Starting phenix.real_space_refine on Wed Dec 13 03:55:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqx_21360/12_2023/6vqx_21360.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqx_21360/12_2023/6vqx_21360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqx_21360/12_2023/6vqx_21360.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqx_21360/12_2023/6vqx_21360.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqx_21360/12_2023/6vqx_21360.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqx_21360/12_2023/6vqx_21360.pdb" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 59 5.49 5 S 23 5.16 5 C 14561 2.51 5 N 4363 2.21 5 O 4690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 14": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 322": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "D PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 190": "NH1" <-> "NH2" Residue "H ARG 51": "NH1" <-> "NH2" Residue "H PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 80": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 23696 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 737 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "B" Number of atoms: 3364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3364 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 24, 'TRANS': 397} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2395 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2272 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Chain: "E" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2579 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 12, 'TRANS': 320} Chain: "F" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2577 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2589 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2573 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2576 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 763 Classifications: {'peptide': 187} Incomplete info: {'backbone_only': 169, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 787 Unresolved non-hydrogen angles: 1125 Unresolved non-hydrogen dihedrals: 520 Unresolved non-hydrogen chiralities: 215 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 11, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 8, 'PHE:plan': 10, 'GLU:plan': 11, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 402 Chain: "K" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1271 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 12, 'rna3p_pur': 20, 'rna3p_pyr': 18} Link IDs: {'rna2p': 20, 'rna3p': 39} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 12.61, per 1000 atoms: 0.53 Number of scatterers: 23696 At special positions: 0 Unit cell: (131.44, 146.28, 150.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 59 15.00 O 4690 8.00 N 4363 7.00 C 14561 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 - 3.50 Amino acid : False - 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: 9.80 Conformation dependent library (CDL) restraints added in 4.5 seconds 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5194 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 38 sheets defined 30.1% alpha, 18.0% beta 1 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 7.63 Creating SS restraints... Processing helix chain 'A' and resid 13 through 23 removed outlier: 3.651A pdb=" N ALA A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 46 removed outlier: 3.616A pdb=" N ALA A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 58 through 70 removed outlier: 3.523A pdb=" N HIS A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A 68 " --> pdb=" O HIS A 64 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 94 removed outlier: 3.612A pdb=" N ALA A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 92 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 29 removed outlier: 3.531A pdb=" N PHE B 20 " --> pdb=" O PHE B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.772A pdb=" N ARG B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 47 removed outlier: 3.604A pdb=" N THR B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 42 through 47' Processing helix chain 'B' and resid 50 through 56 Processing helix chain 'B' and resid 96 through 100 removed outlier: 3.658A pdb=" N GLU B 99 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 100 " --> pdb=" O SER B 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 96 through 100' Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 115 through 121 Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 155 through 160 removed outlier: 3.905A pdb=" N ILE B 160 " --> pdb=" O ARG B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 211 removed outlier: 3.539A pdb=" N VAL B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 225 removed outlier: 3.698A pdb=" N LYS B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N SER B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 251 removed outlier: 3.615A pdb=" N ASN B 250 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 251 " --> pdb=" O PRO B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 251' Processing helix chain 'B' and resid 294 through 307 removed outlier: 3.680A pdb=" N ARG B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 342 removed outlier: 3.780A pdb=" N ALA B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 324 " --> pdb=" O GLN B 320 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 325 " --> pdb=" O ARG B 321 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU B 334 " --> pdb=" O CYS B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 363 Processing helix chain 'B' and resid 376 through 380 Processing helix chain 'B' and resid 385 through 399 removed outlier: 3.924A pdb=" N VAL B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 431 removed outlier: 3.643A pdb=" N GLU B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU B 427 " --> pdb=" O THR B 423 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP B 431 " --> pdb=" O GLU B 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 48 removed outlier: 3.925A pdb=" N PHE C 37 " --> pdb=" O SER C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 121 Processing helix chain 'C' and resid 122 through 135 removed outlier: 3.510A pdb=" N GLN C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN C 133 " --> pdb=" O GLN C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 180 removed outlier: 3.708A pdb=" N ASN C 172 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG C 175 " --> pdb=" O LYS C 171 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU C 176 " --> pdb=" O ASN C 172 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR C 177 " --> pdb=" O GLN C 173 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 179 " --> pdb=" O ARG C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 200 removed outlier: 4.110A pdb=" N LEU C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN C 194 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.703A pdb=" N ASP C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA C 212 " --> pdb=" O THR C 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 207 through 212' Processing helix chain 'C' and resid 297 through 302 removed outlier: 3.933A pdb=" N LEU C 302 " --> pdb=" O SER C 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 147 Processing helix chain 'D' and resid 149 through 162 removed outlier: 3.895A pdb=" N ASN D 159 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU D 160 " --> pdb=" O TYR D 156 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 222 Processing helix chain 'D' and resid 274 through 280 Processing helix chain 'D' and resid 321 through 330 Processing helix chain 'D' and resid 337 through 349 removed outlier: 3.521A pdb=" N HIS D 342 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR D 343 " --> pdb=" O GLU D 339 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 344 " --> pdb=" O GLN D 340 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN D 347 " --> pdb=" O TYR D 343 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU D 348 " --> pdb=" O VAL D 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 54 removed outlier: 3.718A pdb=" N SER E 54 " --> pdb=" O ARG E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 91 removed outlier: 3.562A pdb=" N GLN E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 147 Processing helix chain 'E' and resid 149 through 162 removed outlier: 3.630A pdb=" N HIS E 158 " --> pdb=" O ARG E 154 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 222 removed outlier: 3.629A pdb=" N LEU E 213 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU E 216 " --> pdb=" O ALA E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 283 removed outlier: 3.843A pdb=" N ARG E 283 " --> pdb=" O GLY E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 331 removed outlier: 3.555A pdb=" N ASP E 327 " --> pdb=" O TYR E 323 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TRP E 329 " --> pdb=" O LEU E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 350 removed outlier: 3.527A pdb=" N HIS E 342 " --> pdb=" O VAL E 338 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N TYR E 343 " --> pdb=" O GLU E 339 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA E 346 " --> pdb=" O HIS E 342 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU E 348 " --> pdb=" O VAL E 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 53 Processing helix chain 'F' and resid 81 through 91 removed outlier: 3.542A pdb=" N GLN F 90 " --> pdb=" O ASP F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 147 Processing helix chain 'F' and resid 149 through 162 removed outlier: 3.631A pdb=" N ASN F 159 " --> pdb=" O ARG F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 223 removed outlier: 4.252A pdb=" N LEU F 216 " --> pdb=" O ALA F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 283 removed outlier: 3.618A pdb=" N ARG F 283 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 296 removed outlier: 4.126A pdb=" N LEU F 295 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 331 removed outlier: 3.588A pdb=" N ASP F 327 " --> pdb=" O TYR F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 350 removed outlier: 3.788A pdb=" N HIS F 342 " --> pdb=" O VAL F 338 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N TYR F 343 " --> pdb=" O GLU F 339 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL F 344 " --> pdb=" O GLN F 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 51 removed outlier: 3.692A pdb=" N ARG G 51 " --> pdb=" O TRP G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 90 Processing helix chain 'G' and resid 129 through 147 Processing helix chain 'G' and resid 149 through 158 removed outlier: 3.724A pdb=" N HIS G 158 " --> pdb=" O ARG G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 222 removed outlier: 3.743A pdb=" N GLU G 215 " --> pdb=" O ASP G 211 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU G 216 " --> pdb=" O ALA G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 329 Processing helix chain 'G' and resid 337 through 351 removed outlier: 4.926A pdb=" N TYR G 343 " --> pdb=" O GLU G 339 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL G 344 " --> pdb=" O GLN G 340 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 57 removed outlier: 3.639A pdb=" N GLN H 55 " --> pdb=" O ASP H 52 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU H 56 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TRP H 57 " --> pdb=" O SER H 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 52 through 57' Processing helix chain 'H' and resid 81 through 89 Processing helix chain 'H' and resid 129 through 147 removed outlier: 3.647A pdb=" N ASP H 146 " --> pdb=" O THR H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 162 removed outlier: 3.627A pdb=" N ASN H 159 " --> pdb=" O ARG H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 222 removed outlier: 3.847A pdb=" N LEU H 216 " --> pdb=" O ALA H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 274 through 283 removed outlier: 3.614A pdb=" N ILE H 278 " --> pdb=" O HIS H 274 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG H 283 " --> pdb=" O GLY H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 321 through 331 removed outlier: 3.642A pdb=" N ASP H 327 " --> pdb=" O TYR H 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 351 removed outlier: 3.898A pdb=" N HIS H 342 " --> pdb=" O VAL H 338 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N TYR H 343 " --> pdb=" O GLU H 339 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL H 344 " --> pdb=" O GLN H 340 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU H 348 " --> pdb=" O VAL H 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 54 removed outlier: 3.503A pdb=" N ALA I 53 " --> pdb=" O GLN I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 removed outlier: 3.924A pdb=" N ASP I 86 " --> pdb=" O PRO I 82 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA I 87 " --> pdb=" O ALA I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 129 through 147 Processing helix chain 'I' and resid 149 through 162 removed outlier: 3.508A pdb=" N ARG I 155 " --> pdb=" O GLU I 151 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS I 158 " --> pdb=" O ARG I 154 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN I 159 " --> pdb=" O ARG I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 223 removed outlier: 3.870A pdb=" N LEU I 216 " --> pdb=" O ALA I 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 283 removed outlier: 4.083A pdb=" N ARG I 283 " --> pdb=" O GLY I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 331 removed outlier: 3.533A pdb=" N LEU I 325 " --> pdb=" O ASP I 321 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN I 328 " --> pdb=" O THR I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 337 through 351 removed outlier: 3.617A pdb=" N TYR I 343 " --> pdb=" O GLU I 339 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 69 Processing sheet with id=AA1, first strand: chain 'B' and resid 63 through 65 removed outlier: 3.604A pdb=" N GLN B 64 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 68 through 69 Processing sheet with id=AA3, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.571A pdb=" N HIS B 188 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG C 278 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.571A pdb=" N HIS B 188 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG C 278 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N PHE C 279 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ALA C 257 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU C 281 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR C 255 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LEU C 283 " --> pdb=" O ALA C 253 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TRP C 247 " --> pdb=" O TRP C 289 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA C 253 " --> pdb=" O TRP C 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.502A pdb=" N ILE B 240 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE C 81 " --> pdb=" O ILE B 240 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N LYS B 242 " --> pdb=" O PHE C 81 " (cutoff:3.500A) removed outlier: 10.896A pdb=" N LEU C 83 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.502A pdb=" N ILE B 240 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE C 81 " --> pdb=" O ILE B 240 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N LYS B 242 " --> pdb=" O PHE C 81 " (cutoff:3.500A) removed outlier: 10.896A pdb=" N LEU C 83 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU I 249 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 59 removed outlier: 6.171A pdb=" N GLY C 112 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL C 59 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU C 110 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ALA C 103 " --> pdb=" O ASN C 19 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN C 19 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU C 109 " --> pdb=" O PRO C 13 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU C 11 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL C 113 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU C 9 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER C 16 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 65 through 68 removed outlier: 5.430A pdb=" N ALA C 103 " --> pdb=" O ASN C 19 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN C 19 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU C 109 " --> pdb=" O PRO C 13 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU C 11 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL C 113 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU C 9 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C 157 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 219 through 220 Processing sheet with id=AB1, first strand: chain 'D' and resid 126 through 127 Processing sheet with id=AB2, first strand: chain 'D' and resid 37 through 38 removed outlier: 4.311A pdb=" N VAL D 227 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA D 175 " --> pdb=" O ARG D 236 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE D 180 " --> pdb=" O TRP D 192 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 37 through 38 removed outlier: 3.638A pdb=" N ALA D 41 " --> pdb=" O ILE D 273 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 63 through 65 removed outlier: 3.791A pdb=" N LYS D 65 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL D 97 " --> pdb=" O LYS D 65 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 284 through 286 Processing sheet with id=AB6, first strand: chain 'E' and resid 126 through 127 Processing sheet with id=AB7, first strand: chain 'E' and resid 188 through 195 removed outlier: 6.590A pdb=" N HIS E 182 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA E 191 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE E 180 " --> pdb=" O ALA E 191 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ARG E 193 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL E 178 " --> pdb=" O ARG E 193 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASP E 195 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL E 176 " --> pdb=" O ASP E 195 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU E 228 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL E 227 " --> pdb=" O VAL E 117 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 63 through 69 Processing sheet with id=AB9, first strand: chain 'F' and resid 30 through 31 Processing sheet with id=AC1, first strand: chain 'F' and resid 37 through 38 removed outlier: 4.113A pdb=" N VAL F 227 " --> pdb=" O VAL F 117 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 37 through 38 Processing sheet with id=AC3, first strand: chain 'F' and resid 62 through 68 Processing sheet with id=AC4, first strand: chain 'F' and resid 284 through 286 Processing sheet with id=AC5, first strand: chain 'G' and resid 37 through 38 removed outlier: 4.485A pdb=" N VAL G 227 " --> pdb=" O VAL G 117 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU G 228 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL G 176 " --> pdb=" O ASP G 195 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ASP G 195 " --> pdb=" O VAL G 176 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL G 178 " --> pdb=" O ARG G 193 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ARG G 193 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE G 180 " --> pdb=" O ALA G 191 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA G 191 " --> pdb=" O ILE G 180 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N HIS G 182 " --> pdb=" O ALA G 189 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AC7, first strand: chain 'G' and resid 63 through 68 Processing sheet with id=AC8, first strand: chain 'G' and resid 284 through 286 Processing sheet with id=AC9, first strand: chain 'G' and resid 305 through 306 removed outlier: 3.661A pdb=" N LYS G 311 " --> pdb=" O VAL G 306 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 126 through 127 removed outlier: 3.579A pdb=" N ALA H 126 " --> pdb=" O ALA H 31 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY H 352 " --> pdb=" O PHE H 32 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 37 through 38 removed outlier: 4.210A pdb=" N VAL H 227 " --> pdb=" O VAL H 117 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 37 through 38 Processing sheet with id=AD4, first strand: chain 'H' and resid 62 through 67 removed outlier: 4.587A pdb=" N ALA H 100 " --> pdb=" O VAL H 243 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 62 through 67 removed outlier: 7.000A pdb=" N ASP H 98 " --> pdb=" O SER H 261 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 126 through 127 removed outlier: 3.802A pdb=" N LEU I 30 " --> pdb=" O PHE I 354 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 116 through 117 removed outlier: 3.886A pdb=" N GLU I 230 " --> pdb=" O ASN I 181 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 116 through 117 removed outlier: 5.021A pdb=" N ALA I 271 " --> pdb=" O MET I 43 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 62 through 68 removed outlier: 4.649A pdb=" N ALA I 100 " --> pdb=" O VAL I 243 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 305 through 306 removed outlier: 3.537A pdb=" N VAL I 306 " --> pdb=" O LYS I 311 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS I 311 " --> pdb=" O VAL I 306 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 3 through 5 801 hydrogen bonds defined for protein. 2205 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2 hydrogen bonds 4 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 7.45 Time building geometry restraints manager: 10.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6853 1.33 - 1.45: 4749 1.45 - 1.58: 12517 1.58 - 1.70: 118 1.70 - 1.82: 35 Bond restraints: 24272 Sorted by residual: bond pdb=" C THR B 350 " pdb=" N PRO B 351 " ideal model delta sigma weight residual 1.335 1.376 -0.041 8.70e-03 1.32e+04 2.18e+01 bond pdb=" C PHE C 152 " pdb=" N PRO C 153 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.28e+00 bond pdb=" CA LEU B 130 " pdb=" C LEU B 130 " ideal model delta sigma weight residual 1.526 1.553 -0.027 1.39e-02 5.18e+03 3.86e+00 bond pdb=" CG1 ILE G 278 " pdb=" CD1 ILE G 278 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.47e+00 bond pdb=" C ALA C 154 " pdb=" N PRO C 155 " ideal model delta sigma weight residual 1.330 1.348 -0.018 1.22e-02 6.72e+03 2.30e+00 ... (remaining 24267 not shown) Histogram of bond angle deviations from ideal: 99.97 - 106.82: 1007 106.82 - 113.67: 13240 113.67 - 120.52: 9528 120.52 - 127.38: 8997 127.38 - 134.23: 378 Bond angle restraints: 33150 Sorted by residual: angle pdb=" C ARG H 268 " pdb=" N ASP H 269 " pdb=" CA ASP H 269 " ideal model delta sigma weight residual 121.54 130.80 -9.26 1.91e+00 2.74e-01 2.35e+01 angle pdb=" C PHE B 307 " pdb=" N LEU B 308 " pdb=" CA LEU B 308 " ideal model delta sigma weight residual 121.54 130.23 -8.69 1.91e+00 2.74e-01 2.07e+01 angle pdb=" N ARG C 77 " pdb=" CA ARG C 77 " pdb=" C ARG C 77 " ideal model delta sigma weight residual 114.56 108.93 5.63 1.27e+00 6.20e-01 1.97e+01 angle pdb=" CA LEU B 189 " pdb=" CB LEU B 189 " pdb=" CG LEU B 189 " ideal model delta sigma weight residual 116.30 131.10 -14.80 3.50e+00 8.16e-02 1.79e+01 angle pdb=" CA LEU B 343 " pdb=" CB LEU B 343 " pdb=" CG LEU B 343 " ideal model delta sigma weight residual 116.30 130.88 -14.58 3.50e+00 8.16e-02 1.73e+01 ... (remaining 33145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.36: 14034 31.36 - 62.71: 263 62.71 - 94.07: 75 94.07 - 125.43: 0 125.43 - 156.78: 2 Dihedral angle restraints: 14374 sinusoidal: 6155 harmonic: 8219 Sorted by residual: dihedral pdb=" O4' U K 21 " pdb=" C1' U K 21 " pdb=" N1 U K 21 " pdb=" C2 U K 21 " ideal model delta sinusoidal sigma weight residual 200.00 43.22 156.78 1 1.50e+01 4.44e-03 8.19e+01 dihedral pdb=" CA TRP F 48 " pdb=" C TRP F 48 " pdb=" N ALA F 49 " pdb=" CA ALA F 49 " ideal model delta harmonic sigma weight residual -180.00 -141.33 -38.67 0 5.00e+00 4.00e-02 5.98e+01 dihedral pdb=" CA LEU C 216 " pdb=" C LEU C 216 " pdb=" N CYS C 217 " pdb=" CA CYS C 217 " ideal model delta harmonic sigma weight residual 180.00 141.51 38.49 0 5.00e+00 4.00e-02 5.93e+01 ... (remaining 14371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3278 0.082 - 0.163: 333 0.163 - 0.245: 11 0.245 - 0.326: 4 0.326 - 0.408: 1 Chirality restraints: 3627 Sorted by residual: chirality pdb=" CB ILE G 285 " pdb=" CA ILE G 285 " pdb=" CG1 ILE G 285 " pdb=" CG2 ILE G 285 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CB VAL C 249 " pdb=" CA VAL C 249 " pdb=" CG1 VAL C 249 " pdb=" CG2 VAL C 249 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CB ILE F 285 " pdb=" CA ILE F 285 " pdb=" CG1 ILE F 285 " pdb=" CG2 ILE F 285 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 3624 not shown) Planarity restraints: 4215 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 249 " 0.044 5.00e-02 4.00e+02 6.73e-02 7.25e+00 pdb=" N PRO C 250 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 250 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 250 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 71 " 0.043 5.00e-02 4.00e+02 6.35e-02 6.46e+00 pdb=" N PRO B 72 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 72 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 72 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 329 " -0.020 2.00e-02 2.50e+03 1.60e-02 6.37e+00 pdb=" CG TRP E 329 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP E 329 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP E 329 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 329 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 329 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 329 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 329 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 329 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 329 " -0.002 2.00e-02 2.50e+03 ... (remaining 4212 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1429 2.72 - 3.27: 22365 3.27 - 3.81: 38818 3.81 - 4.36: 47475 4.36 - 4.90: 79539 Nonbonded interactions: 189626 Sorted by model distance: nonbonded pdb=" CB CYS J 175 " pdb=" OP2 G K 57 " model vdw 2.180 3.440 nonbonded pdb=" O GLU F 301 " pdb=" OH TYR F 343 " model vdw 2.255 2.440 nonbonded pdb=" CD1 LEU B 65 " pdb=" OG SER B 106 " model vdw 2.257 3.460 nonbonded pdb=" OH TYR D 289 " pdb=" O GLY D 296 " model vdw 2.274 2.440 nonbonded pdb=" O SER D 66 " pdb=" O2' U K 47 " model vdw 2.281 2.440 ... (remaining 189621 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'D' and (resid 24 through 290 or (resid 291 through 293 and (name N or na \ me CA or name C or name O or name CB )) or resid 294 through 356)) selection = (chain 'E' and (resid 24 through 66 or resid 95 through 249 or resid 262 through \ 290 or (resid 291 through 293 and (name N or name CA or name C or name O or nam \ e CB )) or resid 294 through 356)) selection = (chain 'F' and (resid 24 through 66 or resid 95 through 249 or resid 262 through \ 356)) selection = (chain 'G' and (resid 24 through 66 or resid 95 through 249 or resid 262 through \ 290 or (resid 291 through 293 and (name N or name CA or name C or name O or nam \ e CB )) or resid 294 through 356)) selection = (chain 'H' and (resid 24 through 66 or resid 95 through 249 or resid 262 through \ 291 or (resid 292 through 293 and (name N or name CA or name C or name O or nam \ e CB )) or resid 294 through 356)) selection = (chain 'I' and (resid 24 through 66 or resid 95 through 249 or resid 262 through \ 291 or (resid 292 through 293 and (name N or name CA or name C or name O or nam \ e CB )) or resid 294 through 356)) } 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.670 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 67.040 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.090 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24272 Z= 0.324 Angle : 0.829 14.798 33150 Z= 0.456 Chirality : 0.049 0.408 3627 Planarity : 0.006 0.067 4215 Dihedral : 12.724 156.782 9180 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.72 % Favored : 91.24 % Rotamer: Outliers : 0.04 % Allowed : 1.98 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -4.44 (0.12), residues: 2946 helix: -4.05 (0.08), residues: 840 sheet: -1.21 (0.24), residues: 421 loop : -2.90 (0.12), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP E 329 HIS 0.011 0.002 HIS G 342 PHE 0.027 0.003 PHE B 211 TYR 0.022 0.002 TYR F 156 ARG 0.012 0.001 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 628 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 628 average time/residue: 0.4686 time to fit residues: 414.3757 Evaluate side-chains 340 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 2.770 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 252 optimal weight: 8.9990 chunk 226 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 142 optimal weight: 0.8980 chunk 174 optimal weight: 7.9990 chunk 271 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS B 26 GLN B 148 ASN B 289 HIS B 376 GLN B 393 ASN C 82 ASN C 86 ASN C 133 GLN C 149 ASN C 194 GLN C 196 HIS ** C 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 HIS ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 GLN F 318 GLN G 50 GLN G 247 GLN H 147 GLN ** I 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 GLN I 241 GLN I 259 GLN I 340 GLN I 342 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 24272 Z= 0.378 Angle : 0.708 13.405 33150 Z= 0.375 Chirality : 0.043 0.249 3627 Planarity : 0.005 0.062 4215 Dihedral : 13.842 143.116 4118 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 2.42 % Allowed : 10.78 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.14), residues: 2946 helix: -1.73 (0.15), residues: 873 sheet: -0.77 (0.25), residues: 431 loop : -2.59 (0.14), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP E 329 HIS 0.007 0.001 HIS C 42 PHE 0.027 0.002 PHE A 6 TYR 0.024 0.002 TYR E 156 ARG 0.009 0.001 ARG B 397 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 356 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 31 residues processed: 394 average time/residue: 0.4664 time to fit residues: 262.8780 Evaluate side-chains 327 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 296 time to evaluate : 2.800 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2494 time to fit residues: 17.3163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 150 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 225 optimal weight: 0.9990 chunk 184 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 272 optimal weight: 3.9990 chunk 293 optimal weight: 8.9990 chunk 242 optimal weight: 0.9980 chunk 269 optimal weight: 0.3980 chunk 92 optimal weight: 7.9990 chunk 218 optimal weight: 7.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN D 145 ASN D 147 GLN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN F 147 GLN ** H 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24272 Z= 0.270 Angle : 0.624 13.064 33150 Z= 0.328 Chirality : 0.041 0.181 3627 Planarity : 0.004 0.056 4215 Dihedral : 13.667 142.661 4118 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 1.26 % Allowed : 11.72 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.15), residues: 2946 helix: -0.70 (0.17), residues: 881 sheet: -0.50 (0.25), residues: 426 loop : -2.40 (0.14), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 57 HIS 0.006 0.001 HIS B 47 PHE 0.022 0.002 PHE B 16 TYR 0.025 0.002 TYR B 235 ARG 0.008 0.001 ARG I 184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 316 time to evaluate : 2.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 9 residues processed: 333 average time/residue: 0.4641 time to fit residues: 221.8882 Evaluate side-chains 302 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 293 time to evaluate : 2.474 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2638 time to fit residues: 7.6957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 268 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 chunk 272 optimal weight: 7.9990 chunk 289 optimal weight: 0.0370 chunk 142 optimal weight: 1.9990 chunk 258 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 GLN C 21 ASN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 HIS C 269 ASN D 95 GLN D 101 ASN ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24272 Z= 0.183 Angle : 0.573 12.032 33150 Z= 0.300 Chirality : 0.039 0.171 3627 Planarity : 0.004 0.056 4215 Dihedral : 13.528 143.348 4118 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 1.03 % Allowed : 12.66 % Favored : 86.30 % 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: -1.89 (0.15), residues: 2946 helix: -0.14 (0.18), residues: 880 sheet: -0.25 (0.25), residues: 434 loop : -2.28 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 57 HIS 0.006 0.001 HIS C 196 PHE 0.023 0.001 PHE A 6 TYR 0.025 0.002 TYR B 235 ARG 0.017 0.001 ARG B 397 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 324 time to evaluate : 2.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 17 residues processed: 337 average time/residue: 0.4817 time to fit residues: 232.4796 Evaluate side-chains 296 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 279 time to evaluate : 2.689 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2694 time to fit residues: 11.6604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 240 optimal weight: 7.9990 chunk 164 optimal weight: 8.9990 chunk 4 optimal weight: 0.5980 chunk 215 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 246 optimal weight: 3.9990 chunk 199 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 147 optimal weight: 9.9990 chunk 259 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN B 416 GLN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN D 147 GLN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 ASN H 226 HIS ** H 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 24272 Z= 0.476 Angle : 0.707 15.091 33150 Z= 0.371 Chirality : 0.043 0.206 3627 Planarity : 0.005 0.074 4215 Dihedral : 13.704 142.737 4118 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 1.48 % Allowed : 13.56 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.15), residues: 2946 helix: -0.22 (0.17), residues: 893 sheet: -0.20 (0.25), residues: 431 loop : -2.29 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 147 HIS 0.007 0.002 HIS F 182 PHE 0.027 0.002 PHE B 16 TYR 0.019 0.002 TYR D 132 ARG 0.012 0.001 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 306 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 18 residues processed: 329 average time/residue: 0.4796 time to fit residues: 226.3634 Evaluate side-chains 300 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 282 time to evaluate : 2.638 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2830 time to fit residues: 11.9886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 97 optimal weight: 3.9990 chunk 260 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 169 optimal weight: 0.0370 chunk 71 optimal weight: 7.9990 chunk 289 optimal weight: 40.0000 chunk 240 optimal weight: 9.9990 chunk 133 optimal weight: 0.9980 chunk 24 optimal weight: 0.0670 chunk 95 optimal weight: 10.0000 chunk 151 optimal weight: 20.0000 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 HIS D 95 GLN D 101 ASN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24272 Z= 0.178 Angle : 0.583 11.642 33150 Z= 0.304 Chirality : 0.040 0.179 3627 Planarity : 0.004 0.057 4215 Dihedral : 13.480 143.883 4118 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.21 % Allowed : 14.28 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.15), residues: 2946 helix: 0.25 (0.18), residues: 885 sheet: -0.02 (0.25), residues: 436 loop : -2.12 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 414 HIS 0.004 0.001 HIS B 74 PHE 0.016 0.001 PHE B 118 TYR 0.023 0.002 TYR D 132 ARG 0.010 0.000 ARG I 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 313 time to evaluate : 2.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 10 residues processed: 327 average time/residue: 0.4617 time to fit residues: 219.2950 Evaluate side-chains 283 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 273 time to evaluate : 2.766 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2504 time to fit residues: 8.1411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 278 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 211 optimal weight: 9.9990 chunk 163 optimal weight: 0.8980 chunk 243 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 288 optimal weight: 20.0000 chunk 180 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 133 optimal weight: 0.0570 overall best weight: 2.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24272 Z= 0.267 Angle : 0.627 20.608 33150 Z= 0.323 Chirality : 0.041 0.164 3627 Planarity : 0.004 0.052 4215 Dihedral : 13.442 144.699 4118 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 1.08 % Allowed : 15.85 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.15), residues: 2946 helix: 0.37 (0.18), residues: 876 sheet: -0.01 (0.25), residues: 455 loop : -2.13 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 414 HIS 0.005 0.001 HIS H 226 PHE 0.016 0.001 PHE B 16 TYR 0.021 0.002 TYR D 132 ARG 0.010 0.001 ARG G 193 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 289 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 304 average time/residue: 0.4668 time to fit residues: 207.3808 Evaluate side-chains 287 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 274 time to evaluate : 2.751 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2409 time to fit residues: 9.0920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 178 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 172 optimal weight: 0.1980 chunk 86 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 183 optimal weight: 9.9990 chunk 196 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 226 optimal weight: 0.0470 overall best weight: 2.2484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24272 Z= 0.256 Angle : 0.617 15.918 33150 Z= 0.319 Chirality : 0.041 0.173 3627 Planarity : 0.004 0.054 4215 Dihedral : 13.422 146.671 4118 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.54 % Allowed : 16.61 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.15), residues: 2946 helix: 0.47 (0.18), residues: 876 sheet: 0.12 (0.25), residues: 448 loop : -2.11 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 414 HIS 0.005 0.001 HIS B 203 PHE 0.020 0.001 PHE B 118 TYR 0.014 0.002 TYR D 289 ARG 0.009 0.001 ARG I 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 287 time to evaluate : 2.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 295 average time/residue: 0.4677 time to fit residues: 201.6648 Evaluate side-chains 274 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 267 time to evaluate : 2.764 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2044 time to fit residues: 5.7432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 262 optimal weight: 4.9990 chunk 276 optimal weight: 0.0170 chunk 251 optimal weight: 0.9980 chunk 268 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 210 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 242 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 overall best weight: 1.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 HIS D 101 ASN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN H 147 GLN ** H 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24272 Z= 0.192 Angle : 0.594 13.869 33150 Z= 0.307 Chirality : 0.040 0.203 3627 Planarity : 0.004 0.052 4215 Dihedral : 13.332 148.611 4118 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.58 % Allowed : 16.88 % Favored : 82.53 % 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 (0.15), residues: 2946 helix: 0.56 (0.18), residues: 869 sheet: 0.20 (0.25), residues: 457 loop : -2.03 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 414 HIS 0.004 0.001 HIS C 305 PHE 0.011 0.001 PHE D 165 TYR 0.014 0.001 TYR D 289 ARG 0.010 0.000 ARG I 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 287 time to evaluate : 2.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 293 average time/residue: 0.4590 time to fit residues: 195.8160 Evaluate side-chains 284 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 278 time to evaluate : 2.652 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2463 time to fit residues: 6.2252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 176 optimal weight: 8.9990 chunk 283 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 297 optimal weight: 10.0000 chunk 274 optimal weight: 5.9990 chunk 237 optimal weight: 8.9990 chunk 24 optimal weight: 0.4980 chunk 183 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN D 340 GLN E 241 GLN F 342 HIS ** H 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 24272 Z= 0.416 Angle : 0.716 15.134 33150 Z= 0.371 Chirality : 0.044 0.203 3627 Planarity : 0.005 0.102 4215 Dihedral : 13.536 148.103 4118 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 0.72 % Allowed : 17.51 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.15), residues: 2946 helix: 0.31 (0.18), residues: 877 sheet: 0.21 (0.26), residues: 433 loop : -2.13 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 414 HIS 0.007 0.002 HIS C 305 PHE 0.027 0.002 PHE B 16 TYR 0.025 0.002 TYR E 156 ARG 0.011 0.001 ARG I 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 277 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 285 average time/residue: 0.4687 time to fit residues: 193.9239 Evaluate side-chains 272 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 265 time to evaluate : 2.747 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3490 time to fit residues: 7.5320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 188 optimal weight: 3.9990 chunk 252 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 218 optimal weight: 6.9990 chunk 35 optimal weight: 0.0870 chunk 65 optimal weight: 20.0000 chunk 237 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 243 optimal weight: 0.5980 chunk 30 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN D 101 ASN E 95 GLN ** H 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.115818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.088521 restraints weight = 55176.094| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.62 r_work: 0.3111 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24272 Z= 0.218 Angle : 0.634 14.153 33150 Z= 0.327 Chirality : 0.041 0.196 3627 Planarity : 0.004 0.052 4215 Dihedral : 13.401 147.782 4118 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 0.54 % Allowed : 18.19 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.16), residues: 2946 helix: 0.62 (0.18), residues: 866 sheet: 0.30 (0.26), residues: 435 loop : -2.04 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 414 HIS 0.006 0.001 HIS B 203 PHE 0.014 0.001 PHE B 16 TYR 0.019 0.002 TYR I 156 ARG 0.014 0.001 ARG B 380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5536.72 seconds wall clock time: 100 minutes 57.49 seconds (6057.49 seconds total)