Starting phenix.real_space_refine on Sat Oct 11 11:47:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pk3_17724/10_2025/8pk3_17724.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pk3_17724/10_2025/8pk3_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/cci-nas-00/data/ceres_data/8pk3_17724/10_2025/8pk3_17724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pk3_17724/10_2025/8pk3_17724.map" model { file = "/net/cci-nas-00/data/ceres_data/8pk3_17724/10_2025/8pk3_17724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pk3_17724/10_2025/8pk3_17724.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 3.57, per 1000 atoms: 0.25 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=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: 1.31 Conformation dependent library (CDL) restraints added in 672.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.49 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: 2.31 Time building geometry restraints manager: 1.69 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: 0.00 - 2.95: 19344 2.95 - 5.89: 324 5.89 - 8.84: 46 8.84 - 11.78: 7 11.78 - 14.73: 4 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 3.120 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 Time spend for trying shortcut: 0.01 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: 4.450 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.270 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.750 ------------------------------------------------------------------------------- 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 14615 Z= 0.256 Angle : 0.970 14.730 19842 Z= 0.502 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.018 0.001 ARG A 208 TYR 0.031 0.002 TYR B 302 PHE 0.025 0.002 PHE B 258 TRP 0.016 0.002 TRP I 44 HIS 0.015 0.002 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00533 (14570) covalent geometry : angle 0.95648 (19725) SS BOND : bond 0.00702 ( 18) SS BOND : angle 2.25737 ( 36) hydrogen bonds : bond 0.29514 ( 401) hydrogen bonds : angle 9.65849 ( 1164) link_ALPHA1-3 : bond 0.00695 ( 3) link_ALPHA1-3 : angle 4.76921 ( 9) link_ALPHA1-6 : bond 0.00519 ( 3) link_ALPHA1-6 : angle 1.44330 ( 9) link_BETA1-4 : bond 0.00895 ( 9) link_BETA1-4 : angle 1.33610 ( 27) link_NAG-ASN : bond 0.00702 ( 12) link_NAG-ASN : angle 2.18907 ( 36) *********************** 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 to be fit. rotamer outliers: 11 poor density : 265 time to evaluate : 0.533 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: 0.1296 time to fit residues: 51.3954 Evaluate side-chains 265 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 259 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 250 ASN D 28 ASN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 HIS B 191 GLN E 28 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 ASN H 20 ASN ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.158077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.133762 restraints weight = 21604.438| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 3.09 r_work: 0.3750 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 14615 Z= 0.182 Angle : 0.671 8.012 19842 Z= 0.348 Chirality : 0.046 0.277 2217 Planarity : 0.005 0.054 2543 Dihedral : 11.869 93.318 2453 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 5.25 % Allowed : 27.69 % Favored : 67.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.71 (0.18), residues: 1732 helix: -0.20 (0.24), residues: 372 sheet: -1.01 (0.34), residues: 255 loop : -2.76 (0.15), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 208 TYR 0.013 0.002 TYR C 105 PHE 0.014 0.002 PHE B 125 TRP 0.012 0.002 TRP I 44 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00390 (14570) covalent geometry : angle 0.65355 (19725) SS BOND : bond 0.00310 ( 18) SS BOND : angle 1.72416 ( 36) hydrogen bonds : bond 0.07455 ( 401) hydrogen bonds : angle 6.29928 ( 1164) link_ALPHA1-3 : bond 0.00148 ( 3) link_ALPHA1-3 : angle 4.32297 ( 9) link_ALPHA1-6 : bond 0.00345 ( 3) link_ALPHA1-6 : angle 1.91906 ( 9) link_BETA1-4 : bond 0.00866 ( 9) link_BETA1-4 : angle 1.43322 ( 27) link_NAG-ASN : bond 0.00606 ( 12) link_NAG-ASN : angle 1.92153 ( 36) *********************** 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 343 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 263 time to evaluate : 0.499 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: 0.6670 (mm-30) cc_final: 0.6358 (mm-30) REVERT: G 49 MET cc_start: 0.6888 (tmm) cc_final: 0.6678 (tmm) REVERT: B 18 HIS cc_start: 0.7291 (OUTLIER) cc_final: 0.6066 (p-80) REVERT: B 203 THR cc_start: 0.7276 (m) cc_final: 0.7026 (p) REVERT: E 9 PHE cc_start: 0.6177 (OUTLIER) cc_final: 0.5673 (p90) REVERT: E 45 ILE cc_start: 0.6963 (mt) cc_final: 0.6536 (tp) REVERT: E 86 ASP cc_start: 0.6688 (t0) cc_final: 0.6062 (t0) REVERT: E 90 ASP cc_start: 0.6599 (m-30) cc_final: 0.6330 (m-30) REVERT: E 111 THR cc_start: 0.7326 (p) cc_final: 0.6928 (p) REVERT: H 6 LEU cc_start: 0.5627 (OUTLIER) cc_final: 0.5425 (pp) REVERT: C 261 ARG cc_start: 0.7971 (ttm110) cc_final: 0.7428 (tpp80) REVERT: F 42 GLN cc_start: 0.7952 (tp-100) cc_final: 0.7120 (tp40) REVERT: F 62 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7024 (mmtm) REVERT: F 90 ASP cc_start: 0.6947 (m-30) cc_final: 0.6621 (m-30) REVERT: F 157 TYR cc_start: 0.7673 (t80) cc_final: 0.7452 (t80) outliers start: 80 outliers final: 40 residues processed: 316 average time/residue: 0.1212 time to fit residues: 56.2450 Evaluate side-chains 303 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 259 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 HIS 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 320 MET Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain G residue 32 VAL 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 132 GLN 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 28 ASN Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 137 CYS Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 32 VAL 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 F residue 9 PHE Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 116 ASN 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 32 VAL 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 96 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 132 optimal weight: 0.0980 chunk 157 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 HIS E 28 ASN E 104 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN F 34 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.156459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.132355 restraints weight = 21686.578| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 3.09 r_work: 0.3748 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14615 Z= 0.172 Angle : 0.645 8.249 19842 Z= 0.331 Chirality : 0.045 0.279 2217 Planarity : 0.004 0.055 2543 Dihedral : 11.076 88.811 2446 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 4.72 % Allowed : 28.41 % Favored : 66.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.61 (0.18), residues: 1732 helix: 0.08 (0.24), residues: 372 sheet: -1.10 (0.34), residues: 261 loop : -2.73 (0.16), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 224 TYR 0.012 0.001 TYR C 105 PHE 0.013 0.002 PHE B 125 TRP 0.012 0.002 TRP B 153 HIS 0.004 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00367 (14570) covalent geometry : angle 0.62660 (19725) SS BOND : bond 0.00418 ( 18) SS BOND : angle 1.94035 ( 36) hydrogen bonds : bond 0.06662 ( 401) hydrogen bonds : angle 5.99736 ( 1164) link_ALPHA1-3 : bond 0.00103 ( 3) link_ALPHA1-3 : angle 4.10744 ( 9) link_ALPHA1-6 : bond 0.00329 ( 3) link_ALPHA1-6 : angle 1.86963 ( 9) link_BETA1-4 : bond 0.00743 ( 9) link_BETA1-4 : angle 1.48672 ( 27) link_NAG-ASN : bond 0.00647 ( 12) link_NAG-ASN : angle 1.93510 ( 36) *********************** 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 347 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 275 time to evaluate : 0.551 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: symmetry clash REVERT: D 90 ASP cc_start: 0.6952 (m-30) cc_final: 0.6600 (m-30) REVERT: D 114 GLU cc_start: 0.6704 (mm-30) cc_final: 0.6429 (mm-30) REVERT: G 49 MET cc_start: 0.6897 (tmm) cc_final: 0.6471 (tmm) REVERT: B 18 HIS cc_start: 0.7124 (OUTLIER) cc_final: 0.5988 (p-80) REVERT: B 201 ARG cc_start: 0.7603 (ttp80) cc_final: 0.7340 (ptm-80) REVERT: E 9 PHE cc_start: 0.6212 (OUTLIER) cc_final: 0.5689 (p90) REVERT: E 45 ILE cc_start: 0.6895 (mt) cc_final: 0.6611 (tp) REVERT: E 103 GLU cc_start: 0.7188 (mp0) cc_final: 0.6778 (mm-30) REVERT: E 111 THR cc_start: 0.7297 (p) cc_final: 0.6838 (p) REVERT: C 118 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8001 (tt) REVERT: C 261 ARG cc_start: 0.7956 (ttm110) cc_final: 0.7402 (tpp80) REVERT: F 42 GLN cc_start: 0.8086 (tp40) cc_final: 0.7722 (tp40) REVERT: F 90 ASP cc_start: 0.6945 (m-30) cc_final: 0.6536 (m-30) REVERT: F 135 ASN cc_start: 0.7175 (t0) cc_final: 0.6954 (t0) outliers start: 72 outliers final: 42 residues processed: 320 average time/residue: 0.1238 time to fit residues: 58.3943 Evaluate side-chains 313 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 268 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 92 LYS Chi-restraints excluded: chain A residue 132 GLN 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 320 MET Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 164 ASP 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 132 GLN 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 73 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 137 CYS 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 118 LEU Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 99 LEU 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 74 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 93 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 158 optimal weight: 0.0870 chunk 111 optimal weight: 0.0770 chunk 86 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 overall best weight: 0.5916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 HIS E 28 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.156592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.132751 restraints weight = 21690.134| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 3.04 r_work: 0.3754 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14615 Z= 0.168 Angle : 0.638 8.464 19842 Z= 0.326 Chirality : 0.045 0.278 2217 Planarity : 0.004 0.054 2543 Dihedral : 10.635 84.956 2446 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 5.45 % Allowed : 28.02 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.59 (0.18), residues: 1732 helix: 0.11 (0.24), residues: 375 sheet: -1.25 (0.31), residues: 291 loop : -2.70 (0.16), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 224 TYR 0.015 0.001 TYR C 105 PHE 0.012 0.002 PHE B 125 TRP 0.013 0.001 TRP B 153 HIS 0.005 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00360 (14570) covalent geometry : angle 0.61735 (19725) SS BOND : bond 0.00500 ( 18) SS BOND : angle 2.04974 ( 36) hydrogen bonds : bond 0.06229 ( 401) hydrogen bonds : angle 5.81209 ( 1164) link_ALPHA1-3 : bond 0.00072 ( 3) link_ALPHA1-3 : angle 4.09341 ( 9) link_ALPHA1-6 : bond 0.00316 ( 3) link_ALPHA1-6 : angle 1.80503 ( 9) link_BETA1-4 : bond 0.00710 ( 9) link_BETA1-4 : angle 1.46275 ( 27) link_NAG-ASN : bond 0.00655 ( 12) link_NAG-ASN : angle 2.11877 ( 36) *********************** 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 355 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 272 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.6700 (OUTLIER) cc_final: 0.6449 (t0) REVERT: D 90 ASP cc_start: 0.6998 (m-30) cc_final: 0.6698 (m-30) REVERT: D 114 GLU cc_start: 0.6716 (mm-30) cc_final: 0.6437 (mm-30) REVERT: G 49 MET cc_start: 0.6919 (tmm) cc_final: 0.6554 (tmm) REVERT: B 18 HIS cc_start: 0.7100 (OUTLIER) cc_final: 0.5997 (p-80) REVERT: E 86 ASP cc_start: 0.6770 (t0) cc_final: 0.6485 (t0) REVERT: E 111 THR cc_start: 0.7162 (p) cc_final: 0.6934 (p) REVERT: F 42 GLN cc_start: 0.8131 (tp40) cc_final: 0.7754 (tp40) REVERT: F 90 ASP cc_start: 0.6842 (m-30) cc_final: 0.6478 (m-30) outliers start: 83 outliers final: 53 residues processed: 325 average time/residue: 0.1256 time to fit residues: 59.7007 Evaluate side-chains 319 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 264 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 320 MET Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 104 ASN 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 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 132 GLN 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 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 133 MET Chi-restraints excluded: chain E residue 137 CYS Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 132 GLN 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 193 SER Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 116 ASN 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 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 52 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 159 optimal weight: 0.9980 chunk 135 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 HIS E 34 GLN E 104 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.155734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.131698 restraints weight = 21713.365| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 3.04 r_work: 0.3737 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14615 Z= 0.183 Angle : 0.646 8.535 19842 Z= 0.331 Chirality : 0.045 0.275 2217 Planarity : 0.004 0.056 2543 Dihedral : 10.403 83.009 2446 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 5.25 % Allowed : 29.00 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.63 (0.18), residues: 1732 helix: 0.07 (0.24), residues: 381 sheet: -1.26 (0.31), residues: 291 loop : -2.75 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 208 TYR 0.014 0.002 TYR C 105 PHE 0.014 0.002 PHE B 125 TRP 0.013 0.002 TRP B 153 HIS 0.004 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00394 (14570) covalent geometry : angle 0.62673 (19725) SS BOND : bond 0.00483 ( 18) SS BOND : angle 1.95400 ( 36) hydrogen bonds : bond 0.06269 ( 401) hydrogen bonds : angle 5.77178 ( 1164) link_ALPHA1-3 : bond 0.00102 ( 3) link_ALPHA1-3 : angle 4.03745 ( 9) link_ALPHA1-6 : bond 0.00253 ( 3) link_ALPHA1-6 : angle 1.77901 ( 9) link_BETA1-4 : bond 0.00661 ( 9) link_BETA1-4 : angle 1.50614 ( 27) link_NAG-ASN : bond 0.00624 ( 12) link_NAG-ASN : angle 2.07014 ( 36) *********************** 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 350 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 270 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.6322 (tt) cc_final: 0.6045 (tt) REVERT: A 104 ASP cc_start: 0.6717 (OUTLIER) cc_final: 0.6469 (t0) REVERT: A 297 VAL cc_start: 0.7642 (t) cc_final: 0.7324 (m) REVERT: D 42 GLN cc_start: 0.8400 (tp40) cc_final: 0.7902 (tp40) REVERT: D 90 ASP cc_start: 0.7016 (m-30) cc_final: 0.6697 (m-30) REVERT: D 114 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6506 (mm-30) REVERT: G 23 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7238 (pm20) REVERT: G 36 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7419 (pttm) REVERT: G 49 MET cc_start: 0.6933 (tmm) cc_final: 0.6566 (tmm) REVERT: B 18 HIS cc_start: 0.7106 (OUTLIER) cc_final: 0.5961 (p-80) REVERT: E 27 GLN cc_start: 0.7586 (tm-30) cc_final: 0.7351 (tm-30) REVERT: E 42 GLN cc_start: 0.8315 (tp40) cc_final: 0.8074 (tp40) REVERT: C 64 CYS cc_start: 0.5125 (m) cc_final: 0.4836 (m) REVERT: C 118 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8045 (tt) REVERT: C 191 GLN cc_start: 0.5924 (OUTLIER) cc_final: 0.5504 (tp40) REVERT: F 90 ASP cc_start: 0.6987 (m-30) cc_final: 0.6587 (m-30) outliers start: 80 outliers final: 56 residues processed: 320 average time/residue: 0.1268 time to fit residues: 59.0633 Evaluate side-chains 325 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 263 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 228 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain D residue 28 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 104 ASN 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 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 92 LYS Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 268 MET 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 47 GLN Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 133 MET 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 118 LEU Chi-restraints excluded: chain C residue 132 GLN 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 251 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 283 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 28 ASN Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 140 ILE 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 46 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 67 optimal weight: 0.0980 chunk 44 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 123 optimal weight: 0.1980 chunk 42 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 HIS E 28 ASN E 104 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.157442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.133433 restraints weight = 21660.197| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 3.07 r_work: 0.3755 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14615 Z= 0.144 Angle : 0.627 10.162 19842 Z= 0.319 Chirality : 0.045 0.284 2217 Planarity : 0.004 0.054 2543 Dihedral : 9.869 77.716 2446 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 5.58 % Allowed : 29.59 % Favored : 64.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.57 (0.18), residues: 1732 helix: 0.16 (0.25), residues: 381 sheet: -1.21 (0.31), residues: 291 loop : -2.73 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 170 TYR 0.015 0.001 TYR C 308 PHE 0.010 0.001 PHE B 148 TRP 0.012 0.001 TRP B 153 HIS 0.005 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00307 (14570) covalent geometry : angle 0.60985 (19725) SS BOND : bond 0.00370 ( 18) SS BOND : angle 1.74031 ( 36) hydrogen bonds : bond 0.05835 ( 401) hydrogen bonds : angle 5.65639 ( 1164) link_ALPHA1-3 : bond 0.00051 ( 3) link_ALPHA1-3 : angle 4.17856 ( 9) link_ALPHA1-6 : bond 0.00375 ( 3) link_ALPHA1-6 : angle 1.72258 ( 9) link_BETA1-4 : bond 0.00625 ( 9) link_BETA1-4 : angle 1.42874 ( 27) link_NAG-ASN : bond 0.00586 ( 12) link_NAG-ASN : angle 1.88974 ( 36) *********************** 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 346 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 261 time to evaluate : 0.521 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: 0.6702 (OUTLIER) cc_final: 0.6398 (t0) REVERT: D 42 GLN cc_start: 0.8328 (tp40) cc_final: 0.7757 (tp40) REVERT: D 90 ASP cc_start: 0.6926 (m-30) cc_final: 0.6592 (m-30) REVERT: D 114 GLU cc_start: 0.6780 (mm-30) cc_final: 0.6531 (mm-30) REVERT: G 23 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7266 (pm20) REVERT: G 26 LEU cc_start: 0.5039 (OUTLIER) cc_final: 0.4749 (tt) REVERT: G 49 MET cc_start: 0.6915 (tmm) cc_final: 0.6545 (tmm) REVERT: B 18 HIS cc_start: 0.7110 (OUTLIER) cc_final: 0.6025 (p-80) REVERT: B 70 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6923 (mp) REVERT: E 42 GLN cc_start: 0.8304 (tp40) cc_final: 0.8033 (tp40) REVERT: C 64 CYS cc_start: 0.5147 (OUTLIER) cc_final: 0.4869 (m) REVERT: F 90 ASP cc_start: 0.6929 (OUTLIER) cc_final: 0.6528 (m-30) outliers start: 85 outliers final: 55 residues processed: 317 average time/residue: 0.1162 time to fit residues: 53.9780 Evaluate side-chains 318 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 256 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 227 SER 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 28 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain G residue 23 GLU Chi-restraints excluded: chain G residue 26 LEU 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 33 GLN Chi-restraints excluded: chain B residue 36 VAL 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 121 ILE Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain B residue 280 GLU 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 110 LEU Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 132 GLN 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 193 SER Chi-restraints excluded: chain C residue 204 VAL 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 C residue 283 THR Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 132 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 125 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 HIS E 28 ASN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.157943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.133775 restraints weight = 21542.911| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 3.07 r_work: 0.3733 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14615 Z= 0.204 Angle : 0.669 12.091 19842 Z= 0.342 Chirality : 0.046 0.269 2217 Planarity : 0.004 0.056 2543 Dihedral : 9.995 78.768 2446 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 5.51 % Allowed : 29.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.47 (0.18), residues: 1732 helix: 0.10 (0.24), residues: 381 sheet: 0.39 (0.41), residues: 189 loop : -2.83 (0.15), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 208 TYR 0.015 0.002 TYR C 308 PHE 0.017 0.002 PHE B 125 TRP 0.013 0.002 TRP B 153 HIS 0.007 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00443 (14570) covalent geometry : angle 0.65075 (19725) SS BOND : bond 0.00510 ( 18) SS BOND : angle 2.00335 ( 36) hydrogen bonds : bond 0.06192 ( 401) hydrogen bonds : angle 5.74150 ( 1164) link_ALPHA1-3 : bond 0.00195 ( 3) link_ALPHA1-3 : angle 3.92117 ( 9) link_ALPHA1-6 : bond 0.00220 ( 3) link_ALPHA1-6 : angle 1.76658 ( 9) link_BETA1-4 : bond 0.00630 ( 9) link_BETA1-4 : angle 1.53859 ( 27) link_NAG-ASN : bond 0.00614 ( 12) link_NAG-ASN : angle 2.12462 ( 36) *********************** 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 353 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 269 time to evaluate : 0.636 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: 0.6752 (OUTLIER) cc_final: 0.6455 (t0) REVERT: A 297 VAL cc_start: 0.7704 (t) cc_final: 0.7369 (m) REVERT: A 320 MET cc_start: 0.6406 (OUTLIER) cc_final: 0.6124 (ptp) REVERT: D 42 GLN cc_start: 0.8317 (tp40) cc_final: 0.7809 (tp40) REVERT: D 90 ASP cc_start: 0.7049 (m-30) cc_final: 0.6733 (m-30) REVERT: D 114 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6561 (mm-30) REVERT: D 160 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7464 (t0) REVERT: G 49 MET cc_start: 0.6925 (tmm) cc_final: 0.6573 (tmm) REVERT: B 70 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6933 (mp) REVERT: B 118 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8244 (tt) REVERT: B 201 ARG cc_start: 0.7604 (ttp80) cc_final: 0.7219 (ttp80) REVERT: E 42 GLN cc_start: 0.8335 (tp40) cc_final: 0.7990 (tp40) REVERT: E 86 ASP cc_start: 0.7077 (t0) cc_final: 0.6494 (t0) REVERT: E 90 ASP cc_start: 0.6574 (m-30) cc_final: 0.6013 (m-30) REVERT: E 131 GLU cc_start: 0.7323 (mm-30) cc_final: 0.7100 (mm-30) REVERT: C 34 ILE cc_start: 0.6342 (tt) cc_final: 0.5555 (tp) REVERT: C 191 GLN cc_start: 0.5866 (OUTLIER) cc_final: 0.5422 (tp40) REVERT: F 42 GLN cc_start: 0.8233 (tp40) cc_final: 0.7918 (tp40) REVERT: F 90 ASP cc_start: 0.6932 (OUTLIER) cc_final: 0.6523 (m-30) outliers start: 84 outliers final: 58 residues processed: 323 average time/residue: 0.1158 time to fit residues: 55.5222 Evaluate side-chains 334 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 269 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 227 SER 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 28 ASN Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 160 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 33 GLN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 132 GLN 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 268 MET Chi-restraints excluded: chain B residue 280 GLU 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 47 GLN Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 110 LEU 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 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 251 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 132 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 147 optimal weight: 0.0980 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.158296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.134146 restraints weight = 21536.956| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 3.09 r_work: 0.3738 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14615 Z= 0.188 Angle : 0.667 11.452 19842 Z= 0.343 Chirality : 0.046 0.271 2217 Planarity : 0.004 0.056 2543 Dihedral : 9.749 76.126 2446 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 4.99 % Allowed : 30.31 % Favored : 64.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.60 (0.18), residues: 1732 helix: 0.07 (0.24), residues: 381 sheet: -0.73 (0.36), residues: 249 loop : -2.83 (0.15), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 224 TYR 0.015 0.002 TYR C 105 PHE 0.015 0.002 PHE B 125 TRP 0.014 0.002 TRP B 153 HIS 0.006 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00407 (14570) covalent geometry : angle 0.64845 (19725) SS BOND : bond 0.00466 ( 18) SS BOND : angle 2.09204 ( 36) hydrogen bonds : bond 0.06028 ( 401) hydrogen bonds : angle 5.75861 ( 1164) link_ALPHA1-3 : bond 0.00211 ( 3) link_ALPHA1-3 : angle 3.99253 ( 9) link_ALPHA1-6 : bond 0.00261 ( 3) link_ALPHA1-6 : angle 1.68914 ( 9) link_BETA1-4 : bond 0.00587 ( 9) link_BETA1-4 : angle 1.51571 ( 27) link_NAG-ASN : bond 0.00573 ( 12) link_NAG-ASN : angle 2.08756 ( 36) *********************** 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 344 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 268 time to evaluate : 0.443 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: 0.6764 (OUTLIER) cc_final: 0.6444 (t0) REVERT: A 201 ARG cc_start: 0.7601 (ttp80) cc_final: 0.7211 (ttp80) REVERT: A 297 VAL cc_start: 0.7699 (t) cc_final: 0.7384 (m) REVERT: A 320 MET cc_start: 0.6355 (OUTLIER) cc_final: 0.6123 (ptp) REVERT: D 90 ASP cc_start: 0.7027 (m-30) cc_final: 0.6708 (m-30) REVERT: D 114 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6627 (mm-30) REVERT: D 132 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6764 (tt0) REVERT: D 160 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7416 (t0) REVERT: G 26 LEU cc_start: 0.5074 (OUTLIER) cc_final: 0.4871 (tt) REVERT: G 49 MET cc_start: 0.6963 (tmm) cc_final: 0.6459 (tmm) REVERT: B 18 HIS cc_start: 0.7093 (OUTLIER) cc_final: 0.6305 (p-80) REVERT: B 70 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6942 (mp) REVERT: B 201 ARG cc_start: 0.7575 (ttp80) cc_final: 0.7197 (ttp80) REVERT: B 320 MET cc_start: 0.5887 (ptp) cc_final: 0.5468 (ptp) REVERT: E 42 GLN cc_start: 0.8295 (tp40) cc_final: 0.7936 (tp40) REVERT: E 86 ASP cc_start: 0.7062 (t0) cc_final: 0.6481 (t0) REVERT: E 90 ASP cc_start: 0.6539 (m-30) cc_final: 0.5955 (m-30) REVERT: E 141 TYR cc_start: 0.7015 (m-80) cc_final: 0.6787 (m-80) REVERT: C 104 ASP cc_start: 0.7360 (t70) cc_final: 0.6981 (t70) REVERT: C 191 GLN cc_start: 0.5908 (OUTLIER) cc_final: 0.5457 (tp40) REVERT: F 17 MET cc_start: 0.4140 (mmm) cc_final: 0.2943 (mmm) REVERT: F 90 ASP cc_start: 0.6926 (OUTLIER) cc_final: 0.6575 (m-30) REVERT: F 99 LEU cc_start: 0.6733 (OUTLIER) cc_final: 0.6476 (tt) outliers start: 76 outliers final: 56 residues processed: 321 average time/residue: 0.1278 time to fit residues: 59.7839 Evaluate side-chains 329 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 263 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 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 28 ASN Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 104 ASN 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 160 ASP Chi-restraints excluded: chain G residue 26 LEU 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 92 LYS Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 132 GLN 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 227 SER Chi-restraints excluded: chain E residue 6 ILE 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 110 LEU 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 227 SER 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 C residue 283 THR Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain F residue 132 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 0.5980 chunk 170 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 166 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.158463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.134216 restraints weight = 21610.123| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 3.09 r_work: 0.3735 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14615 Z= 0.191 Angle : 0.672 10.871 19842 Z= 0.345 Chirality : 0.046 0.269 2217 Planarity : 0.005 0.069 2543 Dihedral : 9.642 74.811 2446 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 4.59 % Allowed : 31.23 % Favored : 64.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.59 (0.18), residues: 1732 helix: 0.11 (0.24), residues: 381 sheet: -0.42 (0.38), residues: 219 loop : -2.86 (0.15), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 208 TYR 0.015 0.002 TYR C 308 PHE 0.016 0.002 PHE B 125 TRP 0.013 0.002 TRP B 153 HIS 0.006 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00415 (14570) covalent geometry : angle 0.65359 (19725) SS BOND : bond 0.00474 ( 18) SS BOND : angle 2.05940 ( 36) hydrogen bonds : bond 0.06008 ( 401) hydrogen bonds : angle 5.76233 ( 1164) link_ALPHA1-3 : bond 0.00224 ( 3) link_ALPHA1-3 : angle 3.92935 ( 9) link_ALPHA1-6 : bond 0.00240 ( 3) link_ALPHA1-6 : angle 1.66972 ( 9) link_BETA1-4 : bond 0.00589 ( 9) link_BETA1-4 : angle 1.52935 ( 27) link_NAG-ASN : bond 0.00580 ( 12) link_NAG-ASN : angle 2.10430 ( 36) *********************** 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 334 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 264 time to evaluate : 0.379 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: 0.6783 (OUTLIER) cc_final: 0.6468 (t0) REVERT: A 201 ARG cc_start: 0.7637 (ttp80) cc_final: 0.7304 (ttp80) REVERT: A 297 VAL cc_start: 0.7710 (t) cc_final: 0.7396 (m) REVERT: D 90 ASP cc_start: 0.7050 (m-30) cc_final: 0.6720 (m-30) REVERT: D 114 GLU cc_start: 0.6844 (mm-30) cc_final: 0.6631 (mm-30) REVERT: D 132 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6800 (tt0) REVERT: D 160 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7451 (t0) REVERT: G 26 LEU cc_start: 0.5077 (OUTLIER) cc_final: 0.4873 (tt) REVERT: G 49 MET cc_start: 0.6948 (tmm) cc_final: 0.6440 (tmm) REVERT: B 70 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6967 (mp) REVERT: B 201 ARG cc_start: 0.7596 (ttp80) cc_final: 0.7228 (ttp80) REVERT: B 320 MET cc_start: 0.5845 (ptp) cc_final: 0.5495 (ptp) REVERT: E 42 GLN cc_start: 0.8270 (tp40) cc_final: 0.7932 (tp40) REVERT: E 86 ASP cc_start: 0.7080 (t0) cc_final: 0.6636 (t0) REVERT: E 141 TYR cc_start: 0.7015 (m-80) cc_final: 0.6790 (m-80) REVERT: C 104 ASP cc_start: 0.7420 (t70) cc_final: 0.7006 (t70) REVERT: F 17 MET cc_start: 0.4128 (mmm) cc_final: 0.2805 (mmm) REVERT: F 90 ASP cc_start: 0.6915 (OUTLIER) cc_final: 0.6542 (m-30) REVERT: F 99 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6527 (tt) outliers start: 70 outliers final: 61 residues processed: 310 average time/residue: 0.1168 time to fit residues: 52.9309 Evaluate side-chains 332 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 264 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 97 CYS 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 227 SER 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 28 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 104 ASN 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 160 ASP Chi-restraints excluded: chain G residue 26 LEU 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 92 LYS Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 132 GLN 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 268 MET Chi-restraints excluded: chain E residue 6 ILE 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 110 LEU 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 193 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 227 SER 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 C residue 283 THR Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 114 GLU 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 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 116 optimal weight: 0.4980 chunk 24 optimal weight: 0.3980 chunk 51 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 125 optimal weight: 0.3980 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN E 78 GLN ** E 129 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.158928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.134760 restraints weight = 21562.404| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 3.09 r_work: 0.3742 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14615 Z= 0.174 Angle : 0.673 10.704 19842 Z= 0.347 Chirality : 0.046 0.271 2217 Planarity : 0.004 0.056 2543 Dihedral : 9.405 72.072 2446 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 4.86 % Allowed : 31.17 % Favored : 63.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.56 (0.18), residues: 1732 helix: 0.13 (0.24), residues: 381 sheet: -0.70 (0.35), residues: 249 loop : -2.81 (0.15), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 208 TYR 0.015 0.001 TYR C 105 PHE 0.013 0.002 PHE B 125 TRP 0.013 0.002 TRP B 153 HIS 0.007 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00376 (14570) covalent geometry : angle 0.65540 (19725) SS BOND : bond 0.00471 ( 18) SS BOND : angle 1.99781 ( 36) hydrogen bonds : bond 0.05927 ( 401) hydrogen bonds : angle 5.77587 ( 1164) link_ALPHA1-3 : bond 0.00171 ( 3) link_ALPHA1-3 : angle 3.94819 ( 9) link_ALPHA1-6 : bond 0.00328 ( 3) link_ALPHA1-6 : angle 1.61743 ( 9) link_BETA1-4 : bond 0.00567 ( 9) link_BETA1-4 : angle 1.50460 ( 27) link_NAG-ASN : bond 0.00565 ( 12) link_NAG-ASN : angle 2.04374 ( 36) ********************** 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 333 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 259 time to evaluate : 0.392 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: 0.6764 (OUTLIER) cc_final: 0.6433 (t0) REVERT: A 201 ARG cc_start: 0.7629 (ttp80) cc_final: 0.7292 (ttp80) REVERT: A 297 VAL cc_start: 0.7694 (t) cc_final: 0.7376 (m) REVERT: A 320 MET cc_start: 0.6321 (OUTLIER) cc_final: 0.6063 (ptp) REVERT: D 90 ASP cc_start: 0.7008 (m-30) cc_final: 0.6704 (m-30) REVERT: D 114 GLU cc_start: 0.6865 (mm-30) cc_final: 0.6640 (mm-30) REVERT: D 132 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6818 (tt0) REVERT: D 160 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7467 (t0) REVERT: G 26 LEU cc_start: 0.5094 (OUTLIER) cc_final: 0.4893 (tt) REVERT: G 49 MET cc_start: 0.6927 (tmm) cc_final: 0.6425 (tmm) REVERT: B 18 HIS cc_start: 0.7019 (OUTLIER) cc_final: 0.6387 (p-80) REVERT: B 70 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6951 (mp) REVERT: B 201 ARG cc_start: 0.7553 (ttp80) cc_final: 0.7186 (ttp80) REVERT: B 320 MET cc_start: 0.5809 (ptp) cc_final: 0.5449 (ptp) REVERT: E 42 GLN cc_start: 0.8272 (tp40) cc_final: 0.7935 (tp40) REVERT: E 86 ASP cc_start: 0.7090 (t0) cc_final: 0.6552 (t0) REVERT: E 90 ASP cc_start: 0.6573 (m-30) cc_final: 0.6023 (m-30) REVERT: E 141 TYR cc_start: 0.7000 (m-80) cc_final: 0.6760 (m-80) REVERT: H 49 MET cc_start: 0.7078 (ppp) cc_final: 0.6855 (tmm) REVERT: C 104 ASP cc_start: 0.7412 (t70) cc_final: 0.6994 (t70) REVERT: F 17 MET cc_start: 0.4216 (mmm) cc_final: 0.2921 (mmm) REVERT: F 90 ASP cc_start: 0.6934 (OUTLIER) cc_final: 0.6560 (m-30) outliers start: 74 outliers final: 60 residues processed: 308 average time/residue: 0.1182 time to fit residues: 53.3053 Evaluate side-chains 325 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 257 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 97 CYS 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 227 SER 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 28 ASN Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain G residue 26 LEU 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 33 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 132 GLN 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 227 SER Chi-restraints excluded: chain E residue 6 ILE 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 110 LEU 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 175 ASP Chi-restraints excluded: chain C residue 193 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 227 SER 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 C residue 283 THR Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain F residue 114 GLU 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 23 optimal weight: 0.0040 chunk 80 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN ** E 129 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.158750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.134720 restraints weight = 21593.202| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 3.08 r_work: 0.3739 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14615 Z= 0.174 Angle : 0.672 10.531 19842 Z= 0.345 Chirality : 0.046 0.270 2217 Planarity : 0.004 0.057 2543 Dihedral : 9.309 71.012 2446 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 4.79 % Allowed : 31.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.49 (0.18), residues: 1732 helix: 0.27 (0.24), residues: 372 sheet: -0.69 (0.35), residues: 249 loop : -2.77 (0.16), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 208 TYR 0.026 0.001 TYR D 83 PHE 0.013 0.002 PHE B 125 TRP 0.013 0.002 TRP B 153 HIS 0.007 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00376 (14570) covalent geometry : angle 0.65489 (19725) SS BOND : bond 0.00456 ( 18) SS BOND : angle 1.96613 ( 36) hydrogen bonds : bond 0.05880 ( 401) hydrogen bonds : angle 5.74915 ( 1164) link_ALPHA1-3 : bond 0.00172 ( 3) link_ALPHA1-3 : angle 3.91532 ( 9) link_ALPHA1-6 : bond 0.00335 ( 3) link_ALPHA1-6 : angle 1.59348 ( 9) link_BETA1-4 : bond 0.00552 ( 9) link_BETA1-4 : angle 1.50373 ( 27) link_NAG-ASN : bond 0.00566 ( 12) link_NAG-ASN : angle 2.04027 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3728.96 seconds wall clock time: 64 minutes 53.33 seconds (3893.33 seconds total)