Starting phenix.real_space_refine on Sun Jul 21 12:29:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pk3_17724/07_2024/8pk3_17724.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pk3_17724/07_2024/8pk3_17724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pk3_17724/07_2024/8pk3_17724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pk3_17724/07_2024/8pk3_17724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pk3_17724/07_2024/8pk3_17724.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pk3_17724/07_2024/8pk3_17724.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 8946 2.51 5 N 2427 2.21 5 O 2844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 41": "OE1" <-> "OE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 271": "OD1" <-> "OD2" Residue "D PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 164": "OD1" <-> "OD2" Residue "G TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 85": "OE1" <-> "OE2" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 131": "OE1" <-> "OE2" Residue "E PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 75": "OD1" <-> "OD2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "C ASP 271": "OD1" <-> "OD2" Residue "F TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 85": "OE1" <-> "OE2" Residue "F GLU 97": "OE1" <-> "OE2" Residue "I TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14277 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2482 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 300} Chain: "D" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1417 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 174} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 743 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "B" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2482 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 300} Chain: "E" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1417 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 743 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2482 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 300} Chain: "F" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1417 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 174} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 743 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.81, per 1000 atoms: 0.62 Number of scatterers: 14277 At special positions: 0 Unit cell: (97.18, 97.18, 169.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2844 8.00 N 2427 7.00 C 8946 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS D 137 " distance=2.04 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.02 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS E 137 " distance=2.04 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.02 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.02 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS E 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS F 137 " distance=2.05 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA W 3 " - " MAN W 4 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA W 3 " - " MAN W 5 " " BMA f 3 " - " MAN f 5 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG S 1 " - " NAG S 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG b 1 " - " NAG b 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " NAG-ASN " NAG A 401 " - " ASN A 285 " " NAG A 402 " - " ASN A 38 " " NAG B 401 " - " ASN B 285 " " NAG B 402 " - " ASN B 38 " " NAG C 401 " - " ASN C 285 " " NAG C 402 " - " ASN C 38 " " NAG J 1 " - " ASN A 81 " " NAG N 1 " - " ASN A 165 " " NAG S 1 " - " ASN B 81 " " NAG W 1 " - " ASN B 165 " " NAG b 1 " - " ASN C 81 " " NAG f 1 " - " ASN C 165 " Time building additional restraints: 5.47 Conformation dependent library (CDL) restraints added in 2.5 seconds 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 28 sheets defined 23.3% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.715A pdb=" N GLN A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 57 removed outlier: 3.570A pdb=" N THR D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG D 54 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 125 Processing helix chain 'D' and resid 145 through 153 removed outlier: 3.967A pdb=" N ILE D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 167 removed outlier: 3.621A pdb=" N LEU D 167 " --> pdb=" O ARG D 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.849A pdb=" N LYS G 22 " --> pdb=" O GLU G 18 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU G 23 " --> pdb=" O HIS G 19 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.846A pdb=" N GLY B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 removed outlier: 3.799A pdb=" N GLN B 191 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 57 removed outlier: 3.530A pdb=" N THR E 41 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG E 54 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU E 57 " --> pdb=" O ASN E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 127 removed outlier: 3.504A pdb=" N GLU E 114 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU E 126 " --> pdb=" O THR E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 153 removed outlier: 3.994A pdb=" N ILE E 149 " --> pdb=" O ASP E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing helix chain 'E' and resid 167 through 168 No H-bonds generated for 'chain 'E' and resid 167 through 168' Processing helix chain 'H' and resid 6 through 24 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 104 through 116 removed outlier: 3.825A pdb=" N LEU C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.633A pdb=" N GLN C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 57 removed outlier: 3.503A pdb=" N ALA F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG F 54 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU F 57 " --> pdb=" O ASN F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 125 Processing helix chain 'F' and resid 145 through 153 removed outlier: 3.920A pdb=" N ILE F 149 " --> pdb=" O ASP F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 167 removed outlier: 3.634A pdb=" N LEU F 167 " --> pdb=" O ARG F 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 24 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.144A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 7.233A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ARG A 90 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N PHE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N SER A 270 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N GLU A 89 " --> pdb=" O SER A 270 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.576A pdb=" N ILE A 121 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA6, first strand: chain 'A' and resid 164 through 169 removed outlier: 3.595A pdb=" N SER A 247 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU A 243 " --> pdb=" O MET A 168 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 202 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 213 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 294 through 295 removed outlier: 3.578A pdb=" N GLN A 295 " --> pdb=" O LYS A 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 23 through 26 removed outlier: 3.613A pdb=" N ALA D 35 " --> pdb=" O PHE D 24 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N HIS D 26 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY D 33 " --> pdb=" O HIS D 26 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 29 through 37 removed outlier: 7.499A pdb=" N VAL G 30 " --> pdb=" O LYS G 57 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N LYS G 57 " --> pdb=" O VAL G 30 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL G 32 " --> pdb=" O GLU G 55 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLU G 55 " --> pdb=" O VAL G 32 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS G 34 " --> pdb=" O THR G 53 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR G 50 " --> pdb=" O VAL G 69 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL G 69 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU G 52 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS G 68 " --> pdb=" O GLU G 88 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU G 88 " --> pdb=" O LYS G 68 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 24 through 26 removed outlier: 3.600A pdb=" N THR B 24 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 51 through 52 removed outlier: 6.076A pdb=" N ILE B 51 " --> pdb=" O ASP B 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.003A pdb=" N PHE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N SER B 270 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLU B 89 " --> pdb=" O SER B 270 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 151 through 153 removed outlier: 7.614A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 151 through 153 removed outlier: 7.614A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 164 through 169 removed outlier: 3.507A pdb=" N VAL B 166 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU B 243 " --> pdb=" O MET B 168 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 294 through 295 removed outlier: 3.659A pdb=" N GLN B 295 " --> pdb=" O LYS B 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 25 through 28 removed outlier: 3.878A pdb=" N HIS E 26 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY E 33 " --> pdb=" O HIS E 26 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN E 28 " --> pdb=" O GLY E 31 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY E 31 " --> pdb=" O ASN E 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'H' and resid 29 through 37 removed outlier: 7.248A pdb=" N VAL H 30 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N LYS H 57 " --> pdb=" O VAL H 30 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL H 32 " --> pdb=" O GLU H 55 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLU H 55 " --> pdb=" O VAL H 32 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS H 34 " --> pdb=" O THR H 53 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR H 51 " --> pdb=" O LYS H 36 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR H 50 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL H 69 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU H 52 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU H 88 " --> pdb=" O LYS H 68 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.541A pdb=" N THR C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 51 through 52 removed outlier: 6.134A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 58 through 60 removed outlier: 7.144A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ARG C 90 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N PHE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N SER C 270 " --> pdb=" O PHE C 87 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLU C 89 " --> pdb=" O SER C 270 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 151 through 152 removed outlier: 3.533A pdb=" N ALA C 253 " --> pdb=" O ASN C 152 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.540A pdb=" N LEU C 164 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 247 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU C 243 " --> pdb=" O MET C 168 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE C 213 " --> pdb=" O VAL C 202 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 236 through 237 Processing sheet with id=AC7, first strand: chain 'C' and resid 180 through 184 Processing sheet with id=AC8, first strand: chain 'C' and resid 294 through 295 removed outlier: 3.720A pdb=" N GLN C 295 " --> pdb=" O LYS C 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 23 through 26 removed outlier: 3.623A pdb=" N ALA F 35 " --> pdb=" O PHE F 24 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS F 26 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY F 33 " --> pdb=" O HIS F 26 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 29 through 37 removed outlier: 7.447A pdb=" N VAL I 30 " --> pdb=" O LYS I 57 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N LYS I 57 " --> pdb=" O VAL I 30 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL I 32 " --> pdb=" O GLU I 55 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLU I 55 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS I 34 " --> pdb=" O THR I 53 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR I 51 " --> pdb=" O LYS I 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR I 50 " --> pdb=" O VAL I 69 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL I 69 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS I 68 " --> pdb=" O GLU I 88 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLU I 88 " --> pdb=" O LYS I 68 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP I 70 " --> pdb=" O LEU I 86 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LEU I 86 " --> pdb=" O TRP I 70 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1164 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: 3.43 Time building geometry restraints manager: 6.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4035 1.33 - 1.46: 3494 1.46 - 1.58: 6957 1.58 - 1.71: 0 1.71 - 1.83: 84 Bond restraints: 14570 Sorted by residual: bond pdb=" C3 BMA N 3 " pdb=" O3 BMA N 3 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C3 BMA f 3 " pdb=" O3 BMA f 3 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" N PRO A 9 " pdb=" CD PRO A 9 " ideal model delta sigma weight residual 1.473 1.517 -0.044 1.40e-02 5.10e+03 9.92e+00 bond pdb=" N PRO B 9 " pdb=" CD PRO B 9 " ideal model delta sigma weight residual 1.473 1.516 -0.043 1.40e-02 5.10e+03 9.50e+00 bond pdb=" N PRO C 9 " pdb=" CD PRO C 9 " ideal model delta sigma weight residual 1.473 1.516 -0.043 1.40e-02 5.10e+03 9.38e+00 ... (remaining 14565 not shown) Histogram of bond angle deviations from ideal: 98.64 - 105.73: 246 105.73 - 112.83: 7703 112.83 - 119.93: 5033 119.93 - 127.03: 6566 127.03 - 134.12: 177 Bond angle restraints: 19725 Sorted by residual: angle pdb=" CA PRO B 9 " pdb=" N PRO B 9 " pdb=" CD PRO B 9 " ideal model delta sigma weight residual 112.00 99.99 12.01 1.40e+00 5.10e-01 7.35e+01 angle pdb=" CA PRO C 9 " pdb=" N PRO C 9 " pdb=" CD PRO C 9 " ideal model delta sigma weight residual 112.00 100.04 11.96 1.40e+00 5.10e-01 7.29e+01 angle pdb=" CA PRO A 9 " pdb=" N PRO A 9 " pdb=" CD PRO A 9 " ideal model delta sigma weight residual 112.00 100.04 11.96 1.40e+00 5.10e-01 7.29e+01 angle pdb=" CA ARG E 163 " pdb=" C ARG E 163 " pdb=" N ASP E 164 " ideal model delta sigma weight residual 118.14 112.61 5.53 1.31e+00 5.83e-01 1.78e+01 angle pdb=" CA LEU A 118 " pdb=" CB LEU A 118 " pdb=" CG LEU A 118 " ideal model delta sigma weight residual 116.30 131.03 -14.73 3.50e+00 8.16e-02 1.77e+01 ... (remaining 19720 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.29: 7865 21.29 - 42.59: 949 42.59 - 63.88: 190 63.88 - 85.17: 65 85.17 - 106.46: 20 Dihedral angle restraints: 9089 sinusoidal: 4044 harmonic: 5045 Sorted by residual: dihedral pdb=" CB CYS C 14 " pdb=" SG CYS C 14 " pdb=" SG CYS F 137 " pdb=" CB CYS F 137 " ideal model delta sinusoidal sigma weight residual 93.00 20.42 72.58 1 1.00e+01 1.00e-02 6.73e+01 dihedral pdb=" CB CYS C 281 " pdb=" SG CYS C 281 " pdb=" SG CYS C 305 " pdb=" CB CYS C 305 " ideal model delta sinusoidal sigma weight residual 93.00 25.83 67.17 1 1.00e+01 1.00e-02 5.88e+01 dihedral pdb=" CB CYS B 281 " pdb=" SG CYS B 281 " pdb=" SG CYS B 305 " pdb=" CB CYS B 305 " ideal model delta sinusoidal sigma weight residual 93.00 26.08 66.92 1 1.00e+01 1.00e-02 5.84e+01 ... (remaining 9086 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1898 0.077 - 0.154: 281 0.154 - 0.231: 31 0.231 - 0.308: 4 0.308 - 0.385: 3 Chirality restraints: 2217 Sorted by residual: chirality pdb=" CB VAL E 55 " pdb=" CA VAL E 55 " pdb=" CG1 VAL E 55 " pdb=" CG2 VAL E 55 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CB VAL F 55 " pdb=" CA VAL F 55 " pdb=" CG1 VAL F 55 " pdb=" CG2 VAL F 55 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CB VAL D 55 " pdb=" CA VAL D 55 " pdb=" CG1 VAL D 55 " pdb=" CG2 VAL D 55 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.31 2.00e-01 2.50e+01 2.48e+00 ... (remaining 2214 not shown) Planarity restraints: 2555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 8 " 0.089 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO C 9 " -0.216 5.00e-02 4.00e+02 pdb=" CA PRO C 9 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO C 9 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 8 " -0.084 5.00e-02 4.00e+02 1.18e-01 2.23e+01 pdb=" N PRO B 9 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO B 9 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO B 9 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 8 " -0.083 5.00e-02 4.00e+02 1.16e-01 2.16e+01 pdb=" N PRO A 9 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO A 9 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 9 " -0.059 5.00e-02 4.00e+02 ... (remaining 2552 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.88: 3 1.88 - 2.63: 233 2.63 - 3.39: 18543 3.39 - 4.14: 33205 4.14 - 4.90: 58762 Nonbonded interactions: 110746 Sorted by model distance: nonbonded pdb=" NZ LYS D 174 " pdb=" O GLU E 165 " model vdw 1.122 2.520 nonbonded pdb=" NZ LYS D 174 " pdb=" C GLU E 165 " model vdw 1.303 3.350 nonbonded pdb=" CE LYS D 174 " pdb=" O GLU E 165 " model vdw 1.598 3.440 nonbonded pdb=" OD2 ASP A 8 " pdb=" OE1 GLU D 165 " model vdw 2.040 3.040 nonbonded pdb=" OD2 ASP C 8 " pdb=" OE1 GLU F 165 " model vdw 2.209 3.040 ... (remaining 110741 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'S' selection = chain 'b' } ncs_group { reference = chain 'N' selection = chain 'W' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.900 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: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 38.140 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 14570 Z= 0.349 Angle : 0.956 14.730 19725 Z= 0.499 Chirality : 0.056 0.385 2217 Planarity : 0.007 0.125 2543 Dihedral : 19.403 106.465 5795 Min Nonbonded Distance : 1.122 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.08 % Favored : 91.74 % Rotamer: Outliers : 0.72 % Allowed : 32.28 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % 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: -3.22 (0.17), residues: 1732 helix: -1.44 (0.23), residues: 377 sheet: -1.08 (0.34), residues: 255 loop : -2.82 (0.15), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 44 HIS 0.015 0.002 HIS B 17 PHE 0.025 0.002 PHE B 258 TYR 0.031 0.002 TYR B 302 ARG 0.018 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 265 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 68 LYS cc_start: 0.7722 (ptmt) cc_final: 0.7403 (ptmt) outliers start: 11 outliers final: 6 residues processed: 272 average time/residue: 0.2636 time to fit residues: 103.6675 Evaluate side-chains 265 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 259 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain C residue 167 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 155 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 HIS ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 GLN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 ASN H 20 ASN F 104 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6338 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14570 Z= 0.236 Angle : 0.631 7.842 19725 Z= 0.330 Chirality : 0.046 0.294 2217 Planarity : 0.004 0.052 2543 Dihedral : 11.859 92.430 2453 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 4.86 % Allowed : 29.00 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % 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: -2.80 (0.18), residues: 1732 helix: -0.43 (0.23), residues: 391 sheet: -0.98 (0.34), residues: 255 loop : -2.81 (0.15), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 44 HIS 0.005 0.001 HIS B 17 PHE 0.012 0.001 PHE B 125 TYR 0.012 0.001 TYR C 105 ARG 0.006 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 267 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 114 GLU cc_start: 0.6254 (mm-30) cc_final: 0.6052 (mm-30) REVERT: B 18 HIS cc_start: 0.7144 (OUTLIER) cc_final: 0.6050 (p-80) REVERT: E 45 ILE cc_start: 0.6679 (mt) cc_final: 0.6441 (tp) REVERT: E 86 ASP cc_start: 0.6015 (t0) cc_final: 0.5478 (t0) REVERT: C 196 VAL cc_start: 0.6827 (OUTLIER) cc_final: 0.6488 (m) REVERT: F 42 GLN cc_start: 0.7632 (tp-100) cc_final: 0.6852 (tp40) REVERT: F 62 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.6619 (mmtm) REVERT: F 90 ASP cc_start: 0.6351 (m-30) cc_final: 0.6113 (m-30) outliers start: 74 outliers final: 33 residues processed: 313 average time/residue: 0.2468 time to fit residues: 113.3991 Evaluate side-chains 302 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 266 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain E residue 9 PHE Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain I residue 23 GLU Chi-restraints excluded: chain I residue 74 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 86 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 129 optimal weight: 0.0270 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 250 ASN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 HIS ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN F 65 GLN F 104 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14570 Z= 0.224 Angle : 0.613 8.474 19725 Z= 0.315 Chirality : 0.045 0.280 2217 Planarity : 0.004 0.053 2543 Dihedral : 11.018 87.536 2443 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 5.05 % Allowed : 28.94 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % 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: -2.57 (0.18), residues: 1732 helix: 0.00 (0.24), residues: 375 sheet: -0.90 (0.34), residues: 255 loop : -2.71 (0.16), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 153 HIS 0.005 0.001 HIS B 17 PHE 0.011 0.001 PHE B 125 TYR 0.011 0.001 TYR C 161 ARG 0.006 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 275 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 90 ASP cc_start: 0.6450 (m-30) cc_final: 0.6222 (m-30) REVERT: D 159 HIS cc_start: 0.7159 (p90) cc_final: 0.6928 (p90) REVERT: B 18 HIS cc_start: 0.7050 (OUTLIER) cc_final: 0.6041 (p-80) REVERT: B 320 MET cc_start: 0.5673 (ptp) cc_final: 0.5161 (ptp) REVERT: E 68 LYS cc_start: 0.7722 (mmmm) cc_final: 0.7385 (mmmm) REVERT: C 191 GLN cc_start: 0.5900 (OUTLIER) cc_final: 0.5504 (tp40) REVERT: C 261 ARG cc_start: 0.7453 (ttm110) cc_final: 0.6982 (tpp80) REVERT: F 90 ASP cc_start: 0.6391 (m-30) cc_final: 0.6148 (m-30) outliers start: 77 outliers final: 45 residues processed: 318 average time/residue: 0.2651 time to fit residues: 123.0817 Evaluate side-chains 317 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 270 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain E residue 9 PHE Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 23 GLU Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 74 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 80 optimal weight: 0.0980 chunk 17 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 147 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 HIS ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN F 104 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14570 Z= 0.248 Angle : 0.609 8.651 19725 Z= 0.317 Chirality : 0.045 0.274 2217 Planarity : 0.004 0.054 2543 Dihedral : 10.687 84.324 2443 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 5.45 % Allowed : 29.33 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % 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: -2.58 (0.18), residues: 1732 helix: 0.10 (0.24), residues: 375 sheet: -0.96 (0.34), residues: 255 loop : -2.75 (0.16), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 153 HIS 0.004 0.001 HIS C 18 PHE 0.013 0.002 PHE B 125 TYR 0.013 0.001 TYR B 308 ARG 0.005 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 280 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.6372 (tt) cc_final: 0.6141 (tt) REVERT: D 90 ASP cc_start: 0.6481 (m-30) cc_final: 0.6196 (m-30) REVERT: D 159 HIS cc_start: 0.7144 (p90) cc_final: 0.6916 (p90) REVERT: B 320 MET cc_start: 0.5728 (ptp) cc_final: 0.5411 (ptp) REVERT: E 111 THR cc_start: 0.7441 (p) cc_final: 0.7101 (p) REVERT: C 64 CYS cc_start: 0.3490 (m) cc_final: 0.3184 (m) REVERT: C 191 GLN cc_start: 0.5940 (OUTLIER) cc_final: 0.5523 (tp40) REVERT: C 261 ARG cc_start: 0.7482 (ttm110) cc_final: 0.7042 (tpp80) REVERT: F 90 ASP cc_start: 0.6352 (m-30) cc_final: 0.6116 (m-30) outliers start: 83 outliers final: 55 residues processed: 328 average time/residue: 0.2570 time to fit residues: 122.6097 Evaluate side-chains 329 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 273 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain E residue 9 PHE Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 23 GLU Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 74 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 141 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 HIS ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN F 104 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14570 Z= 0.301 Angle : 0.634 8.481 19725 Z= 0.332 Chirality : 0.046 0.263 2217 Planarity : 0.004 0.059 2543 Dihedral : 10.558 83.338 2443 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 5.97 % Allowed : 29.92 % Favored : 64.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % 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: -2.70 (0.18), residues: 1732 helix: 0.06 (0.25), residues: 372 sheet: -1.04 (0.34), residues: 255 loop : -2.84 (0.15), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 153 HIS 0.007 0.001 HIS C 18 PHE 0.017 0.002 PHE B 125 TYR 0.017 0.002 TYR B 308 ARG 0.004 0.000 ARG C 224 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 278 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.6155 (OUTLIER) cc_final: 0.5808 (t70) REVERT: A 297 VAL cc_start: 0.7450 (t) cc_final: 0.7207 (m) REVERT: D 90 ASP cc_start: 0.6470 (m-30) cc_final: 0.6200 (m-30) REVERT: D 159 HIS cc_start: 0.7215 (p90) cc_final: 0.6957 (p90) REVERT: G 36 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7533 (pttm) REVERT: E 52 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8176 (tt) REVERT: E 90 ASP cc_start: 0.6165 (m-30) cc_final: 0.5887 (m-30) REVERT: C 34 ILE cc_start: 0.6379 (tt) cc_final: 0.5668 (tp) REVERT: C 191 GLN cc_start: 0.6047 (OUTLIER) cc_final: 0.5620 (tp40) REVERT: C 261 ARG cc_start: 0.7495 (ttm110) cc_final: 0.7072 (tpp80) REVERT: F 17 MET cc_start: 0.4284 (mmm) cc_final: 0.2936 (mmm) REVERT: F 90 ASP cc_start: 0.6425 (OUTLIER) cc_final: 0.6147 (m-30) outliers start: 91 outliers final: 63 residues processed: 331 average time/residue: 0.2645 time to fit residues: 127.3987 Evaluate side-chains 338 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 270 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain E residue 9 PHE Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 23 GLU Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 74 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 165 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 76 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN F 104 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14570 Z= 0.335 Angle : 0.658 8.935 19725 Z= 0.345 Chirality : 0.047 0.254 2217 Planarity : 0.005 0.059 2543 Dihedral : 10.508 82.620 2443 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 6.10 % Allowed : 30.71 % Favored : 63.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % 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: -2.82 (0.18), residues: 1732 helix: -0.00 (0.25), residues: 378 sheet: -1.04 (0.34), residues: 255 loop : -2.97 (0.15), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 153 HIS 0.007 0.001 HIS C 18 PHE 0.020 0.002 PHE B 125 TYR 0.028 0.002 TYR C 302 ARG 0.006 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 271 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.6162 (OUTLIER) cc_final: 0.5839 (t70) REVERT: A 297 VAL cc_start: 0.7492 (t) cc_final: 0.7248 (m) REVERT: D 90 ASP cc_start: 0.6475 (m-30) cc_final: 0.6192 (m-30) REVERT: D 132 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6491 (tt0) REVERT: D 159 HIS cc_start: 0.7237 (p90) cc_final: 0.6987 (p90) REVERT: C 34 ILE cc_start: 0.6378 (tt) cc_final: 0.5734 (tp) REVERT: C 191 GLN cc_start: 0.6033 (OUTLIER) cc_final: 0.5593 (tp40) REVERT: F 17 MET cc_start: 0.4426 (mmm) cc_final: 0.2850 (mmm) REVERT: F 90 ASP cc_start: 0.6426 (OUTLIER) cc_final: 0.6164 (m-30) outliers start: 93 outliers final: 69 residues processed: 329 average time/residue: 0.2984 time to fit residues: 144.5622 Evaluate side-chains 341 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 268 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain G residue 23 GLU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain E residue 6 ILE Chi-restraints excluded: chain E residue 9 PHE Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 153 ARG Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 23 GLU Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 74 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 164 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN F 78 GLN F 104 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14570 Z= 0.302 Angle : 0.646 9.079 19725 Z= 0.339 Chirality : 0.046 0.256 2217 Planarity : 0.005 0.058 2543 Dihedral : 10.276 80.002 2443 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Rotamer: Outliers : 5.64 % Allowed : 31.17 % Favored : 63.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % 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: -2.81 (0.18), residues: 1732 helix: 0.06 (0.25), residues: 378 sheet: -1.10 (0.33), residues: 270 loop : -2.99 (0.15), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 70 HIS 0.009 0.001 HIS C 17 PHE 0.016 0.002 PHE B 125 TYR 0.020 0.002 TYR C 302 ARG 0.006 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 275 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.6172 (OUTLIER) cc_final: 0.5827 (t70) REVERT: A 297 VAL cc_start: 0.7464 (t) cc_final: 0.7214 (m) REVERT: D 68 LYS cc_start: 0.7659 (mmtp) cc_final: 0.7457 (mmmm) REVERT: D 90 ASP cc_start: 0.6459 (m-30) cc_final: 0.6173 (m-30) REVERT: D 159 HIS cc_start: 0.7242 (p90) cc_final: 0.6994 (p90) REVERT: G 50 TYR cc_start: 0.7334 (m-10) cc_final: 0.7103 (m-80) REVERT: B 70 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6988 (mp) REVERT: B 78 VAL cc_start: 0.8301 (OUTLIER) cc_final: 0.8000 (t) REVERT: E 52 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8147 (tt) REVERT: E 86 ASP cc_start: 0.6281 (t0) cc_final: 0.5932 (t0) REVERT: E 90 ASP cc_start: 0.6202 (m-30) cc_final: 0.5784 (m-30) REVERT: C 34 ILE cc_start: 0.6357 (tt) cc_final: 0.5706 (tp) REVERT: C 191 GLN cc_start: 0.5991 (OUTLIER) cc_final: 0.5579 (tp40) REVERT: F 17 MET cc_start: 0.4505 (mmm) cc_final: 0.2626 (mmm) REVERT: F 90 ASP cc_start: 0.6406 (OUTLIER) cc_final: 0.6172 (m-30) outliers start: 86 outliers final: 60 residues processed: 329 average time/residue: 0.2635 time to fit residues: 125.7735 Evaluate side-chains 336 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 270 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain E residue 9 PHE Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 153 ARG Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 23 GLU Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 74 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 101 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 104 optimal weight: 0.0030 chunk 112 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 129 optimal weight: 0.1980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN F 78 GLN ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14570 Z= 0.220 Angle : 0.631 10.120 19725 Z= 0.327 Chirality : 0.045 0.266 2217 Planarity : 0.004 0.055 2543 Dihedral : 9.814 74.705 2442 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 4.79 % Allowed : 31.96 % Favored : 63.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % 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: -2.71 (0.18), residues: 1732 helix: 0.18 (0.25), residues: 375 sheet: -1.06 (0.32), residues: 270 loop : -2.92 (0.15), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 70 HIS 0.007 0.001 HIS C 17 PHE 0.011 0.001 PHE B 148 TYR 0.019 0.001 TYR C 308 ARG 0.010 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 267 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.6134 (OUTLIER) cc_final: 0.5772 (t70) REVERT: A 297 VAL cc_start: 0.7451 (OUTLIER) cc_final: 0.7170 (m) REVERT: D 90 ASP cc_start: 0.6457 (m-30) cc_final: 0.6183 (m-30) REVERT: B 18 HIS cc_start: 0.7041 (OUTLIER) cc_final: 0.6154 (p-80) REVERT: B 70 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6911 (mp) REVERT: B 78 VAL cc_start: 0.8245 (OUTLIER) cc_final: 0.7951 (t) REVERT: E 86 ASP cc_start: 0.6237 (t0) cc_final: 0.5951 (t0) REVERT: C 34 ILE cc_start: 0.6323 (tt) cc_final: 0.5695 (tp) REVERT: F 17 MET cc_start: 0.4307 (mmm) cc_final: 0.2409 (mmm) REVERT: F 90 ASP cc_start: 0.6404 (OUTLIER) cc_final: 0.6178 (m-30) outliers start: 73 outliers final: 56 residues processed: 312 average time/residue: 0.2657 time to fit residues: 119.7538 Evaluate side-chains 326 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 264 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain E residue 9 PHE Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 153 ARG Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 23 GLU Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 74 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 0.0570 chunk 157 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 153 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 120 optimal weight: 0.0970 chunk 47 optimal weight: 0.4980 chunk 138 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN F 105 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14570 Z= 0.193 Angle : 0.621 10.212 19725 Z= 0.319 Chirality : 0.045 0.272 2217 Planarity : 0.004 0.052 2543 Dihedral : 9.277 68.629 2442 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 4.07 % Allowed : 32.87 % Favored : 63.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % 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: -2.60 (0.18), residues: 1732 helix: 0.25 (0.25), residues: 375 sheet: -1.01 (0.32), residues: 270 loop : -2.84 (0.16), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 70 HIS 0.006 0.001 HIS B 17 PHE 0.010 0.001 PHE B 148 TYR 0.016 0.001 TYR C 302 ARG 0.006 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 268 time to evaluate : 1.536 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: A 104 ASP cc_start: 0.6102 (OUTLIER) cc_final: 0.5731 (t70) REVERT: A 267 ILE cc_start: 0.5169 (tt) cc_final: 0.4646 (tp) REVERT: D 90 ASP cc_start: 0.6444 (m-30) cc_final: 0.6189 (m-30) REVERT: D 132 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6626 (tt0) REVERT: D 159 HIS cc_start: 0.7227 (p90) cc_final: 0.6966 (p90) REVERT: B 18 HIS cc_start: 0.6987 (OUTLIER) cc_final: 0.6114 (p-80) REVERT: B 70 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6826 (mp) REVERT: B 78 VAL cc_start: 0.8259 (OUTLIER) cc_final: 0.7972 (t) REVERT: B 259 LYS cc_start: 0.8345 (mptt) cc_final: 0.8136 (mptt) REVERT: B 297 VAL cc_start: 0.7477 (t) cc_final: 0.7184 (m) REVERT: E 86 ASP cc_start: 0.6327 (t0) cc_final: 0.6035 (t0) REVERT: E 90 ASP cc_start: 0.6053 (m-30) cc_final: 0.5667 (m-30) REVERT: F 17 MET cc_start: 0.4219 (mmm) cc_final: 0.2598 (mmm) REVERT: F 90 ASP cc_start: 0.6310 (OUTLIER) cc_final: 0.6082 (m-30) outliers start: 62 outliers final: 48 residues processed: 305 average time/residue: 0.2604 time to fit residues: 114.7031 Evaluate side-chains 320 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 266 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain E residue 9 PHE Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 23 GLU Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 77 optimal weight: 0.0030 chunk 112 optimal weight: 0.0970 chunk 170 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 14 optimal weight: 0.0980 chunk 104 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14570 Z= 0.185 Angle : 0.622 9.759 19725 Z= 0.319 Chirality : 0.045 0.276 2217 Planarity : 0.004 0.051 2543 Dihedral : 8.881 63.999 2442 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 3.74 % Allowed : 33.40 % Favored : 62.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % 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: -2.53 (0.18), residues: 1732 helix: 0.30 (0.25), residues: 366 sheet: -0.92 (0.34), residues: 255 loop : -2.76 (0.16), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 70 HIS 0.006 0.001 HIS C 17 PHE 0.009 0.001 PHE B 148 TYR 0.022 0.001 TYR D 83 ARG 0.005 0.000 ARG A 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 264 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.6121 (OUTLIER) cc_final: 0.5763 (t70) REVERT: A 267 ILE cc_start: 0.5139 (tt) cc_final: 0.4620 (tp) REVERT: D 90 ASP cc_start: 0.6434 (m-30) cc_final: 0.6187 (m-30) REVERT: D 132 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6630 (tt0) REVERT: D 159 HIS cc_start: 0.7259 (p90) cc_final: 0.6982 (p90) REVERT: B 18 HIS cc_start: 0.6962 (OUTLIER) cc_final: 0.6132 (p-80) REVERT: B 70 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6806 (mp) REVERT: B 78 VAL cc_start: 0.8254 (OUTLIER) cc_final: 0.7959 (t) REVERT: E 86 ASP cc_start: 0.6330 (t0) cc_final: 0.5987 (t0) REVERT: E 90 ASP cc_start: 0.5993 (m-30) cc_final: 0.5601 (m-30) REVERT: H 57 LYS cc_start: 0.8351 (tptp) cc_final: 0.8075 (tptp) REVERT: F 17 MET cc_start: 0.4005 (mmm) cc_final: 0.2598 (mmm) REVERT: F 90 ASP cc_start: 0.6281 (OUTLIER) cc_final: 0.6069 (m-30) outliers start: 57 outliers final: 49 residues processed: 297 average time/residue: 0.2606 time to fit residues: 112.1295 Evaluate side-chains 317 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 262 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain E residue 9 PHE Chi-restraints excluded: chain E residue 19 ASP Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 23 GLU Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 37 optimal weight: 0.2980 chunk 135 optimal weight: 0.9990 chunk 56 optimal weight: 0.0570 chunk 139 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.158066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.134567 restraints weight = 21537.585| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.92 r_work: 0.3778 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14570 Z= 0.212 Angle : 0.627 9.377 19725 Z= 0.322 Chirality : 0.045 0.269 2217 Planarity : 0.004 0.053 2543 Dihedral : 8.818 62.865 2442 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 4.00 % Allowed : 32.94 % Favored : 63.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % 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: -2.50 (0.18), residues: 1732 helix: 0.41 (0.25), residues: 369 sheet: -0.87 (0.34), residues: 255 loop : -2.79 (0.16), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 70 HIS 0.006 0.001 HIS C 17 PHE 0.010 0.001 PHE B 148 TYR 0.025 0.001 TYR D 83 ARG 0.004 0.000 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3663.23 seconds wall clock time: 65 minutes 59.96 seconds (3959.96 seconds total)