Starting phenix.real_space_refine on Tue May 20 13:20:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ik0_35503/05_2025/8ik0_35503.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ik0_35503/05_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_35503/05_2025/8ik0_35503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ik0_35503/05_2025/8ik0_35503.map" model { file = "/net/cci-nas-00/data/ceres_data/8ik0_35503/05_2025/8ik0_35503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ik0_35503/05_2025/8ik0_35503.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.020 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 6, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 4} 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: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4} 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: {'GLN:plan1': 6, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 4} 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: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4} 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: {'GLN:plan1': 6, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 4} 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: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4} 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: {'GLN:plan1': 6, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 4} 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: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 61 Time building chain proxies: 11.87, per 1000 atoms: 0.61 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: 5.01 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.07 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: 5.62 Time building geometry restraints manager: 5.79 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: 0.05 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 42.200 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.370 ------------------------------------------------------------------------------- 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 : 5.65 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (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 TRP 0.015 0.001 TRP H 214 HIS 0.005 0.000 HIS B 80 PHE 0.023 0.001 PHE A 36 TYR 0.012 0.001 TYR H 226 ARG 0.006 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.13977 ( 1100) hydrogen bonds : angle 6.15029 ( 3249) covalent geometry : bond 0.00220 (19932) covalent geometry : angle 0.57033 (27076) *********************** 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 : 2.260 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: 0.3440 time to fit residues: 176.6556 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 : 2.192 ------------------------------------------------------------------------------- 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 212 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 102 optimal weight: 0.0570 chunk 197 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 chunk 147 optimal weight: 7.9990 chunk 228 optimal weight: 0.9980 overall best weight: 1.5902 ------------------------------------------------------------------------------- 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 342 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 F 271 GLN F 278 GLN F 341 GLN D 159 ASN 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 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 = 0.4595 r_free = 0.4595 target = 0.234715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.199678 restraints weight = 21250.701| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 2.40 r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19932 Z= 0.148 Angle : 0.601 8.225 27076 Z= 0.287 Chirality : 0.040 0.167 3196 Planarity : 0.005 0.074 3384 Dihedral : 3.924 21.598 2766 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.58 % Allowed : 9.80 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.17), residues: 2492 helix: 2.43 (0.14), residues: 1352 sheet: -0.20 (0.29), residues: 296 loop : -1.43 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 336 HIS 0.004 0.001 HIS E 26 PHE 0.016 0.001 PHE G 284 TYR 0.009 0.001 TYR G 226 ARG 0.006 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 1100) hydrogen bonds : angle 4.72322 ( 3249) covalent geometry : bond 0.00350 (19932) covalent geometry : angle 0.60130 (27076) *********************** 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 328 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 296 time to evaluate : 2.047 Fit side-chains REVERT: A 279 ASP cc_start: 0.7885 (t70) cc_final: 0.7617 (t70) REVERT: F 184 MET cc_start: 0.5895 (ttm) cc_final: 0.4908 (mtp) REVERT: H 184 MET cc_start: 0.5989 (ttm) cc_final: 0.5066 (mtp) outliers start: 32 outliers final: 25 residues processed: 310 average time/residue: 0.3446 time to fit residues: 156.4310 Evaluate side-chains 305 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 280 time to evaluate : 2.308 ------------------------------------------------------------------------------- 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 B residue 159 ASN Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 179 ARG 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 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 236 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 Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 151 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 chunk 191 optimal weight: 10.0000 chunk 231 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 188 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 D 83 HIS ** D 341 GLN ** 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** ** E 341 GLN ** 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 = 0.4357 r_free = 0.4357 target = 0.217054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.198083 restraints weight = 20716.601| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 1.06 r_work: 0.3924 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3867 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 19932 Z= 0.276 Angle : 0.731 9.935 27076 Z= 0.352 Chirality : 0.046 0.186 3196 Planarity : 0.005 0.057 3384 Dihedral : 4.489 20.914 2756 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.92 % Allowed : 15.84 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.17), residues: 2492 helix: 1.81 (0.14), residues: 1360 sheet: -0.50 (0.30), residues: 296 loop : -1.72 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 336 HIS 0.006 0.001 HIS D 162 PHE 0.031 0.002 PHE G 284 TYR 0.018 0.003 TYR B 226 ARG 0.008 0.001 ARG E 198 Details of bonding type rmsd hydrogen bonds : bond 0.05381 ( 1100) hydrogen bonds : angle 4.90587 ( 3249) covalent geometry : bond 0.00688 (19932) covalent geometry : angle 0.73067 (27076) *********************** 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 349 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 290 time to evaluate : 2.289 Fit side-chains REVERT: A 341 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.7220 (mp10) REVERT: F 184 MET cc_start: 0.6760 (ttm) cc_final: 0.6018 (mtp) REVERT: D 341 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7190 (mp10) REVERT: H 184 MET cc_start: 0.6689 (ttm) cc_final: 0.6055 (mtp) outliers start: 59 outliers final: 46 residues processed: 323 average time/residue: 0.3531 time to fit residues: 167.0920 Evaluate side-chains 330 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 282 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 167 SER 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 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 190 THR Chi-restraints excluded: chain C residue 317 ILE 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 D residue 57 LEU Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 341 GLN 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 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 E residue 62 LEU Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 135 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 60 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 133 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 136 optimal weight: 0.2980 chunk 88 optimal weight: 0.2980 chunk 182 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** E 26 HIS ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 271 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.233975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.190468 restraints weight = 21273.478| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 3.95 r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19932 Z= 0.104 Angle : 0.549 8.703 27076 Z= 0.262 Chirality : 0.038 0.176 3196 Planarity : 0.004 0.054 3384 Dihedral : 4.019 19.688 2756 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.28 % Allowed : 18.17 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.17), residues: 2492 helix: 2.19 (0.14), residues: 1388 sheet: -0.33 (0.29), residues: 296 loop : -1.65 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 336 HIS 0.003 0.000 HIS G 337 PHE 0.011 0.001 PHE A 36 TYR 0.011 0.001 TYR H 226 ARG 0.007 0.000 ARG E 198 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 1100) hydrogen bonds : angle 4.28874 ( 3249) covalent geometry : bond 0.00220 (19932) covalent geometry : angle 0.54895 (27076) *********************** 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 335 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 289 time to evaluate : 2.152 Fit side-chains REVERT: A 234 ILE cc_start: 0.8314 (mm) cc_final: 0.8088 (mm) REVERT: A 341 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.6281 (mp10) REVERT: F 184 MET cc_start: 0.5990 (ttm) cc_final: 0.5542 (mtp) REVERT: F 226 TYR cc_start: 0.7481 (m-80) cc_final: 0.7226 (m-80) REVERT: D 341 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7287 (mp10) REVERT: H 184 MET cc_start: 0.5487 (ttm) cc_final: 0.5087 (mtp) outliers start: 46 outliers final: 33 residues processed: 313 average time/residue: 0.3437 time to fit residues: 158.1935 Evaluate side-chains 307 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 272 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 186 GLU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 207 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 30 VAL Chi-restraints excluded: chain G residue 62 LEU 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 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 252 ILE Chi-restraints excluded: chain H residue 31 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 249 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 71 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 ** 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 341 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.215807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.192880 restraints weight = 21002.615| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 0.86 r_work: 0.3930 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3873 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 19932 Z= 0.272 Angle : 0.713 9.845 27076 Z= 0.341 Chirality : 0.045 0.195 3196 Planarity : 0.005 0.056 3384 Dihedral : 4.490 21.817 2756 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.96 % Allowed : 19.01 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.17), residues: 2492 helix: 1.78 (0.14), residues: 1372 sheet: -0.58 (0.29), residues: 296 loop : -1.76 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 336 HIS 0.006 0.001 HIS D 162 PHE 0.027 0.002 PHE G 284 TYR 0.016 0.002 TYR B 226 ARG 0.011 0.001 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.05104 ( 1100) hydrogen bonds : angle 4.72585 ( 3249) covalent geometry : bond 0.00674 (19932) covalent geometry : angle 0.71296 (27076) *********************** 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 365 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 285 time to evaluate : 2.332 Fit side-chains REVERT: A 341 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.7317 (mp10) REVERT: C 253 ARG cc_start: 0.6791 (tpt170) cc_final: 0.6589 (tpt170) REVERT: F 184 MET cc_start: 0.6841 (ttm) cc_final: 0.6534 (mtp) REVERT: D 341 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7293 (mp10) REVERT: G 291 GLU cc_start: 0.7223 (tp30) cc_final: 0.7019 (tp30) REVERT: E 341 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.6486 (mt0) REVERT: H 184 MET cc_start: 0.6747 (ttm) cc_final: 0.6266 (mtp) outliers start: 80 outliers final: 62 residues processed: 335 average time/residue: 0.3381 time to fit residues: 167.7308 Evaluate side-chains 345 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 280 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 175 VAL 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 213 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 342 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 179 ARG Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 244 VAL 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 80 HIS 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 F residue 236 THR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 175 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 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 236 THR Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 316 LEU Chi-restraints excluded: chain G residue 339 GLN Chi-restraints excluded: chain G residue 342 GLN Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 341 GLN Chi-restraints excluded: chain H residue 31 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 89 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 196 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.221045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.201909 restraints weight = 20866.945| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 1.05 r_work: 0.3947 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3861 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2017 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= 0.114 Angle : 0.557 8.609 27076 Z= 0.269 Chirality : 0.039 0.203 3196 Planarity : 0.004 0.059 3384 Dihedral : 4.110 21.297 2756 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.42 % Allowed : 20.74 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.17), residues: 2492 helix: 2.19 (0.15), residues: 1372 sheet: -0.44 (0.29), residues: 296 loop : -1.67 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 336 HIS 0.002 0.000 HIS G 337 PHE 0.007 0.001 PHE G 284 TYR 0.010 0.001 TYR H 226 ARG 0.003 0.000 ARG D 286 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 1100) hydrogen bonds : angle 4.22106 ( 3249) covalent geometry : bond 0.00259 (19932) covalent geometry : angle 0.55718 (27076) *********************** 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 354 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 285 time to evaluate : 2.095 Fit side-chains revert: symmetry clash REVERT: A 271 GLN cc_start: 0.7657 (tm-30) cc_final: 0.7454 (tp40) REVERT: A 341 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.7395 (mp10) REVERT: C 341 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7555 (mp10) REVERT: F 184 MET cc_start: 0.6791 (ttm) cc_final: 0.6545 (mtp) REVERT: D 302 ASP cc_start: 0.7853 (m-30) cc_final: 0.7483 (m-30) REVERT: E 341 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.6327 (mt0) REVERT: H 184 MET cc_start: 0.6613 (ttm) cc_final: 0.6233 (mtp) outliers start: 69 outliers final: 49 residues processed: 327 average time/residue: 0.3605 time to fit residues: 174.1894 Evaluate side-chains 329 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 277 time to evaluate : 2.054 ------------------------------------------------------------------------------- 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 249 LEU Chi-restraints excluded: chain A residue 254 ASP 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 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 213 ILE 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 80 HIS Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 341 GLN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 80 HIS 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 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 186 GLU 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 80 HIS Chi-restraints excluded: chain E residue 244 VAL 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 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 216 optimal weight: 0.9990 chunk 230 optimal weight: 7.9990 chunk 205 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 234 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 109 optimal weight: 0.0370 chunk 225 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- 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 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 = 0.4397 r_free = 0.4397 target = 0.219683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.200518 restraints weight = 20966.267| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 1.09 r_work: 0.3930 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3875 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19932 Z= 0.164 Angle : 0.600 8.651 27076 Z= 0.288 Chirality : 0.040 0.207 3196 Planarity : 0.005 0.057 3384 Dihedral : 4.143 20.918 2756 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.86 % Allowed : 21.58 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.17), residues: 2492 helix: 2.06 (0.14), residues: 1388 sheet: -0.48 (0.29), residues: 296 loop : -1.63 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 99 HIS 0.003 0.001 HIS C 84 PHE 0.016 0.001 PHE G 284 TYR 0.009 0.001 TYR B 319 ARG 0.010 0.000 ARG D 23 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 1100) hydrogen bonds : angle 4.29253 ( 3249) covalent geometry : bond 0.00400 (19932) covalent geometry : angle 0.60049 (27076) *********************** 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 356 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 278 time to evaluate : 2.148 Fit side-chains revert: symmetry clash REVERT: B 341 GLN cc_start: 0.8094 (tp40) cc_final: 0.7838 (mt0) REVERT: F 184 MET cc_start: 0.6836 (ttm) cc_final: 0.6532 (mtp) REVERT: D 302 ASP cc_start: 0.7748 (m-30) cc_final: 0.7378 (m-30) REVERT: G 341 GLN cc_start: 0.8116 (tp40) cc_final: 0.7869 (mt0) REVERT: E 341 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.6469 (mt0) REVERT: H 184 MET cc_start: 0.6732 (ttm) cc_final: 0.6341 (mtp) outliers start: 78 outliers final: 63 residues processed: 331 average time/residue: 0.3309 time to fit residues: 161.8946 Evaluate side-chains 339 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 275 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 254 ASP 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 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 230 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 276 MET 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 244 VAL Chi-restraints excluded: chain C residue 341 GLN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 80 HIS 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 F residue 251 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 207 VAL 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 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 236 THR Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 279 ASP Chi-restraints excluded: chain G residue 339 GLN 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 244 VAL 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 137 LEU Chi-restraints excluded: chain H residue 203 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 166 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 199 optimal weight: 20.0000 chunk 145 optimal weight: 0.0470 chunk 95 optimal weight: 0.0870 chunk 96 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 56 optimal weight: 0.0470 overall best weight: 0.8356 ------------------------------------------------------------------------------- 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 F 26 HIS D 341 GLN D 342 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 26 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.221438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.200549 restraints weight = 20968.164| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 1.12 r_work: 0.3951 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3888 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19932 Z= 0.109 Angle : 0.556 9.224 27076 Z= 0.265 Chirality : 0.039 0.214 3196 Planarity : 0.004 0.058 3384 Dihedral : 3.981 20.428 2756 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.12 % Allowed : 22.43 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.17), residues: 2492 helix: 2.25 (0.14), residues: 1388 sheet: -0.39 (0.29), residues: 296 loop : -1.57 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 336 HIS 0.004 0.000 HIS F 26 PHE 0.008 0.001 PHE G 284 TYR 0.008 0.001 TYR H 226 ARG 0.004 0.000 ARG D 179 Details of bonding type rmsd hydrogen bonds : bond 0.03309 ( 1100) hydrogen bonds : angle 4.08887 ( 3249) covalent geometry : bond 0.00245 (19932) covalent geometry : angle 0.55578 (27076) *********************** 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 349 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 286 time to evaluate : 2.159 Fit side-chains REVERT: B 291 GLU cc_start: 0.7110 (tp30) cc_final: 0.6864 (tp30) REVERT: F 31 LEU cc_start: 0.7526 (mm) cc_final: 0.7300 (mm) REVERT: F 184 MET cc_start: 0.6875 (ttm) cc_final: 0.6605 (mtp) REVERT: D 302 ASP cc_start: 0.7831 (m-30) cc_final: 0.7458 (m-30) REVERT: G 291 GLU cc_start: 0.7118 (tp30) cc_final: 0.6871 (tp30) REVERT: E 341 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.6373 (mt0) REVERT: H 31 LEU cc_start: 0.7538 (mm) cc_final: 0.7306 (mm) REVERT: H 184 MET cc_start: 0.6693 (ttm) cc_final: 0.6341 (mtp) outliers start: 63 outliers final: 55 residues processed: 325 average time/residue: 0.3460 time to fit residues: 166.2239 Evaluate side-chains 330 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 274 time to evaluate : 2.124 ------------------------------------------------------------------------------- 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 246 LYS Chi-restraints excluded: chain A residue 249 LEU 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 186 GLU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 276 MET 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 244 VAL Chi-restraints excluded: chain C residue 341 GLN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 80 HIS 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 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 249 LEU 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 130 CYS 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 G residue 251 VAL Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 339 GLN 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 244 VAL Chi-restraints excluded: chain E residue 252 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 80 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 84 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 chunk 202 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 50 optimal weight: 0.0980 chunk 70 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN C 26 HIS ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 GLN D 341 GLN G 159 ASN 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 = 0.4423 r_free = 0.4423 target = 0.222185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.201813 restraints weight = 20817.691| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 1.12 r_work: 0.3963 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3900 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19932 Z= 0.106 Angle : 0.561 9.339 27076 Z= 0.268 Chirality : 0.038 0.217 3196 Planarity : 0.004 0.058 3384 Dihedral : 3.854 19.727 2756 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.42 % Allowed : 22.03 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.17), residues: 2492 helix: 2.32 (0.14), residues: 1392 sheet: -0.37 (0.29), residues: 296 loop : -1.44 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 336 HIS 0.002 0.000 HIS G 162 PHE 0.008 0.001 PHE G 284 TYR 0.007 0.001 TYR H 226 ARG 0.005 0.000 ARG E 189 Details of bonding type rmsd hydrogen bonds : bond 0.03149 ( 1100) hydrogen bonds : angle 4.00042 ( 3249) covalent geometry : bond 0.00235 (19932) covalent geometry : angle 0.56065 (27076) *********************** 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 348 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 279 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 ASP cc_start: 0.7923 (p0) cc_final: 0.7718 (p0) REVERT: B 291 GLU cc_start: 0.7212 (tp30) cc_final: 0.6966 (tp30) REVERT: F 31 LEU cc_start: 0.7486 (mm) cc_final: 0.7251 (mm) REVERT: F 184 MET cc_start: 0.6898 (ttm) cc_final: 0.6625 (mtp) REVERT: D 302 ASP cc_start: 0.7780 (m-30) cc_final: 0.7422 (m-30) REVERT: G 291 GLU cc_start: 0.7180 (tp30) cc_final: 0.6937 (tp30) REVERT: E 153 THR cc_start: 0.8159 (t) cc_final: 0.7823 (p) REVERT: E 341 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.6426 (mt0) REVERT: H 31 LEU cc_start: 0.7507 (mm) cc_final: 0.7274 (mm) REVERT: H 184 MET cc_start: 0.6712 (ttm) cc_final: 0.6367 (mtp) outliers start: 69 outliers final: 58 residues processed: 322 average time/residue: 0.3453 time to fit residues: 164.0729 Evaluate side-chains 336 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 277 time to evaluate : 2.084 ------------------------------------------------------------------------------- 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 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 B residue 276 MET Chi-restraints excluded: chain B residue 342 GLN 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 244 VAL Chi-restraints excluded: chain C residue 341 GLN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 80 HIS 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 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 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 G residue 251 VAL Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 342 GLN 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 244 VAL Chi-restraints excluded: chain E residue 252 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 80 HIS 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 19 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 247 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 142 optimal weight: 0.2980 chunk 11 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 81 optimal weight: 0.0980 chunk 140 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 341 GLN C 26 HIS ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 GLN F 342 GLN D 83 HIS D 341 GLN E 26 HIS ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.223277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.203972 restraints weight = 20814.093| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 1.02 r_work: 0.4010 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3947 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2132 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= 0.098 Angle : 0.550 11.477 27076 Z= 0.260 Chirality : 0.038 0.216 3196 Planarity : 0.004 0.058 3384 Dihedral : 3.783 19.322 2756 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.07 % Allowed : 22.43 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.17), residues: 2492 helix: 2.39 (0.14), residues: 1392 sheet: -0.39 (0.28), residues: 296 loop : -1.36 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 336 HIS 0.003 0.000 HIS A 337 PHE 0.007 0.001 PHE G 284 TYR 0.007 0.001 TYR H 226 ARG 0.004 0.000 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.03031 ( 1100) hydrogen bonds : angle 3.91732 ( 3249) covalent geometry : bond 0.00215 (19932) covalent geometry : angle 0.55000 (27076) ********************** 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 338 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 276 time to evaluate : 2.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 291 GLU cc_start: 0.7006 (tp30) cc_final: 0.6780 (tp30) REVERT: F 31 LEU cc_start: 0.7403 (mm) cc_final: 0.7163 (mm) REVERT: F 184 MET cc_start: 0.6853 (ttm) cc_final: 0.6563 (mtp) REVERT: F 342 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.7097 (tt0) REVERT: D 302 ASP cc_start: 0.7728 (m-30) cc_final: 0.7360 (m-30) REVERT: G 291 GLU cc_start: 0.6997 (tp30) cc_final: 0.6785 (tp30) REVERT: E 341 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.6305 (mt0) REVERT: H 31 LEU cc_start: 0.7456 (mm) cc_final: 0.7208 (mm) REVERT: H 184 MET cc_start: 0.6679 (ttm) cc_final: 0.6322 (mtp) outliers start: 62 outliers final: 52 residues processed: 318 average time/residue: 0.3622 time to fit residues: 169.2494 Evaluate side-chains 326 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 272 time to evaluate : 2.263 ------------------------------------------------------------------------------- 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 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 B residue 342 GLN 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 244 VAL Chi-restraints excluded: chain C residue 341 GLN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 80 HIS 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 F residue 236 THR Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 342 GLN 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 153 THR 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 G residue 339 GLN Chi-restraints excluded: chain G residue 342 GLN 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 244 VAL Chi-restraints excluded: chain E residue 252 ILE 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 137 LEU Chi-restraints excluded: chain H residue 203 LEU 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 5 optimal weight: 7.9990 chunk 240 optimal weight: 0.0370 chunk 115 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 205 optimal weight: 8.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS C 26 HIS ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 HIS D 341 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 = 0.4427 r_free = 0.4427 target = 0.222721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.206191 restraints weight = 20940.061| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 0.87 r_work: 0.4047 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3980 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.263 19932 Z= 0.227 Angle : 0.931 59.198 27076 Z= 0.519 Chirality : 0.043 0.683 3196 Planarity : 0.006 0.188 3384 Dihedral : 3.852 35.506 2756 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.82 % Allowed : 22.48 % Favored : 74.70 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.17), residues: 2492 helix: 2.34 (0.14), residues: 1392 sheet: -0.39 (0.28), residues: 296 loop : -1.36 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 214 HIS 0.005 0.000 HIS F 83 PHE 0.008 0.001 PHE G 284 TYR 0.008 0.001 TYR A 314 ARG 0.003 0.000 ARG D 286 Details of bonding type rmsd hydrogen bonds : bond 0.03230 ( 1100) hydrogen bonds : angle 3.92539 ( 3249) covalent geometry : bond 0.00525 (19932) covalent geometry : angle 0.93143 (27076) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8561.11 seconds wall clock time: 149 minutes 8.25 seconds (8948.25 seconds total)