Starting phenix.real_space_refine on Sun Aug 24 12:58:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ik0_35503/08_2025/8ik0_35503.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ik0_35503/08_2025/8ik0_35503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ik0_35503/08_2025/8ik0_35503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ik0_35503/08_2025/8ik0_35503.map" model { file = "/net/cci-nas-00/data/ceres_data/8ik0_35503/08_2025/8ik0_35503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ik0_35503/08_2025/8ik0_35503.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.020 sd= 0.109 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 720 atoms to isotropic. 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 148 5.16 5 C 12536 2.51 5 N 3436 2.21 5 O 3416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19536 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2435 Classifications: {'peptide': 319} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 21} Link IDs: {'PTRANS': 14, 'TRANS': 304} Chain breaks: 3 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 6, 'GLU:plan': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 2449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2449 Classifications: {'peptide': 320} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 21} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain breaks: 3 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 4, 'GLU:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 61 Chain: "C" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2435 Classifications: {'peptide': 319} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 21} Link IDs: {'PTRANS': 14, 'TRANS': 304} Chain breaks: 3 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 6, 'GLU:plan': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 75 Chain: "F" Number of atoms: 2449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2449 Classifications: {'peptide': 320} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 21} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain breaks: 3 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 4, 'GLU:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 61 Chain: "D" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2435 Classifications: {'peptide': 319} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 21} Link IDs: {'PTRANS': 14, 'TRANS': 304} Chain breaks: 3 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 6, 'GLU:plan': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 75 Chain: "G" Number of atoms: 2449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2449 Classifications: {'peptide': 320} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 21} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain breaks: 3 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 4, 'GLU:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 61 Chain: "E" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2435 Classifications: {'peptide': 319} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 21} Link IDs: {'PTRANS': 14, 'TRANS': 304} Chain breaks: 3 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 6, 'GLU:plan': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 75 Chain: "H" Number of atoms: 2449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2449 Classifications: {'peptide': 320} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 21} Link IDs: {'PTRANS': 14, 'TRANS': 305} Chain breaks: 3 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 4, 'GLU:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 61 Time building chain proxies: 4.33, per 1000 atoms: 0.22 Number of scatterers: 19536 At special positions: 0 Unit cell: (189.435, 101.835, 98.55, 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 148 16.00 O 3416 8.00 N 3436 7.00 C 12536 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 711.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4888 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 12 sheets defined 60.7% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 23 through 41 removed outlier: 3.651A pdb=" N LEU A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 60 removed outlier: 3.578A pdb=" N LEU A 60 " --> pdb=" O GLN A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 76 removed outlier: 3.540A pdb=" N LEU A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 88 through 94 Processing helix chain 'A' and resid 99 through 113 removed outlier: 3.681A pdb=" N LEU A 103 " --> pdb=" O TRP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 140 Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.547A pdb=" N VAL A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 177 removed outlier: 4.392A pdb=" N LYS A 174 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 191 removed outlier: 3.940A pdb=" N GLU A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE A 187 " --> pdb=" O CYS A 183 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 197 Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.615A pdb=" N ALA A 220 " --> pdb=" O ASP A 216 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 221' Processing helix chain 'A' and resid 267 through 278 removed outlier: 3.651A pdb=" N GLN A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 278 " --> pdb=" O CYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 305 removed outlier: 3.512A pdb=" N LEU A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 removed outlier: 3.569A pdb=" N GLY A 332 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN A 341 " --> pdb=" O HIS A 337 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 41 Processing helix chain 'B' and resid 48 through 76 removed outlier: 3.746A pdb=" N ARG B 52 " --> pdb=" O PRO B 48 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 65 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 88 through 95 Processing helix chain 'B' and resid 99 through 113 Processing helix chain 'B' and resid 124 through 140 Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.543A pdb=" N VAL B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 172 removed outlier: 4.561A pdb=" N GLY B 163 " --> pdb=" O ASN B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 180 through 191 Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.833A pdb=" N ALA B 196 " --> pdb=" O MET B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 221 removed outlier: 3.618A pdb=" N ALA B 220 " --> pdb=" O ASP B 216 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 221' Processing helix chain 'B' and resid 267 through 279 removed outlier: 3.597A pdb=" N GLN B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 306 removed outlier: 3.566A pdb=" N SER B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 342 removed outlier: 3.591A pdb=" N GLY B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 41 Processing helix chain 'C' and resid 47 through 60 removed outlier: 3.654A pdb=" N LEU C 60 " --> pdb=" O GLN C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 76 removed outlier: 3.576A pdb=" N LEU C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 88 through 94 Processing helix chain 'C' and resid 99 through 113 Processing helix chain 'C' and resid 124 through 140 Processing helix chain 'C' and resid 145 through 156 removed outlier: 3.736A pdb=" N SER C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 177 removed outlier: 4.384A pdb=" N LYS C 174 " --> pdb=" O ILE C 170 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL C 175 " --> pdb=" O GLY C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 189 removed outlier: 3.945A pdb=" N GLU C 186 " --> pdb=" O GLU C 182 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE C 187 " --> pdb=" O CYS C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 197 Processing helix chain 'C' and resid 216 through 221 removed outlier: 3.876A pdb=" N ALA C 220 " --> pdb=" O ASP C 216 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 221' Processing helix chain 'C' and resid 267 through 278 removed outlier: 3.677A pdb=" N GLN C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN C 278 " --> pdb=" O CYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 306 removed outlier: 3.654A pdb=" N LEU C 290 " --> pdb=" O ARG C 286 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU C 291 " --> pdb=" O GLU C 287 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 340 removed outlier: 3.733A pdb=" N GLY C 332 " --> pdb=" O HIS C 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 41 Processing helix chain 'F' and resid 47 through 76 removed outlier: 4.116A pdb=" N ARG F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY F 63 " --> pdb=" O ALA F 59 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL F 64 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU F 65 " --> pdb=" O GLN F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 Processing helix chain 'F' and resid 88 through 95 Processing helix chain 'F' and resid 99 through 113 Processing helix chain 'F' and resid 124 through 140 Processing helix chain 'F' and resid 145 through 156 removed outlier: 3.584A pdb=" N SER F 156 " --> pdb=" O LEU F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 172 removed outlier: 4.669A pdb=" N GLY F 163 " --> pdb=" O ASN F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 191 Processing helix chain 'F' and resid 192 through 196 removed outlier: 4.226A pdb=" N ALA F 196 " --> pdb=" O MET F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 221 removed outlier: 3.852A pdb=" N ALA F 220 " --> pdb=" O ASP F 216 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 216 through 221' Processing helix chain 'F' and resid 267 through 279 removed outlier: 3.673A pdb=" N GLN F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 306 removed outlier: 3.563A pdb=" N SER F 306 " --> pdb=" O ASP F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 342 Processing helix chain 'D' and resid 23 through 41 removed outlier: 3.656A pdb=" N LEU D 41 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 60 removed outlier: 3.578A pdb=" N LEU D 60 " --> pdb=" O GLN D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 76 removed outlier: 3.532A pdb=" N LEU D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 83 Processing helix chain 'D' and resid 88 through 94 Processing helix chain 'D' and resid 99 through 113 removed outlier: 3.680A pdb=" N LEU D 103 " --> pdb=" O TRP D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 140 Processing helix chain 'D' and resid 145 through 156 removed outlier: 3.549A pdb=" N VAL D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 177 removed outlier: 4.379A pdb=" N LYS D 174 " --> pdb=" O ILE D 170 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL D 175 " --> pdb=" O GLY D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 191 removed outlier: 3.915A pdb=" N GLU D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE D 187 " --> pdb=" O CYS D 183 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR D 190 " --> pdb=" O GLU D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 197 Processing helix chain 'D' and resid 216 through 221 removed outlier: 3.628A pdb=" N ALA D 220 " --> pdb=" O ASP D 216 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 216 through 221' Processing helix chain 'D' and resid 267 through 278 removed outlier: 3.642A pdb=" N GLN D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 306 removed outlier: 3.542A pdb=" N LEU D 290 " --> pdb=" O ARG D 286 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU D 291 " --> pdb=" O GLU D 287 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 342 removed outlier: 3.619A pdb=" N GLY D 332 " --> pdb=" O HIS D 328 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN D 341 " --> pdb=" O HIS D 337 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN D 342 " --> pdb=" O LEU D 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 41 Processing helix chain 'G' and resid 48 through 76 removed outlier: 3.747A pdb=" N ARG G 52 " --> pdb=" O PRO G 48 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL G 64 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU G 65 " --> pdb=" O GLN G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 Processing helix chain 'G' and resid 88 through 95 Processing helix chain 'G' and resid 99 through 113 Processing helix chain 'G' and resid 124 through 140 Processing helix chain 'G' and resid 145 through 156 removed outlier: 3.537A pdb=" N VAL G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 172 removed outlier: 4.569A pdb=" N GLY G 163 " --> pdb=" O ASN G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 180 through 191 Processing helix chain 'G' and resid 192 through 196 removed outlier: 3.793A pdb=" N ALA G 196 " --> pdb=" O MET G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 221 removed outlier: 3.646A pdb=" N ALA G 220 " --> pdb=" O ASP G 216 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP G 221 " --> pdb=" O LEU G 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 216 through 221' Processing helix chain 'G' and resid 267 through 279 removed outlier: 3.585A pdb=" N GLN G 271 " --> pdb=" O ALA G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 285 through 306 removed outlier: 3.538A pdb=" N SER G 306 " --> pdb=" O ASP G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 342 removed outlier: 3.585A pdb=" N GLY G 332 " --> pdb=" O HIS G 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 41 Processing helix chain 'E' and resid 47 through 60 removed outlier: 3.655A pdb=" N LEU E 60 " --> pdb=" O GLN E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 76 removed outlier: 3.578A pdb=" N LEU E 66 " --> pdb=" O LEU E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 Processing helix chain 'E' and resid 88 through 95 removed outlier: 3.866A pdb=" N PHE E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 113 Processing helix chain 'E' and resid 124 through 140 Processing helix chain 'E' and resid 145 through 156 removed outlier: 3.733A pdb=" N SER E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 177 removed outlier: 4.396A pdb=" N LYS E 174 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N VAL E 175 " --> pdb=" O GLY E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 189 removed outlier: 3.948A pdb=" N GLU E 186 " --> pdb=" O GLU E 182 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE E 187 " --> pdb=" O CYS E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 197 Processing helix chain 'E' and resid 216 through 221 removed outlier: 3.875A pdb=" N ALA E 220 " --> pdb=" O ASP E 216 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 216 through 221' Processing helix chain 'E' and resid 267 through 278 removed outlier: 3.688A pdb=" N GLN E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN E 278 " --> pdb=" O CYS E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 306 removed outlier: 3.654A pdb=" N LEU E 290 " --> pdb=" O ARG E 286 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU E 291 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER E 306 " --> pdb=" O ASP E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 342 removed outlier: 3.734A pdb=" N GLY E 332 " --> pdb=" O HIS E 328 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN E 341 " --> pdb=" O HIS E 337 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN E 342 " --> pdb=" O LEU E 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 41 Processing helix chain 'H' and resid 47 through 76 removed outlier: 4.111A pdb=" N ARG H 51 " --> pdb=" O ALA H 47 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY H 63 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL H 64 " --> pdb=" O LEU H 60 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU H 65 " --> pdb=" O GLN H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 Processing helix chain 'H' and resid 88 through 95 Processing helix chain 'H' and resid 99 through 113 Processing helix chain 'H' and resid 124 through 140 Processing helix chain 'H' and resid 145 through 156 removed outlier: 3.605A pdb=" N SER H 156 " --> pdb=" O LEU H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 172 removed outlier: 4.670A pdb=" N GLY H 163 " --> pdb=" O ASN H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 191 Processing helix chain 'H' and resid 192 through 197 removed outlier: 4.226A pdb=" N ALA H 196 " --> pdb=" O MET H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 279 removed outlier: 3.693A pdb=" N GLN H 271 " --> pdb=" O ALA H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 306 removed outlier: 3.564A pdb=" N SER H 306 " --> pdb=" O ASP H 302 " (cutoff:3.500A) Processing helix chain 'H' and resid 329 through 342 Processing sheet with id=AA1, first strand: chain 'A' and resid 224 through 229 removed outlier: 7.118A pdb=" N LEU A 249 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N SER A 248 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU A 264 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU A 203 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE A 317 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE A 205 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N TYR A 319 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL A 207 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 237 removed outlier: 3.965A pdb=" N ARG A 242 " --> pdb=" O GLU B 232 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 224 through 228 removed outlier: 7.001A pdb=" N LEU B 249 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU B 203 " --> pdb=" O ARG B 315 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE B 317 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE B 205 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N TYR B 319 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL B 207 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 224 through 229 removed outlier: 7.137A pdb=" N LEU C 249 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N SER C 248 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU C 264 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU C 203 " --> pdb=" O ARG C 315 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE C 317 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE C 205 " --> pdb=" O ILE C 317 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 233 through 237 removed outlier: 3.984A pdb=" N ARG C 242 " --> pdb=" O GLU F 232 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 224 through 228 removed outlier: 6.865A pdb=" N LEU F 249 " --> pdb=" O LEU F 227 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU F 203 " --> pdb=" O ARG F 315 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE F 317 " --> pdb=" O LEU F 203 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE F 205 " --> pdb=" O ILE F 317 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N TYR F 319 " --> pdb=" O ILE F 205 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL F 207 " --> pdb=" O TYR F 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 224 through 229 removed outlier: 7.149A pdb=" N LEU D 249 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N SER D 248 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU D 264 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU D 203 " --> pdb=" O ARG D 315 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ILE D 317 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE D 205 " --> pdb=" O ILE D 317 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N TYR D 319 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL D 207 " --> pdb=" O TYR D 319 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 233 through 237 removed outlier: 3.941A pdb=" N ARG D 242 " --> pdb=" O GLU G 232 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 224 through 228 removed outlier: 7.006A pdb=" N LEU G 249 " --> pdb=" O LEU G 227 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU G 203 " --> pdb=" O ARG G 315 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE G 317 " --> pdb=" O LEU G 203 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE G 205 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N TYR G 319 " --> pdb=" O ILE G 205 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL G 207 " --> pdb=" O TYR G 319 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 224 through 229 removed outlier: 7.144A pdb=" N LEU E 249 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N SER E 248 " --> pdb=" O LEU E 264 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU E 264 " --> pdb=" O SER E 248 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU E 203 " --> pdb=" O ARG E 315 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE E 317 " --> pdb=" O LEU E 203 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE E 205 " --> pdb=" O ILE E 317 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N TYR E 319 " --> pdb=" O ILE E 205 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL E 207 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 233 through 237 Processing sheet with id=AB3, first strand: chain 'H' and resid 224 through 228 removed outlier: 6.900A pdb=" N LEU H 249 " --> pdb=" O LEU H 227 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU H 203 " --> pdb=" O ARG H 315 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ILE H 317 " --> pdb=" O LEU H 203 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE H 205 " --> pdb=" O ILE H 317 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N TYR H 319 " --> pdb=" O ILE H 205 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL H 207 " --> pdb=" O TYR H 319 " (cutoff:3.500A) 1100 hydrogen bonds defined for protein. 3249 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6356 1.34 - 1.46: 2844 1.46 - 1.58: 10560 1.58 - 1.69: 0 1.69 - 1.81: 172 Bond restraints: 19932 Sorted by residual: bond pdb=" CB PRO H 192 " pdb=" CG PRO H 192 " ideal model delta sigma weight residual 1.492 1.574 -0.082 5.00e-02 4.00e+02 2.71e+00 bond pdb=" CB PRO F 192 " pdb=" CG PRO F 192 " ideal model delta sigma weight residual 1.492 1.573 -0.081 5.00e-02 4.00e+02 2.66e+00 bond pdb=" CE2 PHE B 77 " pdb=" CZ PHE B 77 " ideal model delta sigma weight residual 1.382 1.352 0.030 3.00e-02 1.11e+03 1.01e+00 bond pdb=" CG PRO F 192 " pdb=" CD PRO F 192 " ideal model delta sigma weight residual 1.503 1.536 -0.033 3.40e-02 8.65e+02 9.35e-01 bond pdb=" CG PRO H 192 " pdb=" CD PRO H 192 " ideal model delta sigma weight residual 1.503 1.536 -0.033 3.40e-02 8.65e+02 9.22e-01 ... (remaining 19927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 26643 1.87 - 3.75: 330 3.75 - 5.62: 79 5.62 - 7.49: 22 7.49 - 9.37: 2 Bond angle restraints: 27076 Sorted by residual: angle pdb=" CA LEU C 32 " pdb=" CB LEU C 32 " pdb=" CG LEU C 32 " ideal model delta sigma weight residual 116.30 125.67 -9.37 3.50e+00 8.16e-02 7.16e+00 angle pdb=" N GLU F 186 " pdb=" CA GLU F 186 " pdb=" CB GLU F 186 " ideal model delta sigma weight residual 110.28 114.41 -4.13 1.55e+00 4.16e-01 7.08e+00 angle pdb=" CA LEU E 32 " pdb=" CB LEU E 32 " pdb=" CG LEU E 32 " ideal model delta sigma weight residual 116.30 125.61 -9.31 3.50e+00 8.16e-02 7.08e+00 angle pdb=" CA VAL B 175 " pdb=" C VAL B 175 " pdb=" N VAL B 176 " ideal model delta sigma weight residual 116.60 120.38 -3.78 1.45e+00 4.76e-01 6.80e+00 angle pdb=" N GLU H 186 " pdb=" CA GLU H 186 " pdb=" CB GLU H 186 " ideal model delta sigma weight residual 110.28 114.29 -4.01 1.55e+00 4.16e-01 6.68e+00 ... (remaining 27071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 10595 17.20 - 34.39: 1088 34.39 - 51.59: 266 51.59 - 68.78: 52 68.78 - 85.98: 31 Dihedral angle restraints: 12032 sinusoidal: 4548 harmonic: 7484 Sorted by residual: dihedral pdb=" CA ASP A 254 " pdb=" C ASP A 254 " pdb=" N LYS A 255 " pdb=" CA LYS A 255 " ideal model delta harmonic sigma weight residual 180.00 156.52 23.48 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA ASP H 279 " pdb=" CB ASP H 279 " pdb=" CG ASP H 279 " pdb=" OD1 ASP H 279 " ideal model delta sinusoidal sigma weight residual -30.00 -86.08 56.08 1 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CG ARG D 20 " pdb=" CD ARG D 20 " pdb=" NE ARG D 20 " pdb=" CZ ARG D 20 " ideal model delta sinusoidal sigma weight residual 90.00 133.92 -43.92 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 12029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1909 0.025 - 0.050: 787 0.050 - 0.075: 305 0.075 - 0.100: 112 0.100 - 0.124: 83 Chirality restraints: 3196 Sorted by residual: chirality pdb=" CA VAL B 263 " pdb=" N VAL B 263 " pdb=" C VAL B 263 " pdb=" CB VAL B 263 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA VAL E 251 " pdb=" N VAL E 251 " pdb=" C VAL E 251 " pdb=" CB VAL E 251 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA ILE C 213 " pdb=" N ILE C 213 " pdb=" C ILE C 213 " pdb=" CB ILE C 213 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 3193 not shown) Planarity restraints: 3384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 191 " 0.067 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO B 192 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 192 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 192 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 191 " 0.052 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO G 192 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO G 192 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO G 192 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU G 186 " 0.010 2.00e-02 2.50e+03 2.00e-02 4.01e+00 pdb=" CD GLU G 186 " -0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU G 186 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU G 186 " 0.012 2.00e-02 2.50e+03 ... (remaining 3381 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 368 2.71 - 3.25: 18557 3.25 - 3.80: 29843 3.80 - 4.35: 35371 4.35 - 4.90: 60751 Nonbonded interactions: 144890 Sorted by model distance: nonbonded pdb=" OD1 ASP C 254 " pdb=" N LYS C 255 " model vdw 2.158 3.120 nonbonded pdb=" OD1 ASP E 254 " pdb=" N LYS E 255 " model vdw 2.158 3.120 nonbonded pdb=" OE2 GLU E 232 " pdb=" NZ LYS E 246 " model vdw 2.202 3.120 nonbonded pdb=" OE2 GLU C 232 " pdb=" NZ LYS C 246 " model vdw 2.212 3.120 nonbonded pdb=" OG SER G 156 " pdb=" OD1 ASN G 159 " model vdw 2.293 3.040 ... (remaining 144885 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 56 or (resid 57 through 61 and (na \ me N or name CA or name C or name O or name CB )) or resid 62 through 64 or (res \ id 65 and (name N or name CA or name C or name O or name CB )) or resid 66 throu \ gh 93 or (resid 94 through 95 and (name N or name CA or name C or name O or name \ CB )) or resid 96 through 104 or (resid 105 and (name N or name CA or name C or \ name O or name CB )) or resid 106 through 342)) selection = (chain 'B' and (resid 10 through 14 or (resid 15 and (name N or name CA or name \ C or name O or name CB )) or resid 16 through 55 or (resid 56 through 61 and (na \ me N or name CA or name C or name O or name CB )) or resid 62 through 94 or (res \ id 95 and (name N or name CA or name C or name O or name CB )) or resid 96 throu \ gh 127 or (resid 128 and (name N or name CA or name C or name O or name CB )) or \ resid 129 through 130 or (resid 131 and (name N or name CA or name C or name O \ or name CB )) or resid 132 through 338 or (resid 339 and (name N or name CA or n \ ame C or name O or name CB )) or resid 340 through 342)) selection = (chain 'C' and (resid 10 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 56 or (resid 57 through 61 and (na \ me N or name CA or name C or name O or name CB )) or resid 62 through 64 or (res \ id 65 and (name N or name CA or name C or name O or name CB )) or resid 66 throu \ gh 93 or (resid 94 through 95 and (name N or name CA or name C or name O or name \ CB )) or resid 96 through 104 or (resid 105 and (name N or name CA or name C or \ name O or name CB )) or resid 106 through 342)) selection = (chain 'D' and (resid 10 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 56 or (resid 57 through 61 and (na \ me N or name CA or name C or name O or name CB )) or resid 62 through 64 or (res \ id 65 and (name N or name CA or name C or name O or name CB )) or resid 66 throu \ gh 93 or (resid 94 through 95 and (name N or name CA or name C or name O or name \ CB )) or resid 96 through 104 or (resid 105 and (name N or name CA or name C or \ name O or name CB )) or resid 106 through 342)) selection = (chain 'E' and (resid 10 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 56 or (resid 57 through 61 and (na \ me N or name CA or name C or name O or name CB )) or resid 62 through 64 or (res \ id 65 and (name N or name CA or name C or name O or name CB )) or resid 66 throu \ gh 93 or (resid 94 through 95 and (name N or name CA or name C or name O or name \ CB )) or resid 96 through 104 or (resid 105 and (name N or name CA or name C or \ name O or name CB )) or resid 106 through 342)) selection = (chain 'F' and (resid 10 through 14 or (resid 15 and (name N or name CA or name \ C or name O or name CB )) or resid 16 through 55 or (resid 56 through 61 and (na \ me N or name CA or name C or name O or name CB )) or resid 62 through 94 or (res \ id 95 and (name N or name CA or name C or name O or name CB )) or resid 96 throu \ gh 127 or (resid 128 and (name N or name CA or name C or name O or name CB )) or \ resid 129 through 130 or (resid 131 and (name N or name CA or name C or name O \ or name CB )) or resid 132 through 338 or (resid 339 and (name N or name CA or n \ ame C or name O or name CB )) or resid 340 through 342)) selection = (chain 'G' and (resid 10 through 14 or (resid 15 and (name N or name CA or name \ C or name O or name CB )) or resid 16 through 55 or (resid 56 through 61 and (na \ me N or name CA or name C or name O or name CB )) or resid 62 through 94 or (res \ id 95 and (name N or name CA or name C or name O or name CB )) or resid 96 throu \ gh 127 or (resid 128 and (name N or name CA or name C or name O or name CB )) or \ resid 129 through 130 or (resid 131 and (name N or name CA or name C or name O \ or name CB )) or resid 132 through 338 or (resid 339 and (name N or name CA or n \ ame C or name O or name CB )) or resid 340 through 342)) selection = (chain 'H' and (resid 10 through 14 or (resid 15 and (name N or name CA or name \ C or name O or name CB )) or resid 16 through 55 or (resid 56 through 61 and (na \ me N or name CA or name C or name O or name CB )) or resid 62 through 94 or (res \ id 95 and (name N or name CA or name C or name O or name CB )) or resid 96 throu \ gh 127 or (resid 128 and (name N or name CA or name C or name O or name CB )) or \ resid 129 through 130 or (resid 131 and (name N or name CA or name C or name O \ or name CB )) or resid 132 through 338 or (resid 339 and (name N or name CA or n \ ame C or name O or name CB )) or resid 340 through 342)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.200 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 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 : 0.002 0.082 19932 Z= 0.103 Angle : 0.570 9.367 27076 Z= 0.272 Chirality : 0.037 0.124 3196 Planarity : 0.005 0.103 3384 Dihedral : 15.581 85.977 7144 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.40 % Allowed : 0.84 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.17), residues: 2492 helix: 2.34 (0.14), residues: 1344 sheet: -0.26 (0.32), residues: 244 loop : -1.27 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 23 TYR 0.012 0.001 TYR H 226 PHE 0.023 0.001 PHE A 36 TRP 0.015 0.001 TRP H 214 HIS 0.005 0.000 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00220 (19932) covalent geometry : angle 0.57033 (27076) hydrogen bonds : bond 0.13977 ( 1100) hydrogen bonds : angle 6.15029 ( 3249) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 341 time to evaluate : 0.449 Fit side-chains REVERT: C 191 ASN cc_start: 0.7730 (OUTLIER) cc_final: 0.7266 (t0) REVERT: E 191 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7348 (t0) outliers start: 8 outliers final: 6 residues processed: 349 average time/residue: 0.1380 time to fit residues: 71.2255 Evaluate side-chains 289 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 281 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain C residue 191 ASN Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain H residue 50 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 0.0020 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 247 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 20.0000 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 191 ASN A 340 GLN A 342 GLN ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 HIS ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 GLN F 271 GLN F 278 GLN F 341 GLN D 159 ASN D 340 GLN ** G 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 271 GLN H 278 GLN H 341 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.237517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.200564 restraints weight = 21271.210| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 2.53 r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19932 Z= 0.118 Angle : 0.570 8.273 27076 Z= 0.271 Chirality : 0.039 0.161 3196 Planarity : 0.005 0.073 3384 Dihedral : 3.794 21.461 2766 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.29 % Allowed : 9.01 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.17), residues: 2492 helix: 2.50 (0.14), residues: 1352 sheet: -0.16 (0.29), residues: 296 loop : -1.36 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 286 TYR 0.006 0.001 TYR D 314 PHE 0.015 0.001 PHE A 36 TRP 0.009 0.001 TRP F 99 HIS 0.004 0.001 HIS E 26 Details of bonding type rmsd covalent geometry : bond 0.00263 (19932) covalent geometry : angle 0.57005 (27076) hydrogen bonds : bond 0.03775 ( 1100) hydrogen bonds : angle 4.65818 ( 3249) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 304 time to evaluate : 0.471 Fit side-chains REVERT: A 279 ASP cc_start: 0.7862 (t70) cc_final: 0.7628 (t70) REVERT: F 184 MET cc_start: 0.5784 (ttm) cc_final: 0.4833 (mtp) REVERT: H 184 MET cc_start: 0.5890 (ttm) cc_final: 0.4806 (mtp) outliers start: 26 outliers final: 18 residues processed: 312 average time/residue: 0.1414 time to fit residues: 65.0601 Evaluate side-chains 302 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 284 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain H residue 72 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 75 optimal weight: 9.9990 chunk 133 optimal weight: 9.9990 chunk 185 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 HIS ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 GLN F 271 GLN ** D 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 159 ASN ** G 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 271 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.231516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.197971 restraints weight = 21300.244| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 2.49 r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19932 Z= 0.195 Angle : 0.636 8.975 27076 Z= 0.304 Chirality : 0.042 0.178 3196 Planarity : 0.005 0.057 3384 Dihedral : 4.085 19.026 2756 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.18 % Allowed : 14.65 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.17), residues: 2492 helix: 2.16 (0.14), residues: 1388 sheet: -0.30 (0.29), residues: 296 loop : -1.56 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 198 TYR 0.014 0.002 TYR B 226 PHE 0.023 0.002 PHE G 284 TRP 0.009 0.001 TRP G 201 HIS 0.004 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00478 (19932) covalent geometry : angle 0.63561 (27076) hydrogen bonds : bond 0.04474 ( 1100) hydrogen bonds : angle 4.61801 ( 3249) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 287 time to evaluate : 0.689 Fit side-chains REVERT: A 234 ILE cc_start: 0.8618 (mm) cc_final: 0.8411 (mm) REVERT: A 341 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.6878 (mp10) REVERT: F 184 MET cc_start: 0.6280 (ttm) cc_final: 0.5436 (mtp) REVERT: D 234 ILE cc_start: 0.8607 (mm) cc_final: 0.8406 (mm) REVERT: H 184 MET cc_start: 0.6237 (ttm) cc_final: 0.5454 (mtp) outliers start: 44 outliers final: 34 residues processed: 310 average time/residue: 0.1457 time to fit residues: 66.2109 Evaluate side-chains 313 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 278 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 341 GLN Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 159 ASN Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 207 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 5 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 57 optimal weight: 0.2980 chunk 31 optimal weight: 6.9990 chunk 223 optimal weight: 0.9980 chunk 251 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 170 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 26 HIS ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS ** E 159 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 = 0.4604 r_free = 0.4604 target = 0.235621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.193732 restraints weight = 21308.632| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 3.57 r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19932 Z= 0.100 Angle : 0.538 8.424 27076 Z= 0.256 Chirality : 0.038 0.176 3196 Planarity : 0.004 0.045 3384 Dihedral : 3.814 18.412 2756 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.23 % Allowed : 16.68 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.17), residues: 2492 helix: 2.33 (0.14), residues: 1392 sheet: -0.23 (0.29), residues: 296 loop : -1.48 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 198 TYR 0.005 0.001 TYR H 226 PHE 0.009 0.001 PHE A 36 TRP 0.012 0.001 TRP D 336 HIS 0.002 0.000 HIS E 26 Details of bonding type rmsd covalent geometry : bond 0.00215 (19932) covalent geometry : angle 0.53778 (27076) hydrogen bonds : bond 0.03294 ( 1100) hydrogen bonds : angle 4.21323 ( 3249) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 291 time to evaluate : 0.677 Fit side-chains REVERT: A 234 ILE cc_start: 0.8477 (mm) cc_final: 0.8240 (mm) REVERT: A 341 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.6040 (mp10) REVERT: F 184 MET cc_start: 0.6039 (ttm) cc_final: 0.5384 (mtp) REVERT: D 157 LYS cc_start: 0.8695 (mttm) cc_final: 0.8454 (mttt) REVERT: D 234 ILE cc_start: 0.8487 (mm) cc_final: 0.8242 (mm) REVERT: D 341 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7084 (mp10) REVERT: H 184 MET cc_start: 0.5696 (ttm) cc_final: 0.5167 (mtp) outliers start: 45 outliers final: 28 residues processed: 316 average time/residue: 0.1458 time to fit residues: 67.7734 Evaluate side-chains 307 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 277 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 29 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 341 GLN Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 137 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 175 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 0.0060 chunk 181 optimal weight: 1.9990 chunk 185 optimal weight: 7.9990 chunk 206 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 233 optimal weight: 0.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN B 159 ASN ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 HIS ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 GLN D 341 GLN G 159 ASN ** G 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 341 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.233851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.200222 restraints weight = 21287.449| |-----------------------------------------------------------------------------| r_work (start): 0.4276 rms_B_bonded: 2.49 r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19932 Z= 0.131 Angle : 0.565 8.792 27076 Z= 0.267 Chirality : 0.039 0.186 3196 Planarity : 0.004 0.046 3384 Dihedral : 3.816 19.314 2756 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.87 % Allowed : 17.52 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.17), residues: 2492 helix: 2.34 (0.14), residues: 1388 sheet: -0.28 (0.29), residues: 296 loop : -1.49 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 198 TYR 0.008 0.001 TYR H 226 PHE 0.012 0.001 PHE B 284 TRP 0.010 0.001 TRP A 336 HIS 0.002 0.001 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.00311 (19932) covalent geometry : angle 0.56538 (27076) hydrogen bonds : bond 0.03540 ( 1100) hydrogen bonds : angle 4.18657 ( 3249) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 285 time to evaluate : 0.766 Fit side-chains REVERT: A 234 ILE cc_start: 0.8540 (mm) cc_final: 0.8307 (mm) REVERT: F 31 LEU cc_start: 0.7582 (mm) cc_final: 0.7358 (mm) REVERT: F 184 MET cc_start: 0.6259 (ttm) cc_final: 0.5858 (mtp) REVERT: D 157 LYS cc_start: 0.8776 (mttm) cc_final: 0.8544 (mttt) REVERT: D 253 ARG cc_start: 0.6836 (ttt90) cc_final: 0.6109 (tpt170) REVERT: H 31 LEU cc_start: 0.7572 (mm) cc_final: 0.7342 (mm) REVERT: H 184 MET cc_start: 0.6150 (ttm) cc_final: 0.5688 (mtp) outliers start: 58 outliers final: 47 residues processed: 323 average time/residue: 0.1469 time to fit residues: 70.4678 Evaluate side-chains 320 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 273 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 29 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 341 GLN Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 29 CYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 130 CYS Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 159 ASN Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 279 ASP Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 251 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 140 optimal weight: 0.6980 chunk 156 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 198 optimal weight: 8.9990 chunk 33 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 246 optimal weight: 0.8980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 ASN ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 HIS ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 GLN F 83 HIS G 159 ASN ** G 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.231427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.202304 restraints weight = 21158.483| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 2.14 r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19932 Z= 0.179 Angle : 0.608 8.763 27076 Z= 0.290 Chirality : 0.041 0.205 3196 Planarity : 0.004 0.045 3384 Dihedral : 4.008 19.017 2756 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.22 % Allowed : 18.96 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.17), residues: 2492 helix: 2.12 (0.14), residues: 1404 sheet: -0.39 (0.29), residues: 296 loop : -1.54 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 23 TYR 0.011 0.002 TYR H 226 PHE 0.018 0.001 PHE B 284 TRP 0.012 0.001 TRP H 99 HIS 0.004 0.001 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.00442 (19932) covalent geometry : angle 0.60823 (27076) hydrogen bonds : bond 0.04009 ( 1100) hydrogen bonds : angle 4.31262 ( 3249) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 285 time to evaluate : 0.741 Fit side-chains REVERT: A 234 ILE cc_start: 0.8559 (mm) cc_final: 0.8341 (mm) REVERT: A 341 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.6615 (mp10) REVERT: F 31 LEU cc_start: 0.7530 (mm) cc_final: 0.7293 (mm) REVERT: F 184 MET cc_start: 0.6444 (ttm) cc_final: 0.6053 (mtp) REVERT: D 341 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.5919 (mp10) REVERT: G 342 GLN cc_start: 0.6670 (tt0) cc_final: 0.6440 (pt0) REVERT: E 341 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.6163 (mt0) REVERT: H 184 MET cc_start: 0.6343 (ttm) cc_final: 0.5874 (mtp) outliers start: 65 outliers final: 48 residues processed: 328 average time/residue: 0.1543 time to fit residues: 74.9824 Evaluate side-chains 328 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 277 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 29 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 341 GLN Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 29 CYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 130 CYS Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 159 ASN Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 279 ASP Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 341 GLN Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 251 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 107 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 160 optimal weight: 30.0000 chunk 102 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 235 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 187 optimal weight: 0.0770 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 HIS ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 GLN D 341 GLN ** G 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 271 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.222073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.202687 restraints weight = 20910.721| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 1.03 r_work: 0.3957 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19932 Z= 0.122 Angle : 0.564 8.760 27076 Z= 0.268 Chirality : 0.039 0.206 3196 Planarity : 0.004 0.047 3384 Dihedral : 3.896 19.002 2756 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.82 % Allowed : 20.25 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.17), residues: 2492 helix: 2.28 (0.14), residues: 1392 sheet: -0.36 (0.29), residues: 296 loop : -1.49 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 23 TYR 0.008 0.001 TYR H 226 PHE 0.012 0.001 PHE G 284 TRP 0.011 0.001 TRP A 336 HIS 0.002 0.000 HIS B 337 Details of bonding type rmsd covalent geometry : bond 0.00287 (19932) covalent geometry : angle 0.56368 (27076) hydrogen bonds : bond 0.03426 ( 1100) hydrogen bonds : angle 4.14866 ( 3249) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 285 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 341 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.6216 (mp10) REVERT: B 341 GLN cc_start: 0.8013 (tp40) cc_final: 0.7805 (mt0) REVERT: F 31 LEU cc_start: 0.7553 (mm) cc_final: 0.7331 (mm) REVERT: F 184 MET cc_start: 0.6844 (ttm) cc_final: 0.6447 (mtp) REVERT: G 341 GLN cc_start: 0.8033 (tp40) cc_final: 0.7831 (mt0) REVERT: G 342 GLN cc_start: 0.6927 (tt0) cc_final: 0.6698 (pt0) REVERT: E 341 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.6377 (mt0) REVERT: H 31 LEU cc_start: 0.7566 (mm) cc_final: 0.7336 (mm) REVERT: H 184 MET cc_start: 0.6684 (ttm) cc_final: 0.6239 (mtp) outliers start: 57 outliers final: 46 residues processed: 320 average time/residue: 0.1491 time to fit residues: 69.8844 Evaluate side-chains 325 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 277 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 29 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 341 GLN Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 29 CYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 130 CYS Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 279 ASP Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain E residue 341 GLN Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 251 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 35 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 225 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 HIS ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 GLN F 341 GLN G 159 ASN ** G 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS ** E 159 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 = 0.4396 r_free = 0.4396 target = 0.219569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.198840 restraints weight = 20860.584| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 1.18 r_work: 0.3898 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3829 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19932 Z= 0.174 Angle : 0.618 9.387 27076 Z= 0.293 Chirality : 0.041 0.218 3196 Planarity : 0.004 0.045 3384 Dihedral : 4.039 18.677 2756 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.42 % Allowed : 20.10 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.17), residues: 2492 helix: 2.10 (0.14), residues: 1408 sheet: -0.46 (0.29), residues: 296 loop : -1.50 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 286 TYR 0.012 0.002 TYR H 226 PHE 0.019 0.001 PHE G 284 TRP 0.011 0.001 TRP H 99 HIS 0.004 0.001 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.00427 (19932) covalent geometry : angle 0.61790 (27076) hydrogen bonds : bond 0.03962 ( 1100) hydrogen bonds : angle 4.29337 ( 3249) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 276 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: A 341 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.7380 (mp10) REVERT: F 31 LEU cc_start: 0.7650 (mm) cc_final: 0.7421 (mm) REVERT: F 184 MET cc_start: 0.6966 (ttm) cc_final: 0.6632 (mtp) REVERT: D 341 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.6555 (mp10) REVERT: G 341 GLN cc_start: 0.8072 (tp40) cc_final: 0.7858 (mt0) REVERT: E 341 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.6400 (mt0) REVERT: H 31 LEU cc_start: 0.7634 (mm) cc_final: 0.7405 (mm) REVERT: H 184 MET cc_start: 0.6769 (ttm) cc_final: 0.6345 (mtp) outliers start: 69 outliers final: 57 residues processed: 322 average time/residue: 0.1440 time to fit residues: 68.8611 Evaluate side-chains 331 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 271 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 29 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 341 GLN Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 29 CYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 130 CYS Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 159 ASN Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 279 ASP Chi-restraints excluded: chain G residue 316 LEU Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain E residue 341 GLN Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 251 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 62 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 130 optimal weight: 0.0870 chunk 150 optimal weight: 3.9990 chunk 152 optimal weight: 0.3980 chunk 212 optimal weight: 0.6980 chunk 242 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 208 optimal weight: 4.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 26 HIS ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS ** E 159 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 = 0.4436 r_free = 0.4436 target = 0.223969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.204909 restraints weight = 20641.710| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 1.05 r_work: 0.3996 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3911 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19932 Z= 0.100 Angle : 0.562 9.399 27076 Z= 0.264 Chirality : 0.038 0.214 3196 Planarity : 0.004 0.048 3384 Dihedral : 3.825 18.579 2756 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.57 % Allowed : 20.79 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.17), residues: 2492 helix: 2.37 (0.14), residues: 1396 sheet: -0.30 (0.29), residues: 296 loop : -1.40 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 286 TYR 0.006 0.001 TYR G 314 PHE 0.006 0.001 PHE G 284 TRP 0.014 0.001 TRP A 336 HIS 0.002 0.000 HIS D 337 Details of bonding type rmsd covalent geometry : bond 0.00217 (19932) covalent geometry : angle 0.56248 (27076) hydrogen bonds : bond 0.03094 ( 1100) hydrogen bonds : angle 4.01788 ( 3249) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 278 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: A 341 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.7322 (mp10) REVERT: B 186 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6342 (mp0) REVERT: F 31 LEU cc_start: 0.7504 (mm) cc_final: 0.7275 (mm) REVERT: F 184 MET cc_start: 0.6823 (ttm) cc_final: 0.6468 (mtp) REVERT: D 253 ARG cc_start: 0.7176 (ttt90) cc_final: 0.6363 (tpt170) REVERT: D 341 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.6923 (mp10) REVERT: E 341 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7725 (mp10) REVERT: H 31 LEU cc_start: 0.7514 (mm) cc_final: 0.7282 (mm) REVERT: H 184 MET cc_start: 0.6692 (ttm) cc_final: 0.6294 (mtp) outliers start: 52 outliers final: 43 residues processed: 312 average time/residue: 0.1484 time to fit residues: 67.9013 Evaluate side-chains 320 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 273 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 341 GLN Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 130 CYS Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain E residue 341 GLN Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 80 HIS Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 236 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 116 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 143 optimal weight: 0.0070 chunk 125 optimal weight: 0.9990 chunk 244 optimal weight: 0.8980 chunk 99 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 221 optimal weight: 0.9980 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 HIS ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 GLN D 342 GLN E 26 HIS ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.222255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.204642 restraints weight = 20919.524| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 0.96 r_work: 0.4010 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3955 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19932 Z= 0.122 Angle : 0.581 9.327 27076 Z= 0.272 Chirality : 0.039 0.212 3196 Planarity : 0.004 0.047 3384 Dihedral : 3.786 18.212 2756 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.62 % Allowed : 21.04 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.17), residues: 2492 helix: 2.39 (0.14), residues: 1396 sheet: -0.32 (0.29), residues: 296 loop : -1.37 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 189 TYR 0.008 0.001 TYR H 226 PHE 0.012 0.001 PHE G 284 TRP 0.010 0.001 TRP A 336 HIS 0.002 0.000 HIS G 204 Details of bonding type rmsd covalent geometry : bond 0.00286 (19932) covalent geometry : angle 0.58080 (27076) hydrogen bonds : bond 0.03344 ( 1100) hydrogen bonds : angle 4.04238 ( 3249) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4984 Ramachandran restraints generated. 2492 Oldfield, 0 Emsley, 2492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 274 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 291 GLU cc_start: 0.6832 (tp30) cc_final: 0.6631 (tp30) REVERT: C 253 ARG cc_start: 0.6523 (tpt170) cc_final: 0.6250 (tpt170) REVERT: F 31 LEU cc_start: 0.7453 (mm) cc_final: 0.7222 (mm) REVERT: F 184 MET cc_start: 0.6798 (ttm) cc_final: 0.6359 (mtp) REVERT: E 341 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7747 (mp10) REVERT: H 31 LEU cc_start: 0.7482 (mm) cc_final: 0.7241 (mm) REVERT: H 184 MET cc_start: 0.6682 (ttm) cc_final: 0.6253 (mtp) outliers start: 53 outliers final: 49 residues processed: 307 average time/residue: 0.1542 time to fit residues: 69.7794 Evaluate side-chains 320 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 270 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 341 GLN Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 130 CYS Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 309 GLU Chi-restraints excluded: chain E residue 341 GLN Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 251 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 96 optimal weight: 9.9990 chunk 223 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 239 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 232 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 HIS ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS ** E 159 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 = 0.4405 r_free = 0.4405 target = 0.220470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.202409 restraints weight = 20950.101| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 1.00 r_work: 0.3988 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3931 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19932 Z= 0.156 Angle : 0.619 13.097 27076 Z= 0.290 Chirality : 0.040 0.215 3196 Planarity : 0.004 0.046 3384 Dihedral : 3.911 18.237 2756 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.62 % Allowed : 21.14 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.17), residues: 2492 helix: 2.23 (0.14), residues: 1404 sheet: -0.38 (0.29), residues: 296 loop : -1.41 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 23 TYR 0.009 0.001 TYR H 226 PHE 0.017 0.001 PHE G 284 TRP 0.015 0.001 TRP F 214 HIS 0.003 0.001 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.00380 (19932) covalent geometry : angle 0.61893 (27076) hydrogen bonds : bond 0.03721 ( 1100) hydrogen bonds : angle 4.17379 ( 3249) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3366.35 seconds wall clock time: 58 minutes 43.19 seconds (3523.19 seconds total)