Starting phenix.real_space_refine on Tue Mar 19 08:17:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqx_21360/03_2024/6vqx_21360.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqx_21360/03_2024/6vqx_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_21360/03_2024/6vqx_21360.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqx_21360/03_2024/6vqx_21360.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqx_21360/03_2024/6vqx_21360.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqx_21360/03_2024/6vqx_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 12.92, per 1000 atoms: 0.55 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: 9.79 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: 7.71 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: 7.34 Time building geometry restraints manager: 10.57 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: 14057 31.36 - 62.71: 300 62.71 - 94.07: 75 94.07 - 125.43: 0 125.43 - 156.78: 2 Dihedral angle restraints: 14434 sinusoidal: 6215 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 14431 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 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: 0.030 Extract box with map and model: 3.900 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 68.590 Find NCS groups from input model: 1.520 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: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.110 ------------------------------------------------------------------------------- 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 : 13.062 156.782 9240 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 : 2.660 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 REVERT: A 13 THR cc_start: 0.9136 (p) cc_final: 0.8634 (t) REVERT: A 26 SER cc_start: 0.8626 (t) cc_final: 0.8335 (p) REVERT: A 38 TYR cc_start: 0.9067 (t80) cc_final: 0.8554 (t80) REVERT: A 41 ASP cc_start: 0.8822 (t70) cc_final: 0.8035 (t0) REVERT: B 22 GLN cc_start: 0.7875 (tp40) cc_final: 0.7470 (tm-30) REVERT: B 71 LYS cc_start: 0.8843 (mtpp) cc_final: 0.8594 (mtmt) REVERT: B 82 LEU cc_start: 0.9035 (mt) cc_final: 0.8791 (mt) REVERT: B 118 PHE cc_start: 0.8582 (t80) cc_final: 0.8329 (t80) REVERT: B 153 ARG cc_start: 0.7673 (tpp80) cc_final: 0.7076 (mpt90) REVERT: B 220 GLU cc_start: 0.8632 (tt0) cc_final: 0.8229 (tm-30) REVERT: B 253 GLN cc_start: 0.7031 (tp40) cc_final: 0.6713 (tp-100) REVERT: B 319 ARG cc_start: 0.8061 (mmp80) cc_final: 0.7604 (mpt180) REVERT: B 423 THR cc_start: 0.9011 (m) cc_final: 0.8123 (p) REVERT: B 425 PHE cc_start: 0.9013 (t80) cc_final: 0.8782 (t80) REVERT: C 50 ILE cc_start: 0.9096 (pt) cc_final: 0.8701 (mm) REVERT: C 114 HIS cc_start: 0.6187 (m-70) cc_final: 0.5139 (m170) REVERT: C 116 ASP cc_start: 0.8535 (p0) cc_final: 0.8284 (p0) REVERT: C 159 LEU cc_start: 0.8195 (mp) cc_final: 0.7879 (tt) REVERT: C 170 ARG cc_start: 0.8638 (ttp-110) cc_final: 0.8199 (ttp-110) REVERT: C 171 LYS cc_start: 0.9153 (tptt) cc_final: 0.8751 (tppt) REVERT: C 172 ASN cc_start: 0.9078 (t0) cc_final: 0.8708 (t0) REVERT: C 195 GLN cc_start: 0.8378 (tp40) cc_final: 0.8123 (tp40) REVERT: C 211 ASP cc_start: 0.8829 (m-30) cc_final: 0.8011 (t0) REVERT: C 295 VAL cc_start: 0.8686 (t) cc_final: 0.8465 (p) REVERT: D 57 TRP cc_start: 0.8057 (m100) cc_final: 0.7319 (m100) REVERT: D 128 ASN cc_start: 0.8013 (m110) cc_final: 0.7781 (m110) REVERT: D 242 GLU cc_start: 0.7665 (tt0) cc_final: 0.7178 (tm-30) REVERT: D 249 LEU cc_start: 0.7780 (tp) cc_final: 0.7442 (tp) REVERT: D 328 ASN cc_start: 0.8181 (m-40) cc_final: 0.7960 (m-40) REVERT: D 329 TRP cc_start: 0.8594 (t-100) cc_final: 0.8345 (t-100) REVERT: E 35 LYS cc_start: 0.8434 (mptt) cc_final: 0.8131 (mptt) REVERT: E 171 VAL cc_start: 0.9466 (t) cc_final: 0.9223 (m) REVERT: F 98 ASP cc_start: 0.7834 (m-30) cc_final: 0.7411 (m-30) REVERT: F 260 LYS cc_start: 0.8540 (ttmt) cc_final: 0.8172 (ttmt) REVERT: F 262 LYS cc_start: 0.9160 (ttpt) cc_final: 0.8802 (ttmm) REVERT: G 71 ILE cc_start: 0.8838 (mm) cc_final: 0.8638 (mt) REVERT: G 98 ASP cc_start: 0.7848 (m-30) cc_final: 0.7206 (m-30) REVERT: H 135 LYS cc_start: 0.8900 (tptm) cc_final: 0.8669 (tptm) REVERT: H 211 ASP cc_start: 0.7541 (m-30) cc_final: 0.6624 (m-30) REVERT: H 259 GLN cc_start: 0.7771 (pt0) cc_final: 0.7140 (pm20) REVERT: I 73 ASN cc_start: 0.8579 (m-40) cc_final: 0.8330 (m-40) REVERT: I 135 LYS cc_start: 0.8826 (tptp) cc_final: 0.8264 (tptm) REVERT: I 211 ASP cc_start: 0.8283 (m-30) cc_final: 0.8069 (m-30) outliers start: 1 outliers final: 0 residues processed: 628 average time/residue: 0.4629 time to fit residues: 409.2888 Evaluate side-chains 366 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 2.725 ------------------------------------------------------------------------------- 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: 6.9990 chunk 77 optimal weight: 0.9990 chunk 152 optimal weight: 0.9980 chunk 121 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 174 optimal weight: 7.9990 chunk 271 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 GLN C 82 ASN C 133 GLN C 149 ASN C 194 GLN ** 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** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 GLN F 318 GLN G 50 GLN G 247 GLN I 138 GLN I 147 GLN I 241 GLN I 340 GLN I 342 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24272 Z= 0.271 Angle : 0.649 12.111 33150 Z= 0.344 Chirality : 0.041 0.234 3627 Planarity : 0.005 0.052 4215 Dihedral : 14.382 144.306 4178 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 2.20 % Allowed : 9.70 % Favored : 88.10 % 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: -1.81 (0.15), residues: 869 sheet: -0.61 (0.25), residues: 416 loop : -2.58 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 329 HIS 0.006 0.001 HIS H 158 PHE 0.024 0.002 PHE A 6 TYR 0.022 0.002 TYR E 156 ARG 0.007 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 431 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 382 time to evaluate : 2.202 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: A 26 SER cc_start: 0.8228 (t) cc_final: 0.7892 (p) REVERT: A 37 TYR cc_start: 0.8885 (t80) cc_final: 0.8621 (t80) REVERT: A 38 TYR cc_start: 0.9055 (t80) cc_final: 0.8711 (t80) REVERT: A 41 ASP cc_start: 0.8857 (t70) cc_final: 0.8419 (t70) REVERT: A 45 ASP cc_start: 0.8935 (t0) cc_final: 0.8645 (t0) REVERT: A 85 LEU cc_start: 0.9341 (mm) cc_final: 0.9099 (mm) REVERT: B 82 LEU cc_start: 0.8964 (mt) cc_final: 0.8711 (mt) REVERT: B 118 PHE cc_start: 0.8650 (t80) cc_final: 0.8429 (t80) REVERT: B 153 ARG cc_start: 0.7821 (tpp80) cc_final: 0.7095 (mpp80) REVERT: B 220 GLU cc_start: 0.8689 (tt0) cc_final: 0.8305 (tm-30) REVERT: B 242 LYS cc_start: 0.8671 (mmmt) cc_final: 0.8210 (mmtm) REVERT: B 247 LYS cc_start: 0.8867 (ttmm) cc_final: 0.8563 (mtpp) REVERT: B 302 ARG cc_start: 0.8927 (mtm110) cc_final: 0.8582 (tpt90) REVERT: B 319 ARG cc_start: 0.8508 (mmp80) cc_final: 0.8071 (mmp80) REVERT: B 389 ASN cc_start: 0.9284 (m110) cc_final: 0.8985 (t0) REVERT: C 50 ILE cc_start: 0.9174 (pt) cc_final: 0.8862 (mm) REVERT: C 126 ILE cc_start: 0.9338 (mm) cc_final: 0.9085 (mt) REVERT: C 161 MET cc_start: 0.8514 (ppp) cc_final: 0.7969 (ppp) REVERT: C 166 ASP cc_start: 0.8334 (p0) cc_final: 0.7940 (p0) REVERT: C 170 ARG cc_start: 0.8760 (ttp-110) cc_final: 0.7965 (ttp-110) REVERT: C 171 LYS cc_start: 0.9182 (tptt) cc_final: 0.8961 (tppt) REVERT: C 262 TYR cc_start: 0.7976 (m-80) cc_final: 0.7678 (m-80) REVERT: D 135 LYS cc_start: 0.8712 (tmmt) cc_final: 0.8430 (tptp) REVERT: D 142 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8633 (p) REVERT: D 343 TYR cc_start: 0.7966 (t80) cc_final: 0.7757 (t80) REVERT: E 202 ARG cc_start: 0.7651 (mtp85) cc_final: 0.7439 (mtp85) REVERT: E 311 LYS cc_start: 0.8648 (ptmm) cc_final: 0.8376 (ptmm) REVERT: F 76 LYS cc_start: 0.8236 (mmtt) cc_final: 0.7909 (mmtt) REVERT: F 80 ARG cc_start: 0.8204 (ttm110) cc_final: 0.7853 (ttm110) REVERT: F 86 ASP cc_start: 0.8625 (m-30) cc_final: 0.7906 (t0) REVERT: F 98 ASP cc_start: 0.7830 (m-30) cc_final: 0.7430 (m-30) REVERT: F 260 LYS cc_start: 0.8841 (ttmt) cc_final: 0.8481 (ttmt) REVERT: F 262 LYS cc_start: 0.9259 (ttpt) cc_final: 0.8828 (ttmm) REVERT: H 134 ASP cc_start: 0.8208 (p0) cc_final: 0.7860 (p0) REVERT: H 259 GLN cc_start: 0.7569 (pt0) cc_final: 0.6953 (pm20) REVERT: I 64 GLU cc_start: 0.7686 (mt-10) cc_final: 0.6990 (mt-10) REVERT: I 137 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9126 (mm) REVERT: I 138 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7640 (pp30) REVERT: I 211 ASP cc_start: 0.8450 (m-30) cc_final: 0.8151 (m-30) REVERT: I 260 LYS cc_start: 0.8980 (tttt) cc_final: 0.8632 (tttp) outliers start: 49 outliers final: 31 residues processed: 416 average time/residue: 0.4634 time to fit residues: 275.6354 Evaluate side-chains 354 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 320 time to evaluate : 2.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain G residue 239 ASP Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 57 TRP Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 339 GLU Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 138 GLN Chi-restraints excluded: chain I residue 239 ASP Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 318 GLN 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: 7.9990 chunk 225 optimal weight: 0.5980 chunk 184 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 chunk 272 optimal weight: 0.8980 chunk 293 optimal weight: 9.9990 chunk 242 optimal weight: 0.9980 chunk 269 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 218 optimal weight: 7.9990 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** 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 H 147 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24272 Z= 0.226 Angle : 0.592 11.870 33150 Z= 0.311 Chirality : 0.040 0.182 3627 Planarity : 0.004 0.053 4215 Dihedral : 14.221 144.995 4178 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.20 % Allowed : 11.18 % Favored : 86.62 % 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: -2.29 (0.15), residues: 2946 helix: -0.72 (0.17), residues: 878 sheet: -0.42 (0.25), residues: 423 loop : -2.37 (0.14), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 147 HIS 0.006 0.001 HIS B 47 PHE 0.016 0.001 PHE D 165 TYR 0.023 0.002 TYR B 235 ARG 0.008 0.001 ARG G 202 *********************** 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 397 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 348 time to evaluate : 2.462 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: A 26 SER cc_start: 0.8240 (t) cc_final: 0.7832 (p) REVERT: A 37 TYR cc_start: 0.8869 (t80) cc_final: 0.8597 (t80) REVERT: A 41 ASP cc_start: 0.8806 (t70) cc_final: 0.8218 (t70) REVERT: A 85 LEU cc_start: 0.9320 (mm) cc_final: 0.9042 (mm) REVERT: B 82 LEU cc_start: 0.9037 (mt) cc_final: 0.8748 (mt) REVERT: B 118 PHE cc_start: 0.8618 (t80) cc_final: 0.8397 (t80) REVERT: B 123 LEU cc_start: 0.8204 (mt) cc_final: 0.7954 (pp) REVERT: B 153 ARG cc_start: 0.7804 (tpp80) cc_final: 0.7120 (mpp80) REVERT: B 220 GLU cc_start: 0.8745 (tt0) cc_final: 0.8367 (tm-30) REVERT: B 242 LYS cc_start: 0.8726 (mmmt) cc_final: 0.8252 (mmtm) REVERT: B 247 LYS cc_start: 0.8865 (ttmm) cc_final: 0.8557 (mtpp) REVERT: B 302 ARG cc_start: 0.8940 (mtm110) cc_final: 0.8694 (tpt90) REVERT: B 394 TRP cc_start: 0.7930 (t-100) cc_final: 0.7548 (t-100) REVERT: B 427 GLU cc_start: 0.8978 (mp0) cc_final: 0.8773 (mp0) REVERT: C 19 ASN cc_start: 0.8300 (m-40) cc_final: 0.7953 (t0) REVERT: C 50 ILE cc_start: 0.9163 (pt) cc_final: 0.8864 (mm) REVERT: C 85 ARG cc_start: 0.7744 (mmm-85) cc_final: 0.7498 (mmm-85) REVERT: C 126 ILE cc_start: 0.9361 (mm) cc_final: 0.9114 (mt) REVERT: C 170 ARG cc_start: 0.8737 (ttp-110) cc_final: 0.8119 (ttp-110) REVERT: C 196 HIS cc_start: 0.8413 (t70) cc_final: 0.8088 (t-90) REVERT: C 262 TYR cc_start: 0.8041 (m-80) cc_final: 0.7688 (m-80) REVERT: C 308 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.7004 (pp20) REVERT: E 64 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7385 (tp30) REVERT: E 311 LYS cc_start: 0.8656 (ptmm) cc_final: 0.8352 (ptmm) REVERT: F 51 ARG cc_start: 0.7986 (mpt180) cc_final: 0.7730 (mpt180) REVERT: F 64 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7429 (tt0) REVERT: F 76 LYS cc_start: 0.8310 (mmtt) cc_final: 0.8020 (mmtt) REVERT: F 80 ARG cc_start: 0.8063 (ttm110) cc_final: 0.7654 (ttm110) REVERT: F 98 ASP cc_start: 0.7896 (m-30) cc_final: 0.7509 (m-30) REVERT: F 260 LYS cc_start: 0.8889 (ttmt) cc_final: 0.8140 (ttmm) REVERT: F 262 LYS cc_start: 0.9273 (ttpt) cc_final: 0.8833 (ttmm) REVERT: F 268 ARG cc_start: 0.8280 (mtm-85) cc_final: 0.8049 (mtm-85) REVERT: F 334 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7871 (mt-10) REVERT: G 215 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7566 (mp0) REVERT: H 64 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7154 (mt-10) REVERT: H 86 ASP cc_start: 0.8333 (m-30) cc_final: 0.7914 (m-30) REVERT: H 134 ASP cc_start: 0.8237 (p0) cc_final: 0.7845 (p0) REVERT: H 138 GLN cc_start: 0.7952 (mm-40) cc_final: 0.7686 (mm-40) REVERT: H 260 LYS cc_start: 0.9156 (ttmt) cc_final: 0.8904 (ttmt) REVERT: H 311 LYS cc_start: 0.9103 (pttt) cc_final: 0.8830 (ptmm) REVERT: I 211 ASP cc_start: 0.8446 (m-30) cc_final: 0.8140 (m-30) REVERT: I 255 ASP cc_start: 0.8233 (t70) cc_final: 0.7789 (p0) REVERT: I 260 LYS cc_start: 0.8890 (tttt) cc_final: 0.8679 (tptm) REVERT: I 301 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7455 (mm-30) outliers start: 49 outliers final: 33 residues processed: 382 average time/residue: 0.4953 time to fit residues: 267.4522 Evaluate side-chains 348 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 314 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain G residue 239 ASP Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 57 TRP Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 239 ASP Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 318 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 268 optimal weight: 3.9990 chunk 204 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 chunk 272 optimal weight: 2.9990 chunk 289 optimal weight: 30.0000 chunk 142 optimal weight: 1.9990 chunk 258 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 GLN I 138 GLN I 259 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24272 Z= 0.244 Angle : 0.584 12.698 33150 Z= 0.306 Chirality : 0.040 0.174 3627 Planarity : 0.004 0.053 4215 Dihedral : 14.152 145.444 4178 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 2.83 % Allowed : 11.09 % Favored : 86.08 % 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: -1.87 (0.15), residues: 2946 helix: -0.12 (0.18), residues: 874 sheet: -0.24 (0.25), residues: 441 loop : -2.26 (0.14), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 57 HIS 0.005 0.001 HIS B 47 PHE 0.023 0.001 PHE A 6 TYR 0.025 0.002 TYR B 235 ARG 0.012 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 397 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 334 time to evaluate : 2.654 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: A 26 SER cc_start: 0.8201 (t) cc_final: 0.7789 (p) REVERT: A 37 TYR cc_start: 0.8893 (t80) cc_final: 0.8634 (t80) REVERT: A 41 ASP cc_start: 0.8809 (t70) cc_final: 0.8466 (t70) REVERT: A 86 GLN cc_start: 0.8904 (pt0) cc_final: 0.8612 (pt0) REVERT: B 70 LEU cc_start: 0.9022 (tt) cc_final: 0.8801 (tp) REVERT: B 82 LEU cc_start: 0.9084 (mt) cc_final: 0.8775 (mt) REVERT: B 118 PHE cc_start: 0.8614 (t80) cc_final: 0.8320 (t80) REVERT: B 153 ARG cc_start: 0.7821 (tpp80) cc_final: 0.7123 (mpp80) REVERT: B 220 GLU cc_start: 0.8780 (tt0) cc_final: 0.8482 (tm-30) REVERT: B 242 LYS cc_start: 0.8719 (mmmt) cc_final: 0.8257 (mmtm) REVERT: B 302 ARG cc_start: 0.8978 (mtm110) cc_final: 0.8755 (tpt90) REVERT: C 19 ASN cc_start: 0.8329 (m-40) cc_final: 0.7920 (t0) REVERT: C 50 ILE cc_start: 0.9185 (pt) cc_final: 0.8895 (mm) REVERT: C 85 ARG cc_start: 0.7796 (mmm-85) cc_final: 0.7335 (mmm-85) REVERT: C 126 ILE cc_start: 0.9329 (mm) cc_final: 0.9111 (mt) REVERT: C 170 ARG cc_start: 0.8727 (ttp-110) cc_final: 0.8206 (ttp-110) REVERT: C 171 LYS cc_start: 0.9154 (tppt) cc_final: 0.8942 (tppt) REVERT: C 262 TYR cc_start: 0.8117 (m-80) cc_final: 0.7529 (m-80) REVERT: C 308 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6976 (pp20) REVERT: D 63 ARG cc_start: 0.7870 (ptm160) cc_final: 0.7614 (ptm160) REVERT: E 64 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7322 (tp30) REVERT: E 138 GLN cc_start: 0.8202 (mm-40) cc_final: 0.7987 (mm-40) REVERT: E 311 LYS cc_start: 0.8627 (ptmm) cc_final: 0.8350 (ptmm) REVERT: F 64 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7298 (tt0) REVERT: F 76 LYS cc_start: 0.8263 (mmtt) cc_final: 0.7831 (mmtt) REVERT: F 93 ASN cc_start: 0.8120 (t0) cc_final: 0.7865 (t0) REVERT: F 95 GLN cc_start: 0.8204 (mt0) cc_final: 0.7967 (mt0) REVERT: F 98 ASP cc_start: 0.7896 (m-30) cc_final: 0.7667 (m-30) REVERT: F 260 LYS cc_start: 0.8858 (ttmt) cc_final: 0.8121 (ttmm) REVERT: F 334 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7829 (mt-10) REVERT: G 298 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8263 (tp) REVERT: H 86 ASP cc_start: 0.8414 (m-30) cc_final: 0.8029 (m-30) REVERT: H 311 LYS cc_start: 0.9147 (pttt) cc_final: 0.8828 (ptmm) REVERT: I 112 ARG cc_start: 0.7730 (ttp80) cc_final: 0.7379 (ttt90) REVERT: I 137 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9083 (mm) REVERT: I 211 ASP cc_start: 0.8436 (m-30) cc_final: 0.8146 (m-30) REVERT: I 255 ASP cc_start: 0.8220 (t70) cc_final: 0.7805 (p0) REVERT: I 260 LYS cc_start: 0.8825 (tttt) cc_final: 0.8497 (tttt) REVERT: I 301 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7426 (mm-30) REVERT: I 318 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8081 (mp10) outliers start: 63 outliers final: 40 residues processed: 375 average time/residue: 0.4610 time to fit residues: 247.6369 Evaluate side-chains 358 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 314 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain F residue 303 TYR Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain G residue 239 ASP Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 57 TRP Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 239 ASP Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 303 TYR Chi-restraints excluded: chain I residue 318 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 240 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 215 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 chunk 199 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 259 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 200 HIS ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 HIS ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 HIS I 138 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 24272 Z= 0.386 Angle : 0.656 14.455 33150 Z= 0.344 Chirality : 0.042 0.189 3627 Planarity : 0.004 0.071 4215 Dihedral : 14.269 145.808 4178 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 2.87 % Allowed : 12.80 % Favored : 84.33 % 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: -1.77 (0.15), residues: 2946 helix: -0.02 (0.18), residues: 878 sheet: -0.13 (0.25), residues: 417 loop : -2.21 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 147 HIS 0.007 0.001 HIS B 47 PHE 0.016 0.002 PHE B 425 TYR 0.023 0.002 TYR B 235 ARG 0.018 0.001 ARG B 397 *********************** 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 383 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 319 time to evaluate : 2.518 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: A 26 SER cc_start: 0.8248 (t) cc_final: 0.7765 (p) REVERT: A 37 TYR cc_start: 0.8921 (t80) cc_final: 0.8704 (t80) REVERT: A 41 ASP cc_start: 0.8820 (t70) cc_final: 0.8258 (t0) REVERT: A 85 LEU cc_start: 0.9249 (mm) cc_final: 0.8829 (mm) REVERT: A 86 GLN cc_start: 0.8943 (pt0) cc_final: 0.8499 (pm20) REVERT: B 74 HIS cc_start: 0.8660 (t-90) cc_final: 0.8426 (t-90) REVERT: B 82 LEU cc_start: 0.9141 (mt) cc_final: 0.8794 (mt) REVERT: B 118 PHE cc_start: 0.8716 (t80) cc_final: 0.8304 (t80) REVERT: B 153 ARG cc_start: 0.7922 (tpp80) cc_final: 0.7183 (mpp80) REVERT: B 220 GLU cc_start: 0.8769 (tt0) cc_final: 0.8530 (tm-30) REVERT: B 224 ARG cc_start: 0.8486 (ttm110) cc_final: 0.8218 (ttp-110) REVERT: B 302 ARG cc_start: 0.9000 (mtm110) cc_final: 0.8792 (tpt90) REVERT: B 319 ARG cc_start: 0.8599 (mmp80) cc_final: 0.8080 (mpt180) REVERT: B 328 GLN cc_start: 0.8800 (mm110) cc_final: 0.8482 (mm110) REVERT: B 332 GLU cc_start: 0.9089 (tm-30) cc_final: 0.8850 (tm-30) REVERT: B 393 ASN cc_start: 0.9165 (m110) cc_final: 0.8863 (m110) REVERT: C 50 ILE cc_start: 0.9218 (pt) cc_final: 0.8944 (mm) REVERT: C 85 ARG cc_start: 0.8099 (mmm-85) cc_final: 0.7806 (tpp80) REVERT: C 114 HIS cc_start: 0.6160 (m-70) cc_final: 0.5870 (m-70) REVERT: C 170 ARG cc_start: 0.8740 (ttp-110) cc_final: 0.8105 (ttp-110) REVERT: C 262 TYR cc_start: 0.8067 (m-80) cc_final: 0.7771 (m-80) REVERT: C 308 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7119 (pp20) REVERT: D 63 ARG cc_start: 0.7785 (ptm160) cc_final: 0.7563 (ptm160) REVERT: E 64 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7283 (mm-30) REVERT: E 138 GLN cc_start: 0.8322 (mm-40) cc_final: 0.8110 (mm-40) REVERT: F 64 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7263 (tt0) REVERT: F 260 LYS cc_start: 0.8875 (ttmt) cc_final: 0.8213 (ttmm) REVERT: F 334 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7845 (mt-10) REVERT: G 215 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7662 (mp0) REVERT: G 262 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8769 (tttp) REVERT: H 133 ARG cc_start: 0.8362 (ttm-80) cc_final: 0.8125 (ttm110) REVERT: H 317 LYS cc_start: 0.8298 (mmtt) cc_final: 0.7981 (mmtt) REVERT: I 112 ARG cc_start: 0.7728 (ttp80) cc_final: 0.7497 (ttt-90) REVERT: I 137 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9079 (mm) REVERT: I 138 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7884 (pp30) REVERT: I 211 ASP cc_start: 0.8464 (m-30) cc_final: 0.8151 (m-30) REVERT: I 260 LYS cc_start: 0.8809 (tttt) cc_final: 0.8538 (tttm) REVERT: I 301 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7386 (mm-30) REVERT: I 317 LYS cc_start: 0.8809 (pptt) cc_final: 0.8591 (pptt) outliers start: 64 outliers final: 45 residues processed: 362 average time/residue: 0.4628 time to fit residues: 240.4332 Evaluate side-chains 345 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 296 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain F residue 303 TYR Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 239 ASP Chi-restraints excluded: chain G residue 262 LYS Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 57 TRP Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 138 GLN Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 239 ASP Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 303 TYR Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 318 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 97 optimal weight: 6.9990 chunk 260 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 289 optimal weight: 40.0000 chunk 240 optimal weight: 4.9990 chunk 133 optimal weight: 0.0770 chunk 24 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- 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 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24272 Z= 0.275 Angle : 0.606 13.597 33150 Z= 0.317 Chirality : 0.040 0.178 3627 Planarity : 0.004 0.053 4215 Dihedral : 14.165 145.661 4178 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 3.14 % Allowed : 12.98 % Favored : 83.88 % 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: -1.57 (0.15), residues: 2946 helix: 0.23 (0.18), residues: 874 sheet: -0.14 (0.24), residues: 452 loop : -2.13 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 147 HIS 0.006 0.001 HIS B 203 PHE 0.040 0.001 PHE B 16 TYR 0.018 0.002 TYR B 235 ARG 0.009 0.001 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 378 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 308 time to evaluate : 2.515 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: A 13 THR cc_start: 0.9004 (p) cc_final: 0.7693 (p) REVERT: A 16 GLN cc_start: 0.8448 (mp-120) cc_final: 0.7476 (mp-120) REVERT: A 26 SER cc_start: 0.8242 (t) cc_final: 0.7783 (p) REVERT: A 37 TYR cc_start: 0.8929 (t80) cc_final: 0.8708 (t80) REVERT: A 41 ASP cc_start: 0.8800 (t70) cc_final: 0.8302 (t0) REVERT: A 86 GLN cc_start: 0.8931 (pt0) cc_final: 0.8442 (pm20) REVERT: B 74 HIS cc_start: 0.8658 (t-90) cc_final: 0.8405 (t-90) REVERT: B 82 LEU cc_start: 0.9116 (mt) cc_final: 0.8780 (mt) REVERT: B 118 PHE cc_start: 0.8663 (t80) cc_final: 0.8279 (t80) REVERT: B 153 ARG cc_start: 0.7888 (tpp80) cc_final: 0.7203 (mpt90) REVERT: B 224 ARG cc_start: 0.8430 (ttm110) cc_final: 0.8192 (ttp-110) REVERT: B 247 LYS cc_start: 0.8727 (mttm) cc_final: 0.8512 (mttm) REVERT: B 308 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6058 (pp) REVERT: B 319 ARG cc_start: 0.8575 (mmp80) cc_final: 0.8117 (mpt180) REVERT: B 328 GLN cc_start: 0.8808 (mm110) cc_final: 0.8464 (mm110) REVERT: B 332 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8860 (tm-30) REVERT: C 19 ASN cc_start: 0.8381 (m-40) cc_final: 0.8023 (t0) REVERT: C 50 ILE cc_start: 0.9215 (pt) cc_final: 0.8923 (mm) REVERT: C 85 ARG cc_start: 0.8014 (mmm-85) cc_final: 0.7799 (tpp80) REVERT: C 149 ASN cc_start: 0.7204 (OUTLIER) cc_final: 0.6919 (t160) REVERT: C 170 ARG cc_start: 0.8724 (ttp-110) cc_final: 0.8093 (ttp-110) REVERT: C 308 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6984 (pp20) REVERT: E 64 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7183 (tp30) REVERT: E 138 GLN cc_start: 0.8339 (mm-40) cc_final: 0.8077 (mm-40) REVERT: E 202 ARG cc_start: 0.7656 (mtp85) cc_final: 0.7420 (mtp85) REVERT: F 64 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7355 (tt0) REVERT: F 80 ARG cc_start: 0.8410 (ttp-110) cc_final: 0.8083 (ttp-110) REVERT: F 138 GLN cc_start: 0.8317 (tp-100) cc_final: 0.8071 (tp-100) REVERT: F 260 LYS cc_start: 0.8857 (ttmt) cc_final: 0.8328 (ttmt) REVERT: G 215 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7689 (mp0) REVERT: G 262 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8794 (tttp) REVERT: G 298 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8343 (tp) REVERT: I 211 ASP cc_start: 0.8427 (m-30) cc_final: 0.8128 (m-30) REVERT: I 301 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7372 (mm-30) REVERT: I 318 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8186 (mp10) outliers start: 70 outliers final: 47 residues processed: 353 average time/residue: 0.4557 time to fit residues: 230.4808 Evaluate side-chains 339 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 286 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain F residue 303 TYR Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 239 ASP Chi-restraints excluded: chain G residue 262 LYS Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 303 TYR Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 57 TRP Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 140 VAL Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 239 ASP Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 303 TYR Chi-restraints excluded: chain I residue 318 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 278 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 243 optimal weight: 10.0000 chunk 161 optimal weight: 4.9990 chunk 288 optimal weight: 50.0000 chunk 180 optimal weight: 8.9990 chunk 175 optimal weight: 4.9990 chunk 133 optimal weight: 0.0770 overall best weight: 3.0146 ------------------------------------------------------------------------------- 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 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 24272 Z= 0.310 Angle : 0.636 17.334 33150 Z= 0.330 Chirality : 0.041 0.179 3627 Planarity : 0.004 0.073 4215 Dihedral : 14.148 146.946 4178 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 2.74 % Allowed : 13.92 % Favored : 83.34 % 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: -1.51 (0.15), residues: 2946 helix: 0.26 (0.18), residues: 875 sheet: -0.03 (0.25), residues: 452 loop : -2.12 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 147 HIS 0.007 0.001 HIS B 47 PHE 0.033 0.002 PHE B 16 TYR 0.025 0.002 TYR D 132 ARG 0.011 0.001 ARG I 184 *********************** 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 361 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 300 time to evaluate : 2.962 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: A 13 THR cc_start: 0.8956 (p) cc_final: 0.7591 (p) REVERT: A 16 GLN cc_start: 0.8431 (mp-120) cc_final: 0.7462 (mp-120) REVERT: A 26 SER cc_start: 0.8232 (t) cc_final: 0.7796 (p) REVERT: A 37 TYR cc_start: 0.8935 (t80) cc_final: 0.8718 (t80) REVERT: A 41 ASP cc_start: 0.8816 (t70) cc_final: 0.8126 (t0) REVERT: A 86 GLN cc_start: 0.8941 (pt0) cc_final: 0.8462 (pm20) REVERT: B 22 GLN cc_start: 0.8156 (pt0) cc_final: 0.7868 (pp30) REVERT: B 74 HIS cc_start: 0.8694 (t-90) cc_final: 0.8397 (t-90) REVERT: B 82 LEU cc_start: 0.9133 (mt) cc_final: 0.8790 (mt) REVERT: B 118 PHE cc_start: 0.8671 (t80) cc_final: 0.8296 (t80) REVERT: B 153 ARG cc_start: 0.7926 (tpp80) cc_final: 0.7233 (mpt90) REVERT: B 308 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.5834 (pp) REVERT: B 319 ARG cc_start: 0.8587 (mmp80) cc_final: 0.8081 (mpt180) REVERT: B 332 GLU cc_start: 0.9088 (tm-30) cc_final: 0.8886 (tm-30) REVERT: C 50 ILE cc_start: 0.9213 (pt) cc_final: 0.8932 (mm) REVERT: C 170 ARG cc_start: 0.8792 (ttp-110) cc_final: 0.8284 (ttp-110) REVERT: C 308 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7014 (pp20) REVERT: D 102 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8356 (mp) REVERT: E 64 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7170 (tp30) REVERT: E 138 GLN cc_start: 0.8380 (mm-40) cc_final: 0.8117 (mm-40) REVERT: E 202 ARG cc_start: 0.7675 (mtp85) cc_final: 0.7453 (mtp85) REVERT: F 260 LYS cc_start: 0.8842 (ttmt) cc_final: 0.8477 (ttmt) REVERT: G 262 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8797 (tttp) REVERT: G 298 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8340 (tp) REVERT: I 211 ASP cc_start: 0.8437 (m-30) cc_final: 0.8138 (m-30) REVERT: I 301 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7334 (mm-30) REVERT: I 318 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8179 (mp10) outliers start: 61 outliers final: 48 residues processed: 342 average time/residue: 0.4781 time to fit residues: 235.4513 Evaluate side-chains 329 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 275 time to evaluate : 2.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain F residue 303 TYR Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 239 ASP Chi-restraints excluded: chain G residue 262 LYS Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 303 TYR Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 57 TRP Chi-restraints excluded: chain H residue 79 ASP Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 239 ASP Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 303 TYR Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 318 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 178 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 226 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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** C 149 ASN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24272 Z= 0.264 Angle : 0.615 15.167 33150 Z= 0.319 Chirality : 0.040 0.176 3627 Planarity : 0.004 0.059 4215 Dihedral : 14.068 147.629 4178 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 2.92 % Allowed : 14.01 % 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: -1.42 (0.15), residues: 2946 helix: 0.37 (0.18), residues: 877 sheet: 0.17 (0.25), residues: 441 loop : -2.11 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 414 HIS 0.005 0.001 HIS C 305 PHE 0.025 0.001 PHE B 16 TYR 0.021 0.002 TYR D 132 ARG 0.010 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 365 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 300 time to evaluate : 2.688 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: A 26 SER cc_start: 0.8180 (t) cc_final: 0.7741 (p) REVERT: A 37 TYR cc_start: 0.8934 (t80) cc_final: 0.8723 (t80) REVERT: A 38 TYR cc_start: 0.9098 (t80) cc_final: 0.8533 (t80) REVERT: A 41 ASP cc_start: 0.8712 (t70) cc_final: 0.8001 (t0) REVERT: A 86 GLN cc_start: 0.8932 (pt0) cc_final: 0.8428 (pm20) REVERT: B 22 GLN cc_start: 0.8154 (pt0) cc_final: 0.7947 (pp30) REVERT: B 74 HIS cc_start: 0.8736 (t-90) cc_final: 0.8453 (t-90) REVERT: B 82 LEU cc_start: 0.9112 (mt) cc_final: 0.8785 (mt) REVERT: B 118 PHE cc_start: 0.8640 (t80) cc_final: 0.8258 (t80) REVERT: B 153 ARG cc_start: 0.7911 (tpp80) cc_final: 0.7220 (mpt90) REVERT: B 308 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.5806 (pp) REVERT: B 319 ARG cc_start: 0.8590 (mmp80) cc_final: 0.8052 (mpt180) REVERT: B 332 GLU cc_start: 0.9112 (tm-30) cc_final: 0.8906 (tm-30) REVERT: C 50 ILE cc_start: 0.9175 (pt) cc_final: 0.8896 (mm) REVERT: C 149 ASN cc_start: 0.7240 (OUTLIER) cc_final: 0.6827 (t160) REVERT: C 170 ARG cc_start: 0.8796 (ttp-110) cc_final: 0.8288 (ttp-110) REVERT: E 64 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7183 (tp30) REVERT: E 138 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8051 (mm-40) REVERT: E 202 ARG cc_start: 0.7714 (mtp85) cc_final: 0.7484 (mtp85) REVERT: F 90 GLN cc_start: 0.8630 (mp10) cc_final: 0.8424 (mp10) REVERT: F 260 LYS cc_start: 0.8999 (ttmt) cc_final: 0.8483 (ttmt) REVERT: G 262 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8775 (tttp) REVERT: G 298 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8326 (tp) REVERT: H 28 SER cc_start: 0.9275 (m) cc_final: 0.8916 (t) REVERT: H 51 ARG cc_start: 0.4229 (mmt-90) cc_final: 0.1151 (mtt-85) REVERT: I 211 ASP cc_start: 0.8414 (m-30) cc_final: 0.8115 (m-30) REVERT: I 301 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7373 (mm-30) outliers start: 65 outliers final: 51 residues processed: 343 average time/residue: 0.4606 time to fit residues: 224.2961 Evaluate side-chains 332 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 277 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain F residue 303 TYR Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 239 ASP Chi-restraints excluded: chain G residue 262 LYS Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 303 TYR Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 57 TRP Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 239 ASP Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 303 TYR Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 318 GLN 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: 20.0000 chunk 251 optimal weight: 1.9990 chunk 268 optimal weight: 0.9990 chunk 161 optimal weight: 9.9990 chunk 116 optimal weight: 20.0000 chunk 210 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 242 optimal weight: 0.2980 chunk 253 optimal weight: 7.9990 chunk 267 optimal weight: 0.9980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 ASN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN D 101 ASN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN F 342 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24272 Z= 0.227 Angle : 0.609 14.002 33150 Z= 0.315 Chirality : 0.040 0.175 3627 Planarity : 0.004 0.046 4215 Dihedral : 13.998 148.623 4178 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 2.78 % Allowed : 14.55 % Favored : 82.67 % 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: -1.31 (0.15), residues: 2946 helix: 0.50 (0.18), residues: 876 sheet: 0.16 (0.25), residues: 460 loop : -2.06 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 414 HIS 0.005 0.001 HIS B 47 PHE 0.021 0.001 PHE B 16 TYR 0.023 0.002 TYR D 132 ARG 0.010 0.001 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 359 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 297 time to evaluate : 2.287 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: A 26 SER cc_start: 0.8205 (t) cc_final: 0.7737 (p) REVERT: A 38 TYR cc_start: 0.9093 (t80) cc_final: 0.8554 (t80) REVERT: A 41 ASP cc_start: 0.8698 (t70) cc_final: 0.7955 (t0) REVERT: A 64 HIS cc_start: 0.8843 (m-70) cc_final: 0.8506 (m-70) REVERT: A 86 GLN cc_start: 0.8917 (pt0) cc_final: 0.8414 (pm20) REVERT: B 22 GLN cc_start: 0.8160 (pt0) cc_final: 0.7935 (pp30) REVERT: B 74 HIS cc_start: 0.8675 (t-90) cc_final: 0.8378 (t-90) REVERT: B 82 LEU cc_start: 0.9111 (mt) cc_final: 0.8793 (mt) REVERT: B 118 PHE cc_start: 0.8630 (t80) cc_final: 0.8236 (t80) REVERT: B 242 LYS cc_start: 0.8972 (mmtm) cc_final: 0.8530 (tppt) REVERT: B 308 LEU cc_start: 0.6536 (OUTLIER) cc_final: 0.5741 (pp) REVERT: B 319 ARG cc_start: 0.8444 (mmp80) cc_final: 0.8008 (mmt180) REVERT: B 427 GLU cc_start: 0.9033 (mp0) cc_final: 0.8799 (mp0) REVERT: C 50 ILE cc_start: 0.9160 (pt) cc_final: 0.8926 (mm) REVERT: C 170 ARG cc_start: 0.8785 (ttp-110) cc_final: 0.8318 (ttp-110) REVERT: D 134 ASP cc_start: 0.8765 (t70) cc_final: 0.8554 (t0) REVERT: D 301 GLU cc_start: 0.8394 (mp0) cc_final: 0.8176 (mp0) REVERT: E 64 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7277 (tp30) REVERT: E 138 GLN cc_start: 0.8323 (mm-40) cc_final: 0.8015 (mm-40) REVERT: E 184 ARG cc_start: 0.7124 (mtp85) cc_final: 0.6923 (mtp85) REVERT: E 202 ARG cc_start: 0.7742 (mtp85) cc_final: 0.7511 (mtp85) REVERT: F 64 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7614 (mm-30) REVERT: F 135 LYS cc_start: 0.9045 (tptm) cc_final: 0.8734 (tptm) REVERT: G 298 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8306 (tp) REVERT: H 28 SER cc_start: 0.9263 (m) cc_final: 0.8893 (t) REVERT: H 51 ARG cc_start: 0.4199 (mmt-90) cc_final: 0.1126 (mtt-85) REVERT: H 184 ARG cc_start: 0.8067 (ttm-80) cc_final: 0.7837 (tpp-160) REVERT: I 211 ASP cc_start: 0.8408 (m-30) cc_final: 0.8108 (m-30) REVERT: I 301 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7354 (mm-30) outliers start: 62 outliers final: 54 residues processed: 335 average time/residue: 0.4529 time to fit residues: 218.2759 Evaluate side-chains 327 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 271 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 135 LYS Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain F residue 303 TYR Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 239 ASP Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 303 TYR Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 57 TRP Chi-restraints excluded: chain H residue 146 ASP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 239 ASP Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 303 TYR Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 318 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 176 optimal weight: 1.9990 chunk 283 optimal weight: 8.9990 chunk 173 optimal weight: 0.6980 chunk 134 optimal weight: 0.0060 chunk 197 optimal weight: 1.9990 chunk 297 optimal weight: 10.0000 chunk 274 optimal weight: 3.9990 chunk 237 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN B 22 GLN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 HIS D 95 GLN D 101 ASN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN H 342 HIS ** I 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24272 Z= 0.198 Angle : 0.594 12.434 33150 Z= 0.307 Chirality : 0.040 0.200 3627 Planarity : 0.004 0.047 4215 Dihedral : 13.911 150.094 4178 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 2.51 % Allowed : 14.91 % Favored : 82.58 % 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: -1.18 (0.16), residues: 2946 helix: 0.61 (0.18), residues: 868 sheet: 0.33 (0.25), residues: 456 loop : -2.00 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 414 HIS 0.004 0.001 HIS B 47 PHE 0.014 0.001 PHE B 425 TYR 0.023 0.002 TYR D 132 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 341 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 285 time to evaluate : 2.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 SER cc_start: 0.8182 (t) cc_final: 0.7724 (p) REVERT: A 37 TYR cc_start: 0.8861 (t80) cc_final: 0.8591 (t80) REVERT: A 38 TYR cc_start: 0.8995 (t80) cc_final: 0.8643 (t80) REVERT: A 41 ASP cc_start: 0.8646 (t70) cc_final: 0.7870 (t0) REVERT: A 86 GLN cc_start: 0.8849 (pt0) cc_final: 0.8322 (pm20) REVERT: B 22 GLN cc_start: 0.8132 (pt0) cc_final: 0.7727 (pp30) REVERT: B 49 ARG cc_start: 0.5711 (tpp-160) cc_final: 0.5472 (tpm170) REVERT: B 74 HIS cc_start: 0.8594 (t-90) cc_final: 0.8310 (t-90) REVERT: B 82 LEU cc_start: 0.9045 (mt) cc_final: 0.8768 (mt) REVERT: B 118 PHE cc_start: 0.8564 (t80) cc_final: 0.8156 (t80) REVERT: B 123 LEU cc_start: 0.7918 (mt) cc_final: 0.7703 (pp) REVERT: B 242 LYS cc_start: 0.8959 (mmtm) cc_final: 0.8683 (tppt) REVERT: B 308 LEU cc_start: 0.6348 (OUTLIER) cc_final: 0.5516 (pp) REVERT: B 319 ARG cc_start: 0.8502 (mmp80) cc_final: 0.7842 (mmt180) REVERT: B 424 MET cc_start: 0.8624 (ppp) cc_final: 0.8280 (ppp) REVERT: B 427 GLU cc_start: 0.9017 (mp0) cc_final: 0.8778 (mp0) REVERT: C 50 ILE cc_start: 0.9155 (pt) cc_final: 0.8919 (mm) REVERT: C 170 ARG cc_start: 0.8809 (ttp-110) cc_final: 0.8430 (ttp-110) REVERT: D 134 ASP cc_start: 0.8747 (t70) cc_final: 0.8540 (t0) REVERT: D 301 GLU cc_start: 0.8361 (mp0) cc_final: 0.8160 (mp0) REVERT: E 64 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7387 (tp30) REVERT: E 138 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8065 (mm-40) REVERT: E 184 ARG cc_start: 0.6965 (mtp85) cc_final: 0.6753 (mtp85) REVERT: E 202 ARG cc_start: 0.7709 (mtp85) cc_final: 0.7486 (mtp85) REVERT: H 28 SER cc_start: 0.9234 (m) cc_final: 0.8886 (t) REVERT: H 51 ARG cc_start: 0.4115 (mmt-90) cc_final: 0.1136 (mtt-85) REVERT: I 136 LEU cc_start: 0.9551 (tp) cc_final: 0.9255 (tt) REVERT: I 211 ASP cc_start: 0.8376 (m-30) cc_final: 0.8072 (m-30) outliers start: 56 outliers final: 45 residues processed: 318 average time/residue: 0.4508 time to fit residues: 207.1106 Evaluate side-chains 314 residues out of total 2398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 268 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 172 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 135 LYS Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain F residue 303 TYR Chi-restraints excluded: chain F residue 333 ASP Chi-restraints excluded: chain G residue 68 ARG Chi-restraints excluded: chain G residue 239 ASP Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 303 TYR Chi-restraints excluded: chain G residue 353 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 57 TRP Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 239 ASP Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 303 TYR Chi-restraints excluded: chain I residue 306 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 299 random chunks: chunk 188 optimal weight: 5.9990 chunk 252 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 218 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 237 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 243 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 HIS D 101 ASN ** D 340 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 = 0.3783 r_free = 0.3783 target = 0.118082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.090984 restraints weight = 55069.278| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.63 r_work: 0.3155 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24272 Z= 0.179 Angle : 0.593 11.961 33150 Z= 0.305 Chirality : 0.040 0.215 3627 Planarity : 0.004 0.050 4215 Dihedral : 13.860 150.371 4178 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 2.29 % Allowed : 15.85 % Favored : 81.86 % 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: -1.08 (0.16), residues: 2946 helix: 0.69 (0.18), residues: 874 sheet: 0.42 (0.25), residues: 454 loop : -1.96 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 414 HIS 0.010 0.001 HIS C 293 PHE 0.015 0.001 PHE D 194 TYR 0.022 0.001 TYR D 132 ARG 0.011 0.000 ARG I 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5778.19 seconds wall clock time: 104 minutes 18.87 seconds (6258.87 seconds total)