Starting phenix.real_space_refine on Fri May 16 11:05:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pk3_17724/05_2025/8pk3_17724.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pk3_17724/05_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_17724/05_2025/8pk3_17724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pk3_17724/05_2025/8pk3_17724.map" model { file = "/net/cci-nas-00/data/ceres_data/8pk3_17724/05_2025/8pk3_17724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pk3_17724/05_2025/8pk3_17724.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 8946 2.51 5 N 2427 2.21 5 O 2844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14277 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2482 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 300} Chain: "D" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1417 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 174} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 743 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "B" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2482 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 300} Chain: "E" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1417 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 743 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2482 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 300} Chain: "F" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1417 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 174} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 743 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.81, per 1000 atoms: 0.69 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: 3.92 Conformation dependent library (CDL) restraints added in 1.8 seconds 3464 Ramachandran restraints generated. 1732 Oldfield, 0 Emsley, 1732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 28 sheets defined 23.3% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.715A pdb=" N GLN A 191 " --> pdb=" O THR A 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 57 removed outlier: 3.570A pdb=" N THR D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG D 54 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 125 Processing helix chain 'D' and resid 145 through 153 removed outlier: 3.967A pdb=" N ILE D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 167 removed outlier: 3.621A pdb=" N LEU D 167 " --> pdb=" O ARG D 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.849A pdb=" N LYS G 22 " --> pdb=" O GLU G 18 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU G 23 " --> pdb=" O HIS G 19 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.846A pdb=" N GLY B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 195 removed outlier: 3.799A pdb=" N GLN B 191 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 57 removed outlier: 3.530A pdb=" N THR E 41 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG E 54 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU E 57 " --> pdb=" O ASN E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 127 removed outlier: 3.504A pdb=" N GLU E 114 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU E 126 " --> pdb=" O THR E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 153 removed outlier: 3.994A pdb=" N ILE E 149 " --> pdb=" O ASP E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing helix chain 'E' and resid 167 through 168 No H-bonds generated for 'chain 'E' and resid 167 through 168' Processing helix chain 'H' and resid 6 through 24 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 104 through 116 removed outlier: 3.825A pdb=" N LEU C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.633A pdb=" N GLN C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 57 removed outlier: 3.503A pdb=" N ALA F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG F 54 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU F 57 " --> pdb=" O ASN F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 125 Processing helix chain 'F' and resid 145 through 153 removed outlier: 3.920A pdb=" N ILE F 149 " --> pdb=" O ASP F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 167 removed outlier: 3.634A pdb=" N LEU F 167 " --> pdb=" O ARG F 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 24 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.144A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 7.233A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ARG A 90 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N PHE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N SER A 270 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N GLU A 89 " --> pdb=" O SER A 270 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.576A pdb=" N ILE A 121 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA6, first strand: chain 'A' and resid 164 through 169 removed outlier: 3.595A pdb=" N SER A 247 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU A 243 " --> pdb=" O MET A 168 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 202 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 213 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 294 through 295 removed outlier: 3.578A pdb=" N GLN A 295 " --> pdb=" O LYS A 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 23 through 26 removed outlier: 3.613A pdb=" N ALA D 35 " --> pdb=" O PHE D 24 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N HIS D 26 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY D 33 " --> pdb=" O HIS D 26 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 29 through 37 removed outlier: 7.499A pdb=" N VAL G 30 " --> pdb=" O LYS G 57 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N LYS G 57 " --> pdb=" O VAL G 30 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL G 32 " --> pdb=" O GLU G 55 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLU G 55 " --> pdb=" O VAL G 32 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS G 34 " --> pdb=" O THR G 53 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR G 50 " --> pdb=" O VAL G 69 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL G 69 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU G 52 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS G 68 " --> pdb=" O GLU G 88 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU G 88 " --> pdb=" O LYS G 68 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 24 through 26 removed outlier: 3.600A pdb=" N THR B 24 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 51 through 52 removed outlier: 6.076A pdb=" N ILE B 51 " --> pdb=" O ASP B 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.003A pdb=" N PHE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N SER B 270 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLU B 89 " --> pdb=" O SER B 270 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 151 through 153 removed outlier: 7.614A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 151 through 153 removed outlier: 7.614A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 164 through 169 removed outlier: 3.507A pdb=" N VAL B 166 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU B 243 " --> pdb=" O MET B 168 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 294 through 295 removed outlier: 3.659A pdb=" N GLN B 295 " --> pdb=" O LYS B 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 25 through 28 removed outlier: 3.878A pdb=" N HIS E 26 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY E 33 " --> pdb=" O HIS E 26 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN E 28 " --> pdb=" O GLY E 31 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY E 31 " --> pdb=" O ASN E 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'H' and resid 29 through 37 removed outlier: 7.248A pdb=" N VAL H 30 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N LYS H 57 " --> pdb=" O VAL H 30 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL H 32 " --> pdb=" O GLU H 55 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLU H 55 " --> pdb=" O VAL H 32 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS H 34 " --> pdb=" O THR H 53 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR H 51 " --> pdb=" O LYS H 36 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR H 50 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL H 69 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU H 52 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU H 88 " --> pdb=" O LYS H 68 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.541A pdb=" N THR C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 51 through 52 removed outlier: 6.134A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 58 through 60 removed outlier: 7.144A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ARG C 90 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N PHE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N SER C 270 " --> pdb=" O PHE C 87 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLU C 89 " --> pdb=" O SER C 270 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 151 through 152 removed outlier: 3.533A pdb=" N ALA C 253 " --> pdb=" O ASN C 152 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 164 through 169 removed outlier: 3.540A pdb=" N LEU C 164 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 247 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU C 243 " --> pdb=" O MET C 168 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE C 213 " --> pdb=" O VAL C 202 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 236 through 237 Processing sheet with id=AC7, first strand: chain 'C' and resid 180 through 184 Processing sheet with id=AC8, first strand: chain 'C' and resid 294 through 295 removed outlier: 3.720A pdb=" N GLN C 295 " --> pdb=" O LYS C 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 23 through 26 removed outlier: 3.623A pdb=" N ALA F 35 " --> pdb=" O PHE F 24 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS F 26 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY F 33 " --> pdb=" O HIS F 26 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 29 through 37 removed outlier: 7.447A pdb=" N VAL I 30 " --> pdb=" O LYS I 57 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N LYS I 57 " --> pdb=" O VAL I 30 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL I 32 " --> pdb=" O GLU I 55 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLU I 55 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS I 34 " --> pdb=" O THR I 53 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR I 51 " --> pdb=" O LYS I 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR I 50 " --> pdb=" O VAL I 69 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL I 69 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS I 68 " --> pdb=" O GLU I 88 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLU I 88 " --> pdb=" O LYS I 68 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP I 70 " --> pdb=" O LEU I 86 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LEU I 86 " --> pdb=" O TRP I 70 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 4.53 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: 0.02 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: 3.130 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: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 33.870 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.620 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.17), residues: 1732 helix: -1.44 (0.23), residues: 377 sheet: -1.08 (0.34), residues: 255 loop : -2.82 (0.15), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 44 HIS 0.015 0.002 HIS B 17 PHE 0.025 0.002 PHE B 258 TYR 0.031 0.002 TYR B 302 ARG 0.018 0.001 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00702 ( 12) link_NAG-ASN : angle 2.18907 ( 36) 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_ALPHA1-3 : bond 0.00695 ( 3) link_ALPHA1-3 : angle 4.76921 ( 9) hydrogen bonds : bond 0.29514 ( 401) hydrogen bonds : angle 9.65849 ( 1164) SS BOND : bond 0.00702 ( 18) SS BOND : angle 2.25737 ( 36) covalent geometry : bond 0.00533 (14570) covalent geometry : angle 0.95648 (19725) *********************** 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 : 1.569 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: 0.2706 time to fit residues: 106.2458 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 : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 137 CYS Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain C residue 167 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 1.9990 chunk 129 optimal weight: 0.0970 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 81 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 155 optimal weight: 0.1980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 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** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.159136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.134988 restraints weight = 21381.820| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 3.06 r_work: 0.3772 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 14615 Z= 0.157 Angle : 0.650 7.932 19842 Z= 0.337 Chirality : 0.046 0.275 2217 Planarity : 0.004 0.051 2543 Dihedral : 11.678 91.421 2453 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 5.25 % Allowed : 27.43 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.18), residues: 1732 helix: -0.40 (0.23), residues: 388 sheet: -0.98 (0.34), residues: 255 loop : -2.79 (0.15), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 44 HIS 0.004 0.001 HIS B 17 PHE 0.011 0.001 PHE B 125 TYR 0.013 0.001 TYR C 105 ARG 0.005 0.001 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00616 ( 12) link_NAG-ASN : angle 1.79718 ( 36) link_ALPHA1-6 : bond 0.00501 ( 3) link_ALPHA1-6 : angle 1.96455 ( 9) link_BETA1-4 : bond 0.00740 ( 9) link_BETA1-4 : angle 1.39033 ( 27) link_ALPHA1-3 : bond 0.00333 ( 3) link_ALPHA1-3 : angle 4.39539 ( 9) hydrogen bonds : bond 0.06873 ( 401) hydrogen bonds : angle 6.23473 ( 1164) SS BOND : bond 0.00734 ( 18) SS BOND : angle 1.65157 ( 36) covalent geometry : bond 0.00333 (14570) covalent geometry : angle 0.63320 (19725) *********************** 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 345 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 265 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 114 GLU cc_start: 0.6703 (mm-30) cc_final: 0.6381 (mm-30) REVERT: G 49 MET cc_start: 0.6860 (tmm) cc_final: 0.6635 (tmm) REVERT: B 201 ARG cc_start: 0.7590 (ttp80) cc_final: 0.7267 (ptm-80) REVERT: E 45 ILE cc_start: 0.6981 (mt) cc_final: 0.6555 (tp) REVERT: E 86 ASP cc_start: 0.6703 (t0) cc_final: 0.6014 (t0) REVERT: E 90 ASP cc_start: 0.6572 (m-30) cc_final: 0.6269 (m-30) REVERT: E 104 ASN cc_start: 0.7055 (m110) cc_final: 0.6840 (m110) REVERT: H 6 LEU cc_start: 0.5633 (OUTLIER) cc_final: 0.5430 (pp) REVERT: C 196 VAL cc_start: 0.6926 (OUTLIER) cc_final: 0.6570 (m) REVERT: F 42 GLN cc_start: 0.7950 (tp-100) cc_final: 0.7124 (tp40) REVERT: F 62 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.6996 (mmtm) REVERT: F 90 ASP cc_start: 0.6889 (m-30) cc_final: 0.6514 (m-30) outliers start: 80 outliers final: 38 residues processed: 316 average time/residue: 0.2634 time to fit residues: 120.7043 Evaluate side-chains 302 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 261 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 262 THR 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 152 ILE Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain G residue 32 VAL 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 204 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain E residue 9 PHE Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 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 132 GLN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain 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 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 116 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 13 optimal weight: 0.0270 chunk 99 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 HIS B 191 GLN E 28 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 = 0.4184 r_free = 0.4184 target = 0.157639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.133495 restraints weight = 21455.683| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 3.04 r_work: 0.3748 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.1393 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= 0.180 Angle : 0.644 8.089 19842 Z= 0.330 Chirality : 0.046 0.278 2217 Planarity : 0.004 0.055 2543 Dihedral : 11.167 89.179 2443 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 4.86 % Allowed : 27.95 % Favored : 67.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.18), residues: 1732 helix: 0.09 (0.25), residues: 372 sheet: -1.06 (0.34), residues: 261 loop : -2.73 (0.15), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 153 HIS 0.004 0.001 HIS B 184 PHE 0.014 0.002 PHE B 125 TYR 0.012 0.001 TYR C 161 ARG 0.006 0.000 ARG B 224 Details of bonding type rmsd link_NAG-ASN : bond 0.00655 ( 12) link_NAG-ASN : angle 2.21554 ( 36) link_ALPHA1-6 : bond 0.00288 ( 3) link_ALPHA1-6 : angle 1.89340 ( 9) link_BETA1-4 : bond 0.00736 ( 9) link_BETA1-4 : angle 1.50022 ( 27) link_ALPHA1-3 : bond 0.00115 ( 3) link_ALPHA1-3 : angle 4.04505 ( 9) hydrogen bonds : bond 0.06611 ( 401) hydrogen bonds : angle 5.97696 ( 1164) SS BOND : bond 0.00448 ( 18) SS BOND : angle 1.97183 ( 36) covalent geometry : bond 0.00388 (14570) covalent geometry : angle 0.62384 (19725) *********************** 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 349 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 275 time to evaluate : 1.435 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: D 114 GLU cc_start: 0.6674 (mm-30) cc_final: 0.6413 (mm-30) REVERT: G 49 MET cc_start: 0.6875 (tmm) cc_final: 0.6467 (tmm) REVERT: B 18 HIS cc_start: 0.7278 (OUTLIER) cc_final: 0.6238 (p-80) REVERT: B 201 ARG cc_start: 0.7607 (ttp80) cc_final: 0.7349 (ptm-80) REVERT: E 45 ILE cc_start: 0.6884 (mt) cc_final: 0.6609 (tp) REVERT: C 118 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8021 (tt) REVERT: C 261 ARG cc_start: 0.7985 (ttm110) cc_final: 0.7432 (tpp80) REVERT: F 42 GLN cc_start: 0.8056 (tp40) cc_final: 0.7703 (tp40) REVERT: F 90 ASP cc_start: 0.6926 (m-30) cc_final: 0.6529 (m-30) REVERT: I 49 MET cc_start: 0.6888 (tmm) cc_final: 0.6609 (tmm) outliers start: 74 outliers final: 41 residues processed: 321 average time/residue: 0.2792 time to fit residues: 130.7504 Evaluate side-chains 308 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 265 time to evaluate : 1.431 ------------------------------------------------------------------------------- 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 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 B residue 318 THR Chi-restraints excluded: chain E residue 9 PHE 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 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 166 VAL Chi-restraints excluded: chain C residue 167 THR 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 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 42 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 11 optimal weight: 0.3980 chunk 113 optimal weight: 0.4980 chunk 121 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.155794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.131850 restraints weight = 21575.007| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 3.03 r_work: 0.3745 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14615 Z= 0.179 Angle : 0.638 8.414 19842 Z= 0.326 Chirality : 0.045 0.277 2217 Planarity : 0.004 0.055 2543 Dihedral : 10.755 85.582 2443 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 5.18 % Allowed : 28.74 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.18), residues: 1732 helix: 0.12 (0.24), residues: 375 sheet: -1.24 (0.31), residues: 291 loop : -2.73 (0.16), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 153 HIS 0.005 0.001 HIS C 17 PHE 0.013 0.002 PHE B 125 TYR 0.015 0.001 TYR C 105 ARG 0.006 0.000 ARG B 224 Details of bonding type rmsd link_NAG-ASN : bond 0.00649 ( 12) link_NAG-ASN : angle 2.11906 ( 36) link_ALPHA1-6 : bond 0.00287 ( 3) link_ALPHA1-6 : angle 1.81141 ( 9) link_BETA1-4 : bond 0.00696 ( 9) link_BETA1-4 : angle 1.49514 ( 27) link_ALPHA1-3 : bond 0.00104 ( 3) link_ALPHA1-3 : angle 4.06558 ( 9) hydrogen bonds : bond 0.06250 ( 401) hydrogen bonds : angle 5.82563 ( 1164) SS BOND : bond 0.00523 ( 18) SS BOND : angle 1.99833 ( 36) covalent geometry : bond 0.00385 (14570) covalent geometry : angle 0.61812 (19725) *********************** 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 348 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 269 time to evaluate : 1.450 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: 0.6311 (tt) cc_final: 0.6042 (tt) REVERT: A 104 ASP cc_start: 0.6708 (OUTLIER) cc_final: 0.6455 (t0) REVERT: A 201 ARG cc_start: 0.7477 (ttp80) cc_final: 0.7276 (ttp80) REVERT: D 90 ASP cc_start: 0.7014 (m-30) cc_final: 0.6742 (m-30) REVERT: D 114 GLU cc_start: 0.6706 (mm-30) cc_final: 0.6435 (mm-30) REVERT: G 49 MET cc_start: 0.6942 (tmm) cc_final: 0.6569 (tmm) REVERT: B 18 HIS cc_start: 0.7117 (OUTLIER) cc_final: 0.6272 (p-80) REVERT: B 201 ARG cc_start: 0.7648 (ttp80) cc_final: 0.7239 (ttp80) REVERT: C 64 CYS cc_start: 0.5104 (m) cc_final: 0.4799 (m) REVERT: C 261 ARG cc_start: 0.7977 (ttm110) cc_final: 0.7428 (tpp80) REVERT: F 42 GLN cc_start: 0.8138 (tp40) cc_final: 0.7761 (tp40) REVERT: F 90 ASP cc_start: 0.6860 (m-30) cc_final: 0.6503 (m-30) REVERT: F 135 ASN cc_start: 0.7228 (t0) cc_final: 0.7028 (t0) REVERT: I 49 MET cc_start: 0.6947 (tmm) cc_final: 0.6716 (tmm) outliers start: 79 outliers final: 48 residues processed: 320 average time/residue: 0.2475 time to fit residues: 115.5862 Evaluate side-chains 311 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 261 time to evaluate : 1.629 ------------------------------------------------------------------------------- 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 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 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 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 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 69 GLU 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 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 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 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 164 ASP Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 23 GLU Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain I residue 74 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 154 optimal weight: 0.6980 chunk 60 optimal weight: 0.0970 chunk 7 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 116 optimal weight: 0.0770 chunk 98 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 140 optimal weight: 0.0170 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 ASN ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.158223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.134115 restraints weight = 21610.660| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 3.05 r_work: 0.3773 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14615 Z= 0.128 Angle : 0.603 9.391 19842 Z= 0.307 Chirality : 0.044 0.288 2217 Planarity : 0.004 0.051 2543 Dihedral : 9.959 78.249 2443 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 4.99 % Allowed : 29.79 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.18), residues: 1732 helix: 0.19 (0.25), residues: 381 sheet: -1.21 (0.31), residues: 291 loop : -2.68 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 153 HIS 0.005 0.001 HIS C 17 PHE 0.009 0.001 PHE B 148 TYR 0.014 0.001 TYR C 105 ARG 0.004 0.000 ARG F 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00590 ( 12) link_NAG-ASN : angle 1.81077 ( 36) link_ALPHA1-6 : bond 0.00438 ( 3) link_ALPHA1-6 : angle 1.72270 ( 9) link_BETA1-4 : bond 0.00620 ( 9) link_BETA1-4 : angle 1.39061 ( 27) link_ALPHA1-3 : bond 0.00075 ( 3) link_ALPHA1-3 : angle 4.25442 ( 9) hydrogen bonds : bond 0.05682 ( 401) hydrogen bonds : angle 5.62865 ( 1164) SS BOND : bond 0.00232 ( 18) SS BOND : angle 1.76498 ( 36) covalent geometry : bond 0.00271 (14570) covalent geometry : angle 0.58496 (19725) *********************** 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 349 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 273 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.6227 (tt) cc_final: 0.5949 (tt) REVERT: A 104 ASP cc_start: 0.6657 (OUTLIER) cc_final: 0.6395 (t0) REVERT: D 42 GLN cc_start: 0.8387 (tp40) cc_final: 0.7955 (tp40) REVERT: D 90 ASP cc_start: 0.6936 (m-30) cc_final: 0.6650 (m-30) REVERT: D 114 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6513 (mm-30) REVERT: G 23 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7217 (pm20) REVERT: G 26 LEU cc_start: 0.4994 (OUTLIER) cc_final: 0.4698 (tt) REVERT: G 36 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7391 (pttm) REVERT: G 49 MET cc_start: 0.6931 (tmm) cc_final: 0.6598 (tmm) REVERT: B 71 LEU cc_start: 0.7729 (mm) cc_final: 0.7482 (mm) REVERT: E 42 GLN cc_start: 0.8209 (tp40) cc_final: 0.7958 (tp40) REVERT: E 86 ASP cc_start: 0.7037 (t0) cc_final: 0.6492 (t0) REVERT: E 90 ASP cc_start: 0.6556 (m-30) cc_final: 0.6137 (m-30) REVERT: C 104 ASP cc_start: 0.7275 (t70) cc_final: 0.6915 (t70) REVERT: F 90 ASP cc_start: 0.6964 (OUTLIER) cc_final: 0.6555 (m-30) REVERT: I 49 MET cc_start: 0.6961 (tmm) cc_final: 0.6709 (tmm) outliers start: 76 outliers final: 45 residues processed: 322 average time/residue: 0.2509 time to fit residues: 117.9308 Evaluate side-chains 316 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 266 time to evaluate : 1.486 ------------------------------------------------------------------------------- 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 132 GLN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 262 THR 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 G residue 36 LYS Chi-restraints excluded: chain B residue 12 THR 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 175 ASP Chi-restraints excluded: chain B residue 204 VAL 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 114 GLU 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 40 THR 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 251 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 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 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 93 optimal weight: 0.6980 chunk 148 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 113 optimal weight: 0.0030 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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 78 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.157318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.133221 restraints weight = 21728.193| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 3.05 r_work: 0.3767 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14615 Z= 0.153 Angle : 0.618 8.685 19842 Z= 0.315 Chirality : 0.045 0.282 2217 Planarity : 0.004 0.051 2543 Dihedral : 9.790 76.500 2443 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 4.59 % Allowed : 29.92 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.18), residues: 1732 helix: 0.15 (0.25), residues: 378 sheet: -1.19 (0.31), residues: 291 loop : -2.68 (0.16), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 153 HIS 0.004 0.001 HIS C 17 PHE 0.011 0.001 PHE B 125 TYR 0.017 0.001 TYR C 308 ARG 0.003 0.000 ARG F 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00584 ( 12) link_NAG-ASN : angle 1.88266 ( 36) link_ALPHA1-6 : bond 0.00326 ( 3) link_ALPHA1-6 : angle 1.73327 ( 9) link_BETA1-4 : bond 0.00624 ( 9) link_BETA1-4 : angle 1.42803 ( 27) link_ALPHA1-3 : bond 0.00075 ( 3) link_ALPHA1-3 : angle 4.08409 ( 9) hydrogen bonds : bond 0.05751 ( 401) hydrogen bonds : angle 5.60262 ( 1164) SS BOND : bond 0.00474 ( 18) SS BOND : angle 1.75388 ( 36) covalent geometry : bond 0.00329 (14570) covalent geometry : angle 0.59994 (19725) *********************** 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 340 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 270 time to evaluate : 1.505 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: 0.6701 (OUTLIER) cc_final: 0.6396 (t0) REVERT: D 90 ASP cc_start: 0.6938 (m-30) cc_final: 0.6661 (m-30) REVERT: D 114 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6524 (mm-30) REVERT: G 23 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7281 (pm20) REVERT: G 26 LEU cc_start: 0.5000 (OUTLIER) cc_final: 0.4711 (tt) REVERT: G 49 MET cc_start: 0.6886 (tmm) cc_final: 0.6529 (tmm) REVERT: B 70 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6873 (mp) REVERT: B 71 LEU cc_start: 0.7679 (mm) cc_final: 0.7465 (mm) REVERT: B 118 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8162 (tt) REVERT: E 42 GLN cc_start: 0.8248 (tp40) cc_final: 0.7939 (tp40) REVERT: C 34 ILE cc_start: 0.6267 (tt) cc_final: 0.5521 (tp) REVERT: C 104 ASP cc_start: 0.7341 (t70) cc_final: 0.6970 (t70) REVERT: F 90 ASP cc_start: 0.6936 (OUTLIER) cc_final: 0.6519 (m-30) REVERT: I 49 MET cc_start: 0.6949 (tmm) cc_final: 0.6689 (tmm) outliers start: 70 outliers final: 52 residues processed: 316 average time/residue: 0.2587 time to fit residues: 118.5315 Evaluate side-chains 325 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 267 time to evaluate : 1.402 ------------------------------------------------------------------------------- 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 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 70 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 118 LEU 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 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 103 GLU Chi-restraints excluded: chain E residue 114 GLU 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 40 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 5 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.158301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.133906 restraints weight = 21658.148| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 3.10 r_work: 0.3732 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.2027 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= 0.199 Angle : 0.653 9.626 19842 Z= 0.335 Chirality : 0.046 0.270 2217 Planarity : 0.004 0.056 2543 Dihedral : 9.829 76.748 2443 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 4.92 % Allowed : 29.86 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.18), residues: 1732 helix: 0.17 (0.24), residues: 381 sheet: -0.41 (0.36), residues: 231 loop : -2.82 (0.15), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.006 0.001 HIS C 18 PHE 0.016 0.002 PHE B 125 TYR 0.015 0.002 TYR C 308 ARG 0.005 0.000 ARG C 224 Details of bonding type rmsd link_NAG-ASN : bond 0.00601 ( 12) link_NAG-ASN : angle 2.13362 ( 36) link_ALPHA1-6 : bond 0.00203 ( 3) link_ALPHA1-6 : angle 1.72748 ( 9) link_BETA1-4 : bond 0.00616 ( 9) link_BETA1-4 : angle 1.52878 ( 27) link_ALPHA1-3 : bond 0.00158 ( 3) link_ALPHA1-3 : angle 3.91354 ( 9) hydrogen bonds : bond 0.06000 ( 401) hydrogen bonds : angle 5.70711 ( 1164) SS BOND : bond 0.00518 ( 18) SS BOND : angle 1.91399 ( 36) covalent geometry : bond 0.00433 (14570) covalent geometry : angle 0.63456 (19725) *********************** 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 348 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 273 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ILE cc_start: 0.6366 (tt) cc_final: 0.6089 (tt) REVERT: A 104 ASP cc_start: 0.6760 (OUTLIER) cc_final: 0.6457 (t0) REVERT: D 42 GLN cc_start: 0.8416 (tp40) cc_final: 0.7893 (tp40) REVERT: D 90 ASP cc_start: 0.7028 (m-30) cc_final: 0.6746 (m-30) REVERT: D 114 GLU cc_start: 0.6797 (mm-30) cc_final: 0.6581 (mm-30) REVERT: D 160 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7494 (t0) REVERT: G 49 MET cc_start: 0.6915 (tmm) cc_final: 0.6575 (tmm) REVERT: B 70 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6927 (mp) REVERT: B 78 VAL cc_start: 0.8279 (OUTLIER) cc_final: 0.8075 (t) REVERT: B 118 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8225 (tt) REVERT: E 42 GLN cc_start: 0.8276 (tp40) cc_final: 0.8005 (tp40) REVERT: E 86 ASP cc_start: 0.7138 (t0) cc_final: 0.6687 (t0) REVERT: C 34 ILE cc_start: 0.6398 (tt) cc_final: 0.5649 (tp) REVERT: C 118 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8078 (tt) REVERT: F 42 GLN cc_start: 0.8220 (tp40) cc_final: 0.7900 (tp40) REVERT: F 90 ASP cc_start: 0.6946 (OUTLIER) cc_final: 0.6547 (m-30) REVERT: I 49 MET cc_start: 0.6950 (tmm) cc_final: 0.6682 (tmm) outliers start: 75 outliers final: 51 residues processed: 320 average time/residue: 0.2457 time to fit residues: 114.7336 Evaluate side-chains 327 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 269 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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 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 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 70 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 118 LEU 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 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 114 GLU 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 0.0000 chunk 160 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 152 optimal weight: 0.0980 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN F 104 ASN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.159617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.135470 restraints weight = 21562.595| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 3.11 r_work: 0.3757 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14615 Z= 0.152 Angle : 0.635 9.326 19842 Z= 0.324 Chirality : 0.045 0.283 2217 Planarity : 0.004 0.053 2543 Dihedral : 9.284 71.553 2443 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 4.53 % Allowed : 30.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.18), residues: 1732 helix: 0.23 (0.24), residues: 381 sheet: -1.16 (0.32), residues: 291 loop : -2.77 (0.16), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 153 HIS 0.006 0.001 HIS B 17 PHE 0.011 0.001 PHE B 148 TYR 0.014 0.001 TYR C 105 ARG 0.005 0.000 ARG B 224 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 12) link_NAG-ASN : angle 1.90108 ( 36) link_ALPHA1-6 : bond 0.00342 ( 3) link_ALPHA1-6 : angle 1.62427 ( 9) link_BETA1-4 : bond 0.00565 ( 9) link_BETA1-4 : angle 1.46492 ( 27) link_ALPHA1-3 : bond 0.00197 ( 3) link_ALPHA1-3 : angle 4.07508 ( 9) hydrogen bonds : bond 0.05602 ( 401) hydrogen bonds : angle 5.62037 ( 1164) SS BOND : bond 0.00418 ( 18) SS BOND : angle 1.79858 ( 36) covalent geometry : bond 0.00325 (14570) covalent geometry : angle 0.61733 (19725) *********************** 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 334 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 265 time to evaluate : 1.557 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: 0.6731 (OUTLIER) cc_final: 0.6416 (t0) REVERT: D 42 GLN cc_start: 0.8347 (tp40) cc_final: 0.7338 (tp40) REVERT: D 46 ASP cc_start: 0.7396 (m-30) cc_final: 0.6994 (m-30) REVERT: D 90 ASP cc_start: 0.7012 (m-30) cc_final: 0.6709 (m-30) REVERT: D 114 GLU cc_start: 0.6896 (mm-30) cc_final: 0.6636 (mm-30) REVERT: D 160 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7512 (t0) REVERT: G 26 LEU cc_start: 0.5046 (OUTLIER) cc_final: 0.4843 (tt) REVERT: G 49 MET cc_start: 0.6916 (tmm) cc_final: 0.6411 (tmm) REVERT: B 70 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6877 (mp) REVERT: B 71 LEU cc_start: 0.7670 (mm) cc_final: 0.7457 (mm) REVERT: B 118 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8203 (tt) REVERT: B 201 ARG cc_start: 0.7577 (ttp-110) cc_final: 0.7302 (ptm-80) REVERT: E 45 ILE cc_start: 0.6885 (mt) cc_final: 0.6540 (tp) REVERT: E 86 ASP cc_start: 0.7117 (t0) cc_final: 0.6532 (t0) REVERT: E 90 ASP cc_start: 0.6506 (m-30) cc_final: 0.5953 (m-30) REVERT: C 34 ILE cc_start: 0.6335 (tt) cc_final: 0.5613 (tp) REVERT: C 104 ASP cc_start: 0.7406 (t70) cc_final: 0.7009 (t70) REVERT: F 17 MET cc_start: 0.4055 (mmm) cc_final: 0.2875 (mmm) REVERT: F 90 ASP cc_start: 0.6887 (OUTLIER) cc_final: 0.6470 (m-30) REVERT: I 49 MET cc_start: 0.6935 (tmm) cc_final: 0.6650 (tmm) outliers start: 69 outliers final: 51 residues processed: 311 average time/residue: 0.2586 time to fit residues: 116.7503 Evaluate side-chains 320 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 263 time to evaluate : 1.513 ------------------------------------------------------------------------------- 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 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 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 33 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 118 LEU 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 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 103 GLU Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 165 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 0.1980 chunk 142 optimal weight: 0.3980 chunk 161 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.159676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.135493 restraints weight = 21631.044| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 3.10 r_work: 0.3752 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14615 Z= 0.158 Angle : 0.642 9.314 19842 Z= 0.328 Chirality : 0.045 0.276 2217 Planarity : 0.004 0.078 2543 Dihedral : 9.114 69.701 2443 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 4.59 % Allowed : 30.31 % Favored : 65.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.18), residues: 1732 helix: 0.30 (0.24), residues: 381 sheet: -1.18 (0.31), residues: 306 loop : -2.76 (0.16), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 153 HIS 0.006 0.001 HIS B 17 PHE 0.012 0.001 PHE B 125 TYR 0.015 0.001 TYR C 105 ARG 0.012 0.000 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 12) link_NAG-ASN : angle 1.92801 ( 36) link_ALPHA1-6 : bond 0.00372 ( 3) link_ALPHA1-6 : angle 1.60236 ( 9) link_BETA1-4 : bond 0.00565 ( 9) link_BETA1-4 : angle 1.44678 ( 27) link_ALPHA1-3 : bond 0.00152 ( 3) link_ALPHA1-3 : angle 3.97948 ( 9) hydrogen bonds : bond 0.05600 ( 401) hydrogen bonds : angle 5.57816 ( 1164) SS BOND : bond 0.00409 ( 18) SS BOND : angle 1.93764 ( 36) covalent geometry : bond 0.00340 (14570) covalent geometry : angle 0.62402 (19725) *********************** 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 336 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 266 time to evaluate : 1.445 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: 0.6735 (OUTLIER) cc_final: 0.6425 (t0) REVERT: D 42 GLN cc_start: 0.8336 (tp40) cc_final: 0.7306 (tp40) REVERT: D 46 ASP cc_start: 0.7401 (m-30) cc_final: 0.6980 (m-30) REVERT: D 90 ASP cc_start: 0.7019 (OUTLIER) cc_final: 0.6743 (m-30) REVERT: D 114 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6696 (mm-30) REVERT: D 132 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6809 (tt0) REVERT: D 160 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7524 (t0) REVERT: G 26 LEU cc_start: 0.5046 (OUTLIER) cc_final: 0.4844 (tt) REVERT: G 49 MET cc_start: 0.6938 (tmm) cc_final: 0.6408 (tmm) REVERT: B 70 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6891 (mp) REVERT: B 71 LEU cc_start: 0.7744 (mm) cc_final: 0.7506 (mm) REVERT: B 118 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8178 (tt) REVERT: B 201 ARG cc_start: 0.7581 (ttp-110) cc_final: 0.7308 (ptm-80) REVERT: E 45 ILE cc_start: 0.6879 (mt) cc_final: 0.6542 (tp) REVERT: E 90 ASP cc_start: 0.6454 (m-30) cc_final: 0.6163 (m-30) REVERT: C 34 ILE cc_start: 0.6358 (tt) cc_final: 0.5618 (tp) REVERT: C 70 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.7042 (mp) REVERT: C 104 ASP cc_start: 0.7407 (t70) cc_final: 0.6995 (t70) REVERT: F 17 MET cc_start: 0.4101 (mmm) cc_final: 0.2911 (mmm) REVERT: F 90 ASP cc_start: 0.6836 (OUTLIER) cc_final: 0.6438 (m-30) REVERT: I 49 MET cc_start: 0.6940 (tmm) cc_final: 0.6641 (tmm) outliers start: 70 outliers final: 57 residues processed: 308 average time/residue: 0.2610 time to fit residues: 115.8384 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 : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 18 HIS Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain D residue 9 PHE Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 90 ASP 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 33 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 118 LEU 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 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 103 GLU Chi-restraints excluded: chain E residue 114 GLU 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 70 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 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 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 37 optimal weight: 0.6980 chunk 109 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 0.0970 chunk 65 optimal weight: 0.6980 chunk 144 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 149 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.159651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.135641 restraints weight = 21495.622| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 3.06 r_work: 0.3756 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14615 Z= 0.157 Angle : 0.648 9.408 19842 Z= 0.331 Chirality : 0.046 0.281 2217 Planarity : 0.004 0.053 2543 Dihedral : 8.870 67.140 2443 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 4.46 % Allowed : 30.51 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.18), residues: 1732 helix: 0.47 (0.24), residues: 372 sheet: -1.16 (0.31), residues: 306 loop : -2.73 (0.16), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 153 HIS 0.007 0.001 HIS B 17 PHE 0.012 0.001 PHE B 125 TYR 0.020 0.001 TYR D 83 ARG 0.007 0.000 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00554 ( 12) link_NAG-ASN : angle 1.92105 ( 36) link_ALPHA1-6 : bond 0.00442 ( 3) link_ALPHA1-6 : angle 1.54219 ( 9) link_BETA1-4 : bond 0.00561 ( 9) link_BETA1-4 : angle 1.44291 ( 27) link_ALPHA1-3 : bond 0.00142 ( 3) link_ALPHA1-3 : angle 3.94668 ( 9) hydrogen bonds : bond 0.05515 ( 401) hydrogen bonds : angle 5.57459 ( 1164) SS BOND : bond 0.00426 ( 18) SS BOND : angle 1.89012 ( 36) covalent geometry : bond 0.00337 (14570) covalent geometry : angle 0.63119 (19725) ********************** 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 329 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 261 time to evaluate : 1.459 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: 0.6742 (OUTLIER) cc_final: 0.6434 (t0) REVERT: D 42 GLN cc_start: 0.8381 (tp40) cc_final: 0.7448 (tp40) REVERT: D 46 ASP cc_start: 0.7375 (m-30) cc_final: 0.6939 (m-30) REVERT: D 90 ASP cc_start: 0.7018 (OUTLIER) cc_final: 0.6760 (m-30) REVERT: D 114 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6605 (mm-30) REVERT: D 132 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6817 (tt0) REVERT: D 160 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7519 (t0) REVERT: G 49 MET cc_start: 0.6909 (tmm) cc_final: 0.6402 (tmm) REVERT: B 70 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6890 (mp) REVERT: B 71 LEU cc_start: 0.7754 (mm) cc_final: 0.7510 (mm) REVERT: B 118 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8207 (tt) REVERT: B 201 ARG cc_start: 0.7562 (ttp-110) cc_final: 0.7301 (ptm-80) REVERT: E 45 ILE cc_start: 0.6894 (mt) cc_final: 0.6582 (tp) REVERT: E 90 ASP cc_start: 0.6445 (m-30) cc_final: 0.6162 (m-30) REVERT: C 70 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6873 (mp) REVERT: C 104 ASP cc_start: 0.7420 (t70) cc_final: 0.6999 (t70) REVERT: C 118 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8004 (tt) REVERT: F 17 MET cc_start: 0.4078 (mmm) cc_final: 0.2777 (mmm) REVERT: F 90 ASP cc_start: 0.6920 (OUTLIER) cc_final: 0.6545 (m-30) REVERT: I 49 MET cc_start: 0.6949 (tmm) cc_final: 0.6675 (tmm) outliers start: 68 outliers final: 55 residues processed: 304 average time/residue: 0.2548 time to fit residues: 112.3504 Evaluate side-chains 323 residues out of total 1527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 259 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 92 LYS Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 167 THR 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 D residue 9 PHE Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 90 ASP 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 32 VAL Chi-restraints excluded: chain B residue 12 THR 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 118 LEU 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 204 VAL Chi-restraints excluded: chain B residue 227 SER 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 103 GLU Chi-restraints excluded: chain E residue 114 GLU 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 70 LEU 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 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 C residue 320 MET Chi-restraints excluded: chain F residue 9 PHE Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 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 94 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 152 optimal weight: 0.3980 chunk 107 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN F 105 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 = 0.4194 r_free = 0.4194 target = 0.159226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.134951 restraints weight = 21688.116| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 3.11 r_work: 0.3740 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.2252 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= 0.174 Angle : 0.653 9.461 19842 Z= 0.334 Chirality : 0.046 0.278 2217 Planarity : 0.004 0.053 2543 Dihedral : 8.888 67.291 2443 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 4.86 % Allowed : 30.58 % Favored : 64.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.18), residues: 1732 helix: 0.49 (0.25), residues: 372 sheet: -1.16 (0.31), residues: 306 loop : -2.74 (0.16), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 153 HIS 0.007 0.001 HIS B 17 PHE 0.014 0.002 PHE B 125 TYR 0.020 0.001 TYR D 83 ARG 0.007 0.000 ARG A 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00563 ( 12) link_NAG-ASN : angle 1.96719 ( 36) link_ALPHA1-6 : bond 0.00437 ( 3) link_ALPHA1-6 : angle 1.52558 ( 9) link_BETA1-4 : bond 0.00558 ( 9) link_BETA1-4 : angle 1.47780 ( 27) link_ALPHA1-3 : bond 0.00213 ( 3) link_ALPHA1-3 : angle 3.88676 ( 9) hydrogen bonds : bond 0.05624 ( 401) hydrogen bonds : angle 5.57300 ( 1164) SS BOND : bond 0.00461 ( 18) SS BOND : angle 1.90062 ( 36) covalent geometry : bond 0.00377 (14570) covalent geometry : angle 0.63623 (19725) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7930.11 seconds wall clock time: 138 minutes 8.51 seconds (8288.51 seconds total)