 115.22 -5.58 5.38e-01 3.45e+00 1.07e+02 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 ... (remaining 51127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.89: 21400 33.89 - 67.77: 720 67.77 - 101.66: 80 101.66 - 135.54: 16 135.54 - 169.43: 16 Dihedral angle restraints: 22232 sinusoidal: 9408 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 22229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4752 0.069 - 0.138: 847 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 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. 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: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 15.540 Check model and map are aligned: 0.520 Convert atoms to be neutral: 0.320 Process input model: 101.060 Find NCS groups from input model: 2.760 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 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= 0.884 Angle : 1.409 20.498 51132 Z= 0.591 Chirality : 0.060 0.345 5756 Planarity : 0.019 0.341 6196 Dihedral : 17.750 169.427 13872 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 % 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 *********************** 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 : 4.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 353 average time/residue: 0.5719 time to fit residues: 310.4659 Evaluate side-chains 238 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 4.422 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6783 ------------------------------------------------------------------------------- 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: 0.8599 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 37788 Z= 0.276 Angle : 0.545 8.997 51132 Z= 0.283 Chirality : 0.041 0.156 5756 Planarity : 0.004 0.047 6196 Dihedral : 15.759 143.361 5820 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 1.81 % 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: -1.63 (0.12), residues: 4332 helix: -0.64 (0.10), residues: 2128 sheet: -1.32 (0.22), residues: 532 loop : -1.39 (0.15), residues: 1672 *********************** 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 315 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 245 time to evaluate : 4.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 28 residues processed: 293 average time/residue: 0.4613 time to fit residues: 229.9266 Evaluate side-chains 252 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 224 time to evaluate : 4.546 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3403 time to fit residues: 24.0441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 326 optimal weight: 2.9990 chunk 267 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 393 optimal weight: 0.9980 chunk 424 optimal weight: 6.9990 chunk 350 optimal weight: 0.6980 chunk 389 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 315 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN A 267 GLN A 465 ASN B 216 GLN B 465 ASN C 216 GLN C 267 GLN C 465 ASN D 216 GLN D 465 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 37788 Z= 0.194 Angle : 0.464 7.563 51132 Z= 0.242 Chirality : 0.039 0.149 5756 Planarity : 0.003 0.033 6196 Dihedral : 14.355 126.413 5820 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 1.11 % 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: -0.78 (0.13), residues: 4332 helix: 0.10 (0.11), residues: 2136 sheet: -0.92 (0.23), residues: 524 loop : -1.04 (0.15), residues: 1672 *********************** 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 303 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 260 time to evaluate : 4.919 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 outliers start: 43 outliers final: 28 residues processed: 295 average time/residue: 0.5125 time to fit residues: 251.7967 Evaluate side-chains 254 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 226 time to evaluate : 4.771 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3257 time to fit residues: 23.2567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 6.9990 chunk 295 optimal weight: 6.9990 chunk 203 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 263 optimal weight: 0.1980 chunk 394 optimal weight: 1.9990 chunk 417 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 373 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN A 254 HIS ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN E2124 GLN E2165 HIS B 216 GLN B 254 HIS B 267 GLN ** B 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2165 HIS C 216 GLN C 254 HIS ** C 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2091 ASN G2165 HIS D 216 GLN D 254 HIS D 816 GLN ** D 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2091 ASN H2165 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.045 37788 Z= 0.389 Angle : 0.563 6.449 51132 Z= 0.291 Chirality : 0.043 0.153 5756 Planarity : 0.004 0.033 6196 Dihedral : 14.487 111.580 5820 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 1.21 % 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: 0.29 (0.11), residues: 2136 sheet: -0.92 (0.23), residues: 532 loop : -0.78 (0.16), residues: 1664 *********************** 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 291 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 244 time to evaluate : 4.570 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 outliers start: 47 outliers final: 23 residues processed: 281 average time/residue: 0.5096 time to fit residues: 237.0097 Evaluate side-chains 248 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 225 time to evaluate : 4.802 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3603 time to fit residues: 20.8929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 0.6980 chunk 237 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 310 optimal weight: 0.0370 chunk 172 optimal weight: 5.9990 chunk 356 optimal weight: 1.9990 chunk 288 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 213 optimal weight: 3.9990 chunk 374 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN A1008 ASN B 216 GLN B 816 GLN B1008 ASN C 216 GLN C 267 GLN C1008 ASN G2091 ASN D 216 GLN D 267 GLN D1008 ASN H2091 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 37788 Z= 0.174 Angle : 0.457 6.305 51132 Z= 0.236 Chirality : 0.039 0.146 5756 Planarity : 0.003 0.031 6196 Dihedral : 13.548 100.784 5820 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 0.83 % 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: -0.13 (0.13), residues: 4332 helix: 0.64 (0.11), residues: 2128 sheet: -0.76 (0.23), residues: 524 loop : -0.68 (0.16), residues: 1680 *********************** 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 280 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 248 time to evaluate : 4.663 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 outliers start: 32 outliers final: 11 residues processed: 271 average time/residue: 0.4946 time to fit residues: 224.5166 Evaluate side-chains 247 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 236 time to evaluate : 4.404 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3760 time to fit residues: 13.1801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 0.7980 chunk 376 optimal weight: 4.9990 chunk 82 optimal weight: 0.2980 chunk 245 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 417 optimal weight: 10.0000 chunk 346 optimal weight: 0.9980 chunk 193 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 219 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 816 GLN F2124 GLN C 216 GLN G2124 GLN D 216 GLN H2124 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 37788 Z= 0.185 Angle : 0.455 6.245 51132 Z= 0.237 Chirality : 0.040 0.224 5756 Planarity : 0.003 0.031 6196 Dihedral : 13.125 96.962 5820 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 0.88 % 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: 0.08 (0.13), residues: 4332 helix: 0.83 (0.11), residues: 2140 sheet: -0.81 (0.23), residues: 540 loop : -0.53 (0.16), residues: 1652 *********************** 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 292 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 258 time to evaluate : 4.651 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 outliers start: 34 outliers final: 11 residues processed: 290 average time/residue: 0.5254 time to fit residues: 250.6369 Evaluate side-chains 251 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 240 time to evaluate : 4.543 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3390 time to fit residues: 13.0573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 238 optimal weight: 0.5980 chunk 305 optimal weight: 2.9990 chunk 236 optimal weight: 0.8980 chunk 351 optimal weight: 3.9990 chunk 233 optimal weight: 0.6980 chunk 416 optimal weight: 2.9990 chunk 260 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.093 37788 Z= 0.160 Angle : 0.445 8.254 51132 Z= 0.231 Chirality : 0.039 0.191 5756 Planarity : 0.003 0.032 6196 Dihedral : 12.622 90.560 5820 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 0.70 % 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: 0.30 (0.13), residues: 4332 helix: 1.00 (0.11), residues: 2144 sheet: -0.70 (0.23), residues: 548 loop : -0.42 (0.16), residues: 1640 *********************** 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 301 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 274 time to evaluate : 4.420 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 outliers start: 27 outliers final: 4 residues processed: 300 average time/residue: 0.5425 time to fit residues: 265.2581 Evaluate side-chains 258 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 254 time to evaluate : 4.435 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3983 time to fit residues: 9.6207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 248 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 80 optimal weight: 0.5980 chunk 264 optimal weight: 1.9990 chunk 283 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 327 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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: 0.8565 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 37788 Z= 0.178 Angle : 0.462 12.483 51132 Z= 0.237 Chirality : 0.039 0.177 5756 Planarity : 0.003 0.032 6196 Dihedral : 12.462 89.513 5820 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 0.59 % 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: 0.38 (0.13), residues: 4332 helix: 1.07 (0.11), residues: 2136 sheet: -0.71 (0.23), residues: 548 loop : -0.35 (0.16), residues: 1648 *********************** 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 285 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 262 time to evaluate : 4.487 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 outliers start: 23 outliers final: 5 residues processed: 280 average time/residue: 0.5160 time to fit residues: 237.1376 Evaluate side-chains 255 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 250 time to evaluate : 4.359 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3410 time to fit residues: 8.9110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 5.9990 chunk 398 optimal weight: 1.9990 chunk 363 optimal weight: 2.9990 chunk 388 optimal weight: 5.9990 chunk 233 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 304 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 350 optimal weight: 0.6980 chunk 366 optimal weight: 2.9990 chunk 386 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN A 816 GLN B 216 GLN B 957 ASN C 216 GLN C 816 GLN C 957 ASN D 216 GLN D 957 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 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 : 0.004 0.044 37788 Z= 0.244 Angle : 0.496 11.472 51132 Z= 0.253 Chirality : 0.041 0.167 5756 Planarity : 0.003 0.032 6196 Dihedral : 12.579 88.957 5820 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 0.39 % 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: 0.35 (0.13), residues: 4332 helix: 0.97 (0.11), residues: 2144 sheet: -0.74 (0.23), residues: 536 loop : -0.26 (0.17), residues: 1652 *********************** 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 269 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 254 time to evaluate : 4.590 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 outliers start: 15 outliers final: 11 residues processed: 268 average time/residue: 0.5275 time to fit residues: 232.7231 Evaluate side-chains 255 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 244 time to evaluate : 4.699 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4237 time to fit residues: 14.1479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 0.8980 chunk 410 optimal weight: 0.0060 chunk 250 optimal weight: 3.9990 chunk 194 optimal weight: 0.0470 chunk 285 optimal weight: 0.7980 chunk 430 optimal weight: 1.9990 chunk 396 optimal weight: 0.9980 chunk 342 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 264 optimal weight: 2.9990 chunk 210 optimal weight: 0.0070 overall best weight: 0.3112 ------------------------------------------------------------------------------- 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 ** E2154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** F2154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN C 816 GLN ** G2154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN H2154 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 37788 Z= 0.119 Angle : 0.443 11.936 51132 Z= 0.227 Chirality : 0.038 0.167 5756 Planarity : 0.003 0.032 6196 Dihedral : 11.755 87.660 5820 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 0.18 % 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: 0.54 (0.13), residues: 4332 helix: 1.16 (0.12), residues: 2140 sheet: -0.64 (0.23), residues: 536 loop : -0.21 (0.16), residues: 1656 ********************** 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 283 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 276 time to evaluate : 4.718 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 outliers start: 7 outliers final: 3 residues processed: 279 average time/residue: 0.5105 time to fit residues: 238.0283 Evaluate side-chains 268 residues out of total 3872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 265 time to evaluate : 4.536 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4005 time to fit residues: 8.0580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 0.0070 chunk 365 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 316 optimal weight: 1.9990 chunk 50 optimal weight: 0.0670 chunk 95 optimal weight: 3.9990 chunk 343 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 352 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E2154 GLN F2154 GLN G2091 ASN ** G2154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2091 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.091803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.068427 restraints weight = 85654.410| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.71 r_work: 0.2968 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work: 0.2945 rms_B_bonded: 2.48 restraints_weight: 0.1250 r_work: 0.2933 rms_B_bonded: 2.54 restraints_weight: 0.0625 r_work: 0.2921 rms_B_bonded: 2.62 restraints_weight: 0.0312 r_work: 0.2909 rms_B_bonded: 2.74 restraints_weight: 0.0156 r_work: 0.2895 rms_B_bonded: 2.88 restraints_weight: 0.0078 r_work: 0.2882 rms_B_bonded: 3.05 restraints_weight: 0.0039 r_work: 0.2867 rms_B_bonded: 3.24 restraints_weight: 0.0020 r_work: 0.2852 rms_B_bonded: 3.47 restraints_weight: 0.0010 r_work: 0.2836 rms_B_bonded: 3.73 restraints_weight: 0.0005 r_work: 0.2818 rms_B_bonded: 4.02 restraints_weight: 0.0002 r_work: 0.2800 rms_B_bonded: 4.35 restraints_weight: 0.0001 r_work: 0.2781 rms_B_bonded: 4.72 restraints_weight: 0.0001 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 37788 Z= 0.147 Angle : 0.448 11.771 51132 Z= 0.229 Chirality : 0.039 0.163 5756 Planarity : 0.003 0.032 6196 Dihedral : 11.566 87.221 5820 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 0.21 % 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: 0.60 (0.13), residues: 4332 helix: 1.21 (0.12), residues: 2132 sheet: -0.57 (0.23), residues: 536 loop : -0.19 (0.17), residues: 1664 =============================================================================== Job complete usr+sys time: 6252.53 seconds wall clock time: 116 minutes 16.23 seconds (6976.23 seconds total)