Starting phenix.real_space_refine on Tue Nov 19 19:56:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik0_35503/11_2024/8ik0_35503.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik0_35503/11_2024/8ik0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik0_35503/11_2024/8ik0_35503.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik0_35503/11_2024/8ik0_35503.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik0_35503/11_2024/8ik0_35503.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik0_35503/11_2024/8ik0_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-5513/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: 12.62, per 1000 atoms: 0.65 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: 5.37 Conformation dependent library (CDL) restraints added in 2.8 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: 2.29 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: 6.34 Time building geometry restraints manager: 5.96 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: 0.00 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.020 Extract box with map and model: 0.820 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 45.770 Find NCS groups from input model: 1.200 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: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.310 ------------------------------------------------------------------------------- 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= 0.152 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 *********************** 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 : 2.233 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: 0.3614 time to fit residues: 183.7574 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 : 2.124 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 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= 0.233 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 *********************** 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 : 2.376 Fit side-chains REVERT: A 279 ASP cc_start: 0.7772 (t70) cc_final: 0.7495 (t70) REVERT: F 184 MET cc_start: 0.5884 (ttm) cc_final: 0.4899 (mtp) REVERT: H 184 MET cc_start: 0.6005 (ttm) cc_final: 0.5083 (mtp) outliers start: 32 outliers final: 25 residues processed: 310 average time/residue: 0.3569 time to fit residues: 161.3704 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 : 2.299 ------------------------------------------------------------------------------- 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 127 optimal weight: 6.9990 chunk 71 optimal weight: 0.3980 chunk 190 optimal weight: 6.9990 chunk 155 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 chunk 229 optimal weight: 7.9990 chunk 247 optimal weight: 0.8980 chunk 204 optimal weight: 0.3980 chunk 227 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 183 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19932 Z= 0.144 Angle : 0.540 8.645 27076 Z= 0.256 Chirality : 0.038 0.166 3196 Planarity : 0.004 0.054 3384 Dihedral : 3.720 19.345 2756 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.58 % Allowed : 13.22 % Favored : 85.20 % 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: 1.40 (0.17), residues: 2492 helix: 2.44 (0.14), residues: 1380 sheet: -0.16 (0.29), residues: 296 loop : -1.38 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 99 HIS 0.003 0.000 HIS E 26 PHE 0.011 0.001 PHE A 36 TYR 0.005 0.001 TYR H 226 ARG 0.007 0.000 ARG E 198 *********************** 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 332 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 300 time to evaluate : 2.288 Fit side-chains REVERT: A 234 ILE cc_start: 0.8537 (mm) cc_final: 0.8313 (mm) REVERT: A 279 ASP cc_start: 0.7801 (t70) cc_final: 0.7541 (t70) REVERT: A 341 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.5974 (mp10) REVERT: C 341 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.6683 (mp10) REVERT: F 184 MET cc_start: 0.5981 (ttm) cc_final: 0.5201 (mtp) REVERT: D 234 ILE cc_start: 0.8562 (mm) cc_final: 0.8352 (mm) REVERT: D 341 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.6954 (mp10) REVERT: H 184 MET cc_start: 0.5944 (ttm) cc_final: 0.5075 (mtp) outliers start: 32 outliers final: 22 residues processed: 313 average time/residue: 0.3609 time to fit residues: 165.2935 Evaluate side-chains 309 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 284 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 159 ASN Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 205 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 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 80 HIS Chi-restraints excluded: chain G residue 159 ASN Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 72 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 153 optimal weight: 0.6980 chunk 230 optimal weight: 8.9990 chunk 243 optimal weight: 0.0050 chunk 120 optimal weight: 0.4980 chunk 218 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 overall best weight: 1.2196 ------------------------------------------------------------------------------- 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 ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19932 Z= 0.189 Angle : 0.549 8.014 27076 Z= 0.259 Chirality : 0.038 0.176 3196 Planarity : 0.004 0.044 3384 Dihedral : 3.727 18.439 2756 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.52 % Allowed : 15.45 % Favored : 82.03 % 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: 1.40 (0.17), residues: 2492 helix: 2.43 (0.14), residues: 1384 sheet: -0.18 (0.29), residues: 296 loop : -1.38 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 99 HIS 0.003 0.000 HIS C 26 PHE 0.012 0.001 PHE H 284 TYR 0.009 0.001 TYR G 226 ARG 0.006 0.000 ARG E 198 *********************** 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 338 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 287 time to evaluate : 2.204 Fit side-chains REVERT: A 36 PHE cc_start: 0.5093 (OUTLIER) cc_final: 0.4759 (m-10) REVERT: A 341 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.5986 (mp10) REVERT: C 341 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7406 (mp10) REVERT: F 31 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7391 (mm) REVERT: F 184 MET cc_start: 0.6306 (ttm) cc_final: 0.5600 (mtp) REVERT: D 36 PHE cc_start: 0.5062 (OUTLIER) cc_final: 0.4861 (m-10) REVERT: D 234 ILE cc_start: 0.8571 (mm) cc_final: 0.8368 (mm) REVERT: D 341 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.6961 (mp10) REVERT: H 184 MET cc_start: 0.6058 (ttm) cc_final: 0.5439 (mtp) outliers start: 51 outliers final: 33 residues processed: 315 average time/residue: 0.3646 time to fit residues: 167.2381 Evaluate side-chains 312 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 273 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 335 LEU 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 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 205 ILE Chi-restraints excluded: chain C residue 252 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 101 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain D residue 36 PHE 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 30 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 159 ASN Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 207 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 3 optimal weight: 0.4980 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 124 optimal weight: 0.0470 chunk 218 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.5084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 HIS ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19932 Z= 0.212 Angle : 0.558 8.102 27076 Z= 0.265 Chirality : 0.039 0.185 3196 Planarity : 0.004 0.045 3384 Dihedral : 3.782 17.804 2756 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.62 % Allowed : 17.03 % Favored : 80.35 % 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: 1.36 (0.17), residues: 2492 helix: 2.42 (0.14), residues: 1380 sheet: -0.20 (0.29), residues: 296 loop : -1.41 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 336 HIS 0.003 0.001 HIS D 197 PHE 0.013 0.001 PHE B 284 TYR 0.007 0.001 TYR H 226 ARG 0.004 0.000 ARG E 198 *********************** 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 340 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 287 time to evaluate : 2.258 Fit side-chains REVERT: A 36 PHE cc_start: 0.5116 (OUTLIER) cc_final: 0.4610 (m-10) REVERT: A 341 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.6043 (mp10) REVERT: C 246 LYS cc_start: 0.8678 (mttp) cc_final: 0.8448 (mttp) REVERT: F 31 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7385 (mm) REVERT: F 184 MET cc_start: 0.6248 (ttm) cc_final: 0.5860 (mtp) REVERT: D 36 PHE cc_start: 0.5094 (OUTLIER) cc_final: 0.4597 (m-10) REVERT: D 157 LYS cc_start: 0.8798 (mttm) cc_final: 0.8583 (mttt) REVERT: D 234 ILE cc_start: 0.8599 (mm) cc_final: 0.8390 (mm) REVERT: D 341 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7054 (mp10) REVERT: H 31 LEU cc_start: 0.7568 (mm) cc_final: 0.7336 (mm) REVERT: H 184 MET cc_start: 0.6102 (ttm) cc_final: 0.5634 (mtp) outliers start: 53 outliers final: 36 residues processed: 319 average time/residue: 0.3667 time to fit residues: 171.1734 Evaluate side-chains 316 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 275 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE 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 130 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain D residue 36 PHE 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 153 THR 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 72 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 207 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 0.9980 chunk 219 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 243 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 20 optimal weight: 0.0030 chunk 80 optimal weight: 0.0870 chunk 128 optimal weight: 8.9990 overall best weight: 1.6172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 HIS ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** H 271 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19932 Z= 0.223 Angle : 0.574 8.425 27076 Z= 0.272 Chirality : 0.040 0.199 3196 Planarity : 0.004 0.045 3384 Dihedral : 3.858 19.699 2756 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.77 % Allowed : 18.07 % Favored : 79.16 % 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: 2.30 (0.14), residues: 1396 sheet: -0.26 (0.29), residues: 296 loop : -1.46 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 99 HIS 0.003 0.001 HIS D 197 PHE 0.014 0.001 PHE G 284 TYR 0.010 0.001 TYR H 226 ARG 0.003 0.000 ARG A 286 *********************** 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 337 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 281 time to evaluate : 2.259 Fit side-chains REVERT: A 36 PHE cc_start: 0.5001 (OUTLIER) cc_final: 0.4450 (m-80) REVERT: C 246 LYS cc_start: 0.8699 (mttp) cc_final: 0.8435 (mttp) REVERT: F 31 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7383 (mm) REVERT: F 184 MET cc_start: 0.6345 (ttm) cc_final: 0.5973 (mtp) REVERT: D 36 PHE cc_start: 0.5024 (OUTLIER) cc_final: 0.4480 (m-80) REVERT: D 234 ILE cc_start: 0.8608 (mm) cc_final: 0.8386 (mm) REVERT: D 253 ARG cc_start: 0.6893 (ttt90) cc_final: 0.6098 (tpt170) REVERT: D 341 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7159 (mp10) REVERT: H 31 LEU cc_start: 0.7575 (mm) cc_final: 0.7336 (mm) REVERT: H 184 MET cc_start: 0.6169 (ttm) cc_final: 0.5727 (mtp) outliers start: 56 outliers final: 45 residues processed: 318 average time/residue: 0.3637 time to fit residues: 168.8009 Evaluate side-chains 322 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 273 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE 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 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 273 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain D residue 36 PHE 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 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 279 ASP Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 251 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 138 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 205 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 242 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 ASN ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 HIS ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 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** H 83 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19932 Z= 0.280 Angle : 0.609 8.898 27076 Z= 0.290 Chirality : 0.041 0.197 3196 Planarity : 0.004 0.045 3384 Dihedral : 4.006 19.086 2756 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.32 % Allowed : 18.42 % Favored : 78.27 % 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: 1.12 (0.17), residues: 2492 helix: 2.15 (0.14), residues: 1404 sheet: -0.33 (0.30), residues: 296 loop : -1.48 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 99 HIS 0.004 0.001 HIS D 197 PHE 0.018 0.001 PHE B 284 TYR 0.012 0.002 TYR H 226 ARG 0.011 0.000 ARG A 23 *********************** 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 351 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 284 time to evaluate : 2.430 Fit side-chains REVERT: A 36 PHE cc_start: 0.4975 (OUTLIER) cc_final: 0.4404 (m-80) REVERT: A 341 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.6330 (mp10) REVERT: C 341 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.6311 (mt0) REVERT: F 31 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7381 (mm) REVERT: F 184 MET cc_start: 0.6518 (ttm) cc_final: 0.6111 (mtp) REVERT: D 36 PHE cc_start: 0.4969 (OUTLIER) cc_final: 0.4417 (m-80) REVERT: D 234 ILE cc_start: 0.8619 (mm) cc_final: 0.8403 (mm) REVERT: D 341 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.7172 (mp10) REVERT: G 342 GLN cc_start: 0.6735 (tt0) cc_final: 0.6493 (pt0) REVERT: E 341 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.6136 (mt0) REVERT: H 31 LEU cc_start: 0.7547 (mm) cc_final: 0.7303 (mm) REVERT: H 184 MET cc_start: 0.6311 (ttm) cc_final: 0.5866 (mtp) outliers start: 67 outliers final: 50 residues processed: 330 average time/residue: 0.3824 time to fit residues: 183.3359 Evaluate side-chains 337 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 280 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 29 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 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 205 ILE 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 31 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain D residue 36 PHE 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 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 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 273 LEU Chi-restraints excluded: chain G residue 279 ASP Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 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 101 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 251 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 220 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 HIS ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 GLN D 342 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.1983 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= 0.239 Angle : 0.593 8.928 27076 Z= 0.281 Chirality : 0.040 0.206 3196 Planarity : 0.004 0.045 3384 Dihedral : 4.004 19.398 2756 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.42 % Allowed : 19.41 % Favored : 77.18 % 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: 2.16 (0.14), residues: 1408 sheet: -0.34 (0.30), residues: 296 loop : -1.48 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.003 0.001 HIS D 197 PHE 0.015 0.001 PHE B 284 TYR 0.011 0.001 TYR H 226 ARG 0.003 0.000 ARG A 286 *********************** 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: 69 poor density : 280 time to evaluate : 2.521 Fit side-chains REVERT: A 36 PHE cc_start: 0.4808 (OUTLIER) cc_final: 0.4274 (m-80) REVERT: A 341 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.6172 (mp10) REVERT: C 341 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.6243 (mt0) REVERT: F 31 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7362 (mm) REVERT: F 184 MET cc_start: 0.6495 (ttm) cc_final: 0.6179 (mtp) REVERT: D 36 PHE cc_start: 0.4819 (OUTLIER) cc_final: 0.4273 (m-80) REVERT: D 234 ILE cc_start: 0.8622 (mm) cc_final: 0.8413 (mm) REVERT: G 341 GLN cc_start: 0.8091 (tp40) cc_final: 0.7799 (mt0) REVERT: E 341 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7445 (mp10) REVERT: H 31 LEU cc_start: 0.7537 (mm) cc_final: 0.7290 (mm) REVERT: H 184 MET cc_start: 0.6295 (ttm) cc_final: 0.5869 (mtp) outliers start: 69 outliers final: 54 residues processed: 326 average time/residue: 0.3682 time to fit residues: 177.2189 Evaluate side-chains 332 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 272 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 279 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 273 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 252 ILE 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 101 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain D residue 36 PHE 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 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 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 273 LEU 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 205 ILE Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 317 ILE Chi-restraints excluded: chain E residue 341 GLN Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 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 232 optimal weight: 3.9990 chunk 212 optimal weight: 0.4980 chunk 226 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 177 optimal weight: 0.2980 chunk 69 optimal weight: 10.0000 chunk 204 optimal weight: 0.6980 chunk 214 optimal weight: 0.9980 chunk 225 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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** ** G 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19932 Z= 0.199 Angle : 0.591 9.226 27076 Z= 0.278 Chirality : 0.040 0.212 3196 Planarity : 0.004 0.046 3384 Dihedral : 3.923 19.164 2756 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.22 % Allowed : 19.70 % Favored : 77.08 % 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: 2.30 (0.14), residues: 1392 sheet: -0.32 (0.29), residues: 296 loop : -1.46 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.003 0.001 HIS D 337 PHE 0.011 0.001 PHE B 284 TYR 0.009 0.001 TYR H 226 ARG 0.006 0.000 ARG D 23 *********************** 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 344 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 279 time to evaluate : 2.203 Fit side-chains REVERT: A 36 PHE cc_start: 0.4818 (OUTLIER) cc_final: 0.4210 (m-80) REVERT: A 341 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7250 (mp10) REVERT: B 341 GLN cc_start: 0.8104 (tp40) cc_final: 0.7821 (mt0) REVERT: C 341 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.6188 (mt0) REVERT: F 31 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7295 (mm) REVERT: F 184 MET cc_start: 0.6510 (ttm) cc_final: 0.6207 (mtp) REVERT: D 36 PHE cc_start: 0.4779 (OUTLIER) cc_final: 0.4239 (m-80) REVERT: D 234 ILE cc_start: 0.8621 (mm) cc_final: 0.8397 (mm) REVERT: G 341 GLN cc_start: 0.8067 (tp40) cc_final: 0.7785 (mt0) REVERT: E 341 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7481 (mp10) REVERT: H 31 LEU cc_start: 0.7537 (mm) cc_final: 0.7296 (mm) REVERT: H 184 MET cc_start: 0.6269 (ttm) cc_final: 0.5860 (mtp) outliers start: 65 outliers final: 55 residues processed: 319 average time/residue: 0.3692 time to fit residues: 171.0559 Evaluate side-chains 337 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 276 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 279 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 29 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 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 252 ILE 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 101 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain D residue 36 PHE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 207 VAL 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 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 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 205 ILE Chi-restraints excluded: chain E residue 229 ASP 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 101 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 236 THR 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 239 optimal weight: 10.0000 chunk 146 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 166 optimal weight: 30.0000 chunk 251 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 chunk 199 optimal weight: 9.9990 chunk 20 optimal weight: 0.4980 chunk 154 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 overall best weight: 2.4988 ------------------------------------------------------------------------------- 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 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 HIS ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19932 Z= 0.315 Angle : 0.656 9.167 27076 Z= 0.311 Chirality : 0.042 0.215 3196 Planarity : 0.005 0.044 3384 Dihedral : 4.171 19.394 2756 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.37 % Allowed : 19.70 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.99 (0.17), residues: 2492 helix: 2.06 (0.14), residues: 1400 sheet: -0.47 (0.29), residues: 296 loop : -1.50 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 99 HIS 0.004 0.001 HIS D 197 PHE 0.021 0.001 PHE B 284 TYR 0.012 0.002 TYR H 226 ARG 0.008 0.000 ARG E 189 ********************** 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 342 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 274 time to evaluate : 2.178 Fit side-chains REVERT: A 36 PHE cc_start: 0.4884 (OUTLIER) cc_final: 0.4097 (m-80) REVERT: A 71 CYS cc_start: 0.7465 (m) cc_final: 0.7119 (m) REVERT: A 341 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.7271 (mp10) REVERT: C 341 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.6330 (mt0) REVERT: F 184 MET cc_start: 0.6588 (ttm) cc_final: 0.6275 (mtp) REVERT: D 36 PHE cc_start: 0.4933 (OUTLIER) cc_final: 0.4178 (m-80) REVERT: D 234 ILE cc_start: 0.8498 (mm) cc_final: 0.8255 (mm) REVERT: E 341 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7521 (mp10) REVERT: H 184 MET cc_start: 0.6460 (ttm) cc_final: 0.6043 (mtp) outliers start: 68 outliers final: 58 residues processed: 315 average time/residue: 0.3717 time to fit residues: 171.7047 Evaluate side-chains 331 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 268 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 279 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 29 CYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 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 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 36 PHE Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 207 VAL 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 186 GLU Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 279 ASP Chi-restraints excluded: chain G residue 316 LEU Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 71 CYS Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 229 ASP Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 341 GLN Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 80 HIS Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 236 THR 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 212 optimal weight: 1.9990 chunk 61 optimal weight: 0.0570 chunk 184 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 205 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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** F 26 HIS F 271 GLN F 342 GLN E 26 HIS ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.222825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.203752 restraints weight = 20843.383| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 1.02 r_work: 0.4079 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.4029 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2107 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= 0.155 Angle : 0.572 9.530 27076 Z= 0.269 Chirality : 0.039 0.216 3196 Planarity : 0.004 0.047 3384 Dihedral : 3.873 19.161 2756 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.77 % Allowed : 20.59 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.29 (0.17), residues: 2492 helix: 2.34 (0.14), residues: 1392 sheet: -0.38 (0.29), residues: 296 loop : -1.39 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F 214 HIS 0.004 0.000 HIS F 26 PHE 0.009 0.001 PHE G 284 TYR 0.007 0.001 TYR H 226 ARG 0.005 0.000 ARG A 286 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4180.73 seconds wall clock time: 76 minutes 54.04 seconds (4614.04 seconds total)