Starting phenix.real_space_refine (version: dev) on Fri Dec 16 22:09:19 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k71_9840/12_2022/6k71_9840.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k71_9840/12_2022/6k71_9840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k71_9840/12_2022/6k71_9840.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k71_9840/12_2022/6k71_9840.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k71_9840/12_2022/6k71_9840.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k71_9840/12_2022/6k71_9840.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.000 sd= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 108": "NH1" <-> "NH2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 108": "NH1" <-> "NH2" Residue "B PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 183": "NH1" <-> "NH2" Residue "D PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 234": "NH1" <-> "NH2" Residue "E TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 234": "NH1" <-> "NH2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "G ARG 321": "NH1" <-> "NH2" Residue "G PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 374": "NH1" <-> "NH2" Residue "G ARG 417": "NH1" <-> "NH2" Residue "G ARG 467": "NH1" <-> "NH2" Residue "H ARG 170": "NH1" <-> "NH2" Residue "H ARG 321": "NH1" <-> "NH2" Residue "H PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 374": "NH1" <-> "NH2" Residue "H ARG 417": "NH1" <-> "NH2" Residue "H ARG 467": "NH1" <-> "NH2" Residue "I ARG 55": "NH1" <-> "NH2" Residue "I PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 428": "NH1" <-> "NH2" Residue "J ARG 55": "NH1" <-> "NH2" Residue "J ARG 428": "NH1" <-> "NH2" Residue "K ARG 53": "NH1" <-> "NH2" Residue "K ARG 54": "NH1" <-> "NH2" Residue "K ARG 57": "NH1" <-> "NH2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K ARG 88": "NH1" <-> "NH2" Residue "K TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 32589 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2055 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 9, 'TRANS': 255} Chain breaks: 3 Chain: "B" Number of atoms: 2055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2055 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 9, 'TRANS': 255} Chain breaks: 3 Chain: "C" Number of atoms: 2486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2486 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Chain: "D" Number of atoms: 2486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2486 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Chain: "E" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2306 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 11, 'TRANS': 324} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 7, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 143 Chain: "F" Number of atoms: 2275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2275 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 11, 'TRANS': 320} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 7, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 143 Chain: "G" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2779 Classifications: {'peptide': 357} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 338} Chain: "H" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2779 Classifications: {'peptide': 357} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 338} Chain: "I" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3312 Classifications: {'peptide': 421} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 402} Chain breaks: 1 Chain: "J" Number of atoms: 4675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4675 Classifications: {'peptide': 588} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 565} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2139 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 8, 'TRANS': 256} Chain: "M" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 145 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "P" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3097 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 19, 'TRANS': 386} Chain breaks: 1 Time building chain proxies: 25.18, per 1000 atoms: 0.77 Number of scatterers: 32589 At special positions: 0 Unit cell: (160.23, 198.45, 173.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 6055 8.00 N 5685 7.00 C 20681 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: 13.99 Conformation dependent library (CDL) restraints added in 4.7 seconds 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8018 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 45 sheets defined 33.6% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 7 through 17 removed outlier: 4.269A pdb=" N ASP A 17 " --> pdb=" O GLN A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 33 removed outlier: 4.109A pdb=" N ALA A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 92 through 106 removed outlier: 3.861A pdb=" N ARG A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 106 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 115 Processing helix chain 'A' and resid 131 through 143 removed outlier: 3.705A pdb=" N LEU A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 170 Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.559A pdb=" N MET A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.779A pdb=" N VAL A 246 " --> pdb=" O GLN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.769A pdb=" N ASP A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 17 removed outlier: 3.948A pdb=" N ASP B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 32 Processing helix chain 'B' and resid 33 through 36 removed outlier: 3.639A pdb=" N ARG B 36 " --> pdb=" O PHE B 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 33 through 36' Processing helix chain 'B' and resid 46 through 58 Processing helix chain 'B' and resid 62 through 76 removed outlier: 4.172A pdb=" N SER B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 116 removed outlier: 3.945A pdb=" N ARG B 96 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG B 108 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ASN B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N HIS B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 141 removed outlier: 4.078A pdb=" N LEU B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 170 Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 186 through 190 Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 247 through 252 Processing helix chain 'B' and resid 295 through 301 Processing helix chain 'C' and resid 11 through 24 Processing helix chain 'C' and resid 31 through 43 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.780A pdb=" N LEU C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 98 Processing helix chain 'C' and resid 128 through 154 removed outlier: 4.132A pdb=" N ASN C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N MET C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 removed outlier: 3.674A pdb=" N HIS C 158 " --> pdb=" O ALA C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 155 through 158' Processing helix chain 'C' and resid 171 through 185 Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 221 through 228 removed outlier: 3.789A pdb=" N ALA C 224 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N MET C 226 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER C 227 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG C 228 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 336 through 344 Processing helix chain 'C' and resid 345 through 350 removed outlier: 3.543A pdb=" N ASP C 348 " --> pdb=" O HIS C 345 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL C 350 " --> pdb=" O ASP C 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 345 through 350' Processing helix chain 'D' and resid 11 through 22 Processing helix chain 'D' and resid 31 through 41 removed outlier: 3.992A pdb=" N ALA D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.649A pdb=" N LEU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 98 Processing helix chain 'D' and resid 128 through 154 removed outlier: 3.877A pdb=" N ASN D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N MET D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N GLU D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 185 Processing helix chain 'D' and resid 200 through 207 Processing helix chain 'D' and resid 218 through 222 removed outlier: 3.900A pdb=" N ILE D 222 " --> pdb=" O ASP D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 259 Processing helix chain 'D' and resid 290 through 294 removed outlier: 3.716A pdb=" N GLU D 293 " --> pdb=" O ALA D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 removed outlier: 3.836A pdb=" N LEU D 320 " --> pdb=" O PRO D 317 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE D 321 " --> pdb=" O PRO D 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 317 through 321' Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 345 through 349 Processing helix chain 'E' and resid 36 through 43 removed outlier: 3.664A pdb=" N LEU E 42 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU E 43 " --> pdb=" O PRO E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 66 removed outlier: 3.937A pdb=" N GLU E 66 " --> pdb=" O LEU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 93 removed outlier: 4.183A pdb=" N ILE E 93 " --> pdb=" O SER E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 123 removed outlier: 3.551A pdb=" N ALA E 123 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 176 Processing helix chain 'E' and resid 183 through 190 removed outlier: 4.234A pdb=" N LEU E 187 " --> pdb=" O LYS E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 217 removed outlier: 3.831A pdb=" N VAL E 212 " --> pdb=" O LYS E 208 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU E 217 " --> pdb=" O ASP E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 229 removed outlier: 3.781A pdb=" N LEU E 228 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE E 229 " --> pdb=" O SER E 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 225 through 229' Processing helix chain 'F' and resid 37 through 41 Processing helix chain 'F' and resid 62 through 66 removed outlier: 4.134A pdb=" N GLU F 66 " --> pdb=" O LEU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 91 Processing helix chain 'F' and resid 116 through 120 Processing helix chain 'F' and resid 184 through 190 Processing helix chain 'F' and resid 208 through 216 removed outlier: 3.881A pdb=" N VAL F 212 " --> pdb=" O LYS F 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 195 removed outlier: 3.894A pdb=" N GLN G 194 " --> pdb=" O SER G 191 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE G 195 " --> pdb=" O LEU G 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 191 through 195' Processing helix chain 'G' and resid 204 through 215 removed outlier: 3.762A pdb=" N VAL G 208 " --> pdb=" O HIS G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 238 Processing helix chain 'G' and resid 251 through 256 Processing helix chain 'G' and resid 256 through 267 Processing helix chain 'G' and resid 270 through 287 removed outlier: 3.522A pdb=" N HIS G 274 " --> pdb=" O SER G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 327 Processing helix chain 'G' and resid 341 through 351 Processing helix chain 'G' and resid 369 through 379 Processing helix chain 'G' and resid 389 through 394 removed outlier: 6.177A pdb=" N SER G 392 " --> pdb=" O PRO G 389 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR G 393 " --> pdb=" O ALA G 390 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL G 394 " --> pdb=" O ALA G 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 389 through 394' Processing helix chain 'G' and resid 421 through 427 removed outlier: 4.081A pdb=" N LEU G 425 " --> pdb=" O ALA G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 443 removed outlier: 3.863A pdb=" N PHE G 443 " --> pdb=" O THR G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 512 through 517 removed outlier: 3.646A pdb=" N LEU G 516 " --> pdb=" O VAL G 512 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 195 removed outlier: 3.655A pdb=" N PHE H 195 " --> pdb=" O LEU H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 215 Processing helix chain 'H' and resid 223 through 238 Processing helix chain 'H' and resid 252 through 267 removed outlier: 3.538A pdb=" N LYS H 257 " --> pdb=" O VAL H 253 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 270 through 287 Processing helix chain 'H' and resid 292 through 327 removed outlier: 3.521A pdb=" N ALA H 296 " --> pdb=" O ARG H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 341 through 351 Processing helix chain 'H' and resid 369 through 379 Processing helix chain 'H' and resid 387 through 391 Processing helix chain 'H' and resid 421 through 429 removed outlier: 3.974A pdb=" N LEU H 425 " --> pdb=" O ALA H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 512 through 518 removed outlier: 3.580A pdb=" N VAL H 518 " --> pdb=" O VAL H 514 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 68 removed outlier: 3.561A pdb=" N LEU I 67 " --> pdb=" O PRO I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 86 removed outlier: 3.731A pdb=" N TYR I 78 " --> pdb=" O ALA I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 107 Processing helix chain 'I' and resid 132 through 142 Processing helix chain 'I' and resid 161 through 176 removed outlier: 3.691A pdb=" N LYS I 176 " --> pdb=" O ARG I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 260 Processing helix chain 'I' and resid 269 through 275 removed outlier: 4.130A pdb=" N VAL I 273 " --> pdb=" O ARG I 269 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG I 274 " --> pdb=" O ASP I 270 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY I 275 " --> pdb=" O ASP I 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 269 through 275' Processing helix chain 'I' and resid 276 through 278 No H-bonds generated for 'chain 'I' and resid 276 through 278' Processing helix chain 'I' and resid 302 through 314 Processing helix chain 'I' and resid 338 through 342 removed outlier: 3.524A pdb=" N ASN I 341 " --> pdb=" O SER I 338 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE I 342 " --> pdb=" O ARG I 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 338 through 342' Processing helix chain 'J' and resid 74 through 86 Processing helix chain 'J' and resid 98 through 106 removed outlier: 3.673A pdb=" N ILE J 102 " --> pdb=" O LYS J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 139 Processing helix chain 'J' and resid 161 through 175 removed outlier: 3.520A pdb=" N LEU J 165 " --> pdb=" O ILE J 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 231 removed outlier: 3.677A pdb=" N LEU J 230 " --> pdb=" O PRO J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 262 removed outlier: 3.536A pdb=" N GLN J 258 " --> pdb=" O PRO J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 277 Processing helix chain 'J' and resid 302 through 311 Processing helix chain 'J' and resid 548 through 552 Processing helix chain 'J' and resid 552 through 561 removed outlier: 4.068A pdb=" N GLU J 556 " --> pdb=" O VAL J 552 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL J 557 " --> pdb=" O PHE J 553 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU J 561 " --> pdb=" O VAL J 557 " (cutoff:3.500A) Processing helix chain 'J' and resid 562 through 565 removed outlier: 3.507A pdb=" N LYS J 565 " --> pdb=" O GLN J 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 562 through 565' Processing helix chain 'J' and resid 571 through 584 removed outlier: 3.535A pdb=" N VAL J 575 " --> pdb=" O CYS J 571 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA J 584 " --> pdb=" O SER J 580 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 602 removed outlier: 5.465A pdb=" N GLN J 594 " --> pdb=" O LYS J 590 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 622 Processing helix chain 'J' and resid 622 through 627 Processing helix chain 'J' and resid 638 through 656 Processing helix chain 'J' and resid 657 through 664 removed outlier: 5.135A pdb=" N ILE J 661 " --> pdb=" O ALA J 658 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER J 662 " --> pdb=" O LEU J 659 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET J 663 " --> pdb=" O GLY J 660 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA J 664 " --> pdb=" O ILE J 661 " (cutoff:3.500A) Processing helix chain 'J' and resid 666 through 670 Processing helix chain 'J' and resid 677 through 685 removed outlier: 4.681A pdb=" N ILE J 681 " --> pdb=" O ALA J 677 " (cutoff:3.500A) Processing helix chain 'J' and resid 693 through 699 Processing helix chain 'J' and resid 700 through 714 Processing helix chain 'K' and resid 96 through 114 removed outlier: 3.948A pdb=" N HIS K 114 " --> pdb=" O SER K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 132 removed outlier: 3.828A pdb=" N LEU K 130 " --> pdb=" O GLN K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 135 No H-bonds generated for 'chain 'K' and resid 133 through 135' Processing helix chain 'K' and resid 143 through 156 removed outlier: 4.184A pdb=" N HIS K 155 " --> pdb=" O ASP K 151 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA K 156 " --> pdb=" O ALA K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 178 removed outlier: 4.527A pdb=" N ASN K 178 " --> pdb=" O GLU K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 183 removed outlier: 3.561A pdb=" N ARG K 183 " --> pdb=" O ASN K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 221 Processing helix chain 'K' and resid 245 through 261 removed outlier: 3.938A pdb=" N SER K 249 " --> pdb=" O THR K 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 187 removed outlier: 4.606A pdb=" N PHE M 184 " --> pdb=" O LEU M 180 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 63 removed outlier: 4.130A pdb=" N VAL P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 149 Processing helix chain 'P' and resid 168 through 174 removed outlier: 3.710A pdb=" N GLU P 172 " --> pdb=" O PRO P 168 " (cutoff:3.500A) Processing helix chain 'P' and resid 196 through 209 removed outlier: 3.764A pdb=" N ALA P 200 " --> pdb=" O LYS P 196 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU P 205 " --> pdb=" O LYS P 201 " (cutoff:3.500A) Processing helix chain 'P' and resid 231 through 241 Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 127 Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 201 removed outlier: 3.610A pdb=" N GLY A 205 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN A 208 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AA4, first strand: chain 'B' and resid 151 through 152 removed outlier: 5.816A pdb=" N ILE B 125 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 194 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL B 193 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL B 229 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL B 195 " --> pdb=" O VAL B 229 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 199 through 200 removed outlier: 3.936A pdb=" N GLY B 199 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE B 207 " --> pdb=" O GLY B 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 284 through 285 Processing sheet with id=AA7, first strand: chain 'C' and resid 164 through 168 removed outlier: 5.940A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR C 214 " --> pdb=" O ARG G 483 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 313 through 316 removed outlier: 3.788A pdb=" N LEU C 245 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL C 248 " --> pdb=" O THR C 236 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR C 236 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N CYS C 268 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR C 236 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY C 329 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 306 through 308 removed outlier: 6.259A pdb=" N SER C 307 " --> pdb=" O TYR G 385 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N LEU G 387 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU G 386 " --> pdb=" O VAL G 360 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP G 362 " --> pdb=" O LEU G 386 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU G 334 " --> pdb=" O LEU G 402 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU G 499 " --> pdb=" O VAL G 434 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 215 through 216 removed outlier: 6.703A pdb=" N VAL D 189 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR D 167 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N GLY D 235 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE D 168 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE D 266 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU D 323 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 267 " --> pdb=" O LEU D 323 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AB3, first strand: chain 'E' and resid 51 through 52 removed outlier: 7.348A pdb=" N ALA E 5 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU E 128 " --> pdb=" O TYR E 264 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 170 through 171 Processing sheet with id=AB5, first strand: chain 'E' and resid 181 through 182 Processing sheet with id=AB6, first strand: chain 'E' and resid 357 through 358 removed outlier: 5.951A pdb=" N LEU E 357 " --> pdb=" O ILE E 375 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N VAL E 374 " --> pdb=" O LEU E 392 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU E 391 " --> pdb=" O ILE E 409 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 52 through 53 removed outlier: 6.386A pdb=" N VAL F 6 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 132 through 133 Processing sheet with id=AB9, first strand: chain 'F' and resid 159 through 160 removed outlier: 3.711A pdb=" N ILE F 193 " --> pdb=" O VAL I 240 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE F 195 " --> pdb=" O VAL I 238 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N VAL I 238 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG I 241 " --> pdb=" O VAL I 203 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL I 203 " --> pdb=" O ARG I 241 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 181 through 183 removed outlier: 3.746A pdb=" N PHE I 224 " --> pdb=" O ILE F 182 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 363 through 364 removed outlier: 5.957A pdb=" N GLN F 363 " --> pdb=" O ILE F 381 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU F 380 " --> pdb=" O VAL F 398 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 402 through 404 removed outlier: 7.485A pdb=" N ASN F 403 " --> pdb=" O ILE F 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'G' and resid 414 through 417 removed outlier: 4.044A pdb=" N VAL G 414 " --> pdb=" O THR G 492 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 333 through 334 removed outlier: 3.697A pdb=" N LEU H 334 " --> pdb=" O LYS H 400 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'H' and resid 358 through 360 removed outlier: 6.536A pdb=" N VAL H 358 " --> pdb=" O SER H 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'H' and resid 407 through 408 removed outlier: 3.931A pdb=" N VAL H 414 " --> pdb=" O THR H 492 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR H 492 " --> pdb=" O VAL H 414 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER H 416 " --> pdb=" O ASP H 490 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 436 through 437 Processing sheet with id=AC9, first strand: chain 'I' and resid 46 through 48 Processing sheet with id=AD1, first strand: chain 'I' and resid 94 through 95 removed outlier: 3.914A pdb=" N CYS I 95 " --> pdb=" O ILE I 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'I' and resid 179 through 185 removed outlier: 4.951A pdb=" N SER I 179 " --> pdb=" O GLN I 286 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N HIS I 288 " --> pdb=" O SER I 179 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N MET I 181 " --> pdb=" O HIS I 288 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N HIS I 290 " --> pdb=" O MET I 181 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N MET I 183 " --> pdb=" O HIS I 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'I' and resid 390 through 392 removed outlier: 6.283A pdb=" N VAL I 390 " --> pdb=" O ILE I 408 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'I' and resid 431 through 432 removed outlier: 3.595A pdb=" N THR I 432 " --> pdb=" O ILE I 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'J' and resid 119 through 121 removed outlier: 4.261A pdb=" N THR J 91 " --> pdb=" O VAL J 119 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA J 45 " --> pdb=" O GLU J 90 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL J 151 " --> pdb=" O VAL J 46 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 155 through 157 removed outlier: 4.018A pdb=" N ILE J 156 " --> pdb=" O ALA J 298 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA J 298 " --> pdb=" O ILE J 156 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'J' and resid 179 through 184 removed outlier: 4.259A pdb=" N SER J 179 " --> pdb=" O GLN J 286 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N HIS J 288 " --> pdb=" O SER J 179 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N MET J 181 " --> pdb=" O HIS J 288 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N HIS J 290 " --> pdb=" O MET J 181 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N MET J 183 " --> pdb=" O HIS J 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'J' and resid 212 through 214 removed outlier: 6.449A pdb=" N ALA J 204 " --> pdb=" O LEU J 213 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL J 205 " --> pdb=" O GLU J 239 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 336 through 337 removed outlier: 3.525A pdb=" N ARG J 344 " --> pdb=" O THR J 336 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 355 through 356 removed outlier: 7.106A pdb=" N ILE J 355 " --> pdb=" O ILE J 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 389 through 390 Processing sheet with id=AE3, first strand: chain 'J' and resid 411 through 412 removed outlier: 3.618A pdb=" N LEU J 412 " --> pdb=" O SER J 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'K' and resid 22 through 23 removed outlier: 3.606A pdb=" N VAL K 22 " --> pdb=" O GLU K 69 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU K 69 " --> pdb=" O VAL K 22 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'P' and resid 44 through 45 Processing sheet with id=AE6, first strand: chain 'P' and resid 159 through 160 removed outlier: 7.697A pdb=" N ILE P 159 " --> pdb=" O ASN P 190 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'P' and resid 277 through 278 removed outlier: 3.514A pdb=" N GLY P 277 " --> pdb=" O THR P 341 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLY P 340 " --> pdb=" O VAL P 319 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'P' and resid 419 through 420 removed outlier: 3.586A pdb=" N LYS P 426 " --> pdb=" O ALA P 419 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP P 456 " --> pdb=" O PHE P 376 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 414 through 415 removed outlier: 3.796A pdb=" N ALA P 442 " --> pdb=" O ASN P 407 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG P 452 " --> pdb=" O ARG P 445 " (cutoff:3.500A) 921 hydrogen bonds defined for protein. 2616 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.81 Time building geometry restraints manager: 15.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10239 1.34 - 1.46: 6088 1.46 - 1.58: 16558 1.58 - 1.70: 0 1.70 - 1.82: 259 Bond restraints: 33144 Sorted by residual: bond pdb=" C ASP J 62 " pdb=" N GLN J 63 " ideal model delta sigma weight residual 1.329 1.256 0.073 1.86e-02 2.89e+03 1.54e+01 bond pdb=" C LEU H 499 " pdb=" N VAL H 500 " ideal model delta sigma weight residual 1.329 1.282 0.047 1.38e-02 5.25e+03 1.18e+01 bond pdb=" C LEU A 291 " pdb=" N THR A 292 " ideal model delta sigma weight residual 1.331 1.284 0.048 1.54e-02 4.22e+03 9.58e+00 bond pdb=" C LEU F 28 " pdb=" N PRO F 29 " ideal model delta sigma weight residual 1.334 1.403 -0.069 2.34e-02 1.83e+03 8.74e+00 bond pdb=" C TYR F 94 " pdb=" N PRO F 95 " ideal model delta sigma weight residual 1.336 1.364 -0.028 9.80e-03 1.04e+04 8.16e+00 ... (remaining 33139 not shown) Histogram of bond angle deviations from ideal: 95.09 - 103.53: 426 103.53 - 111.96: 14981 111.96 - 120.40: 16900 120.40 - 128.84: 12368 128.84 - 137.28: 228 Bond angle restraints: 44903 Sorted by residual: angle pdb=" N ILE F 36 " pdb=" CA ILE F 36 " pdb=" C ILE F 36 " ideal model delta sigma weight residual 112.17 105.72 6.45 9.50e-01 1.11e+00 4.61e+01 angle pdb=" N ILE P 192 " pdb=" CA ILE P 192 " pdb=" C ILE P 192 " ideal model delta sigma weight residual 113.20 106.77 6.43 9.60e-01 1.09e+00 4.48e+01 angle pdb=" N ASN K 179 " pdb=" CA ASN K 179 " pdb=" C ASN K 179 " ideal model delta sigma weight residual 111.07 118.23 -7.16 1.07e+00 8.73e-01 4.48e+01 angle pdb=" C CYS C 194 " pdb=" N ALA C 195 " pdb=" CA ALA C 195 " ideal model delta sigma weight residual 123.34 115.03 8.31 1.29e+00 6.01e-01 4.15e+01 angle pdb=" N LEU K 242 " pdb=" CA LEU K 242 " pdb=" C LEU K 242 " ideal model delta sigma weight residual 113.72 105.42 8.30 1.30e+00 5.92e-01 4.08e+01 ... (remaining 44898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 18114 15.91 - 31.82: 1679 31.82 - 47.73: 347 47.73 - 63.65: 16 63.65 - 79.56: 21 Dihedral angle restraints: 20177 sinusoidal: 7838 harmonic: 12339 Sorted by residual: dihedral pdb=" CA GLY E 47 " pdb=" C GLY E 47 " pdb=" N PHE E 48 " pdb=" CA PHE E 48 " ideal model delta harmonic sigma weight residual 180.00 126.78 53.22 0 5.00e+00 4.00e-02 1.13e+02 dihedral pdb=" CA GLN A 156 " pdb=" C GLN A 156 " pdb=" N PRO A 157 " pdb=" CA PRO A 157 " ideal model delta harmonic sigma weight residual 180.00 132.75 47.25 0 5.00e+00 4.00e-02 8.93e+01 dihedral pdb=" CA MET P 180 " pdb=" C MET P 180 " pdb=" N LYS P 181 " pdb=" CA LYS P 181 " ideal model delta harmonic sigma weight residual 180.00 135.26 44.74 0 5.00e+00 4.00e-02 8.01e+01 ... (remaining 20174 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 4643 0.111 - 0.222: 586 0.222 - 0.332: 49 0.332 - 0.443: 3 0.443 - 0.554: 1 Chirality restraints: 5282 Sorted by residual: chirality pdb=" CB ILE G 198 " pdb=" CA ILE G 198 " pdb=" CG1 ILE G 198 " pdb=" CG2 ILE G 198 " both_signs ideal model delta sigma weight residual False 2.64 2.09 0.55 2.00e-01 2.50e+01 7.68e+00 chirality pdb=" CB ILE K 65 " pdb=" CA ILE K 65 " pdb=" CG1 ILE K 65 " pdb=" CG2 ILE K 65 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" CB ILE J 385 " pdb=" CA ILE J 385 " pdb=" CG1 ILE J 385 " pdb=" CG2 ILE J 385 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 5279 not shown) Planarity restraints: 5753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR I 322 " -0.073 5.00e-02 4.00e+02 1.11e-01 1.99e+01 pdb=" N PRO I 323 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO I 323 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO I 323 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 185 " 0.030 2.00e-02 2.50e+03 3.00e-02 1.57e+01 pdb=" CG PHE J 185 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 PHE J 185 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE J 185 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE J 185 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE J 185 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE J 185 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 156 " -0.064 5.00e-02 4.00e+02 9.77e-02 1.53e+01 pdb=" N PRO A 157 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 157 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 157 " -0.053 5.00e-02 4.00e+02 ... (remaining 5750 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 7 2.23 - 2.90: 12436 2.90 - 3.57: 46614 3.57 - 4.23: 72423 4.23 - 4.90: 117115 Nonbonded interactions: 248595 Sorted by model distance: nonbonded pdb=" CB VAL K 157 " pdb=" CD1 ILE K 180 " model vdw 1.563 3.890 nonbonded pdb=" CG1 VAL K 157 " pdb=" CD1 ILE K 180 " model vdw 1.700 3.880 nonbonded pdb=" CG2 VAL K 157 " pdb=" CD1 ILE K 180 " model vdw 1.859 3.880 nonbonded pdb=" ND2 ASN K 178 " pdb=" CD ARG K 182 " model vdw 2.148 3.520 nonbonded pdb=" O ASN K 178 " pdb=" CB ARG K 182 " model vdw 2.156 2.752 ... (remaining 248590 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 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 1 through 267 or resid 276 through 444)) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 20681 2.51 5 N 5685 2.21 5 O 6055 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue 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: 2.640 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: 0.000 Extract box with map and model: 5.890 Check model and map are aligned: 0.420 Convert atoms to be neutral: 0.260 Process input model: 85.010 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 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 : 0.008 0.089 33144 Z= 0.525 Angle : 1.398 20.105 44903 Z= 0.763 Chirality : 0.074 0.554 5282 Planarity : 0.009 0.111 5753 Dihedral : 12.846 79.557 12159 Min Nonbonded Distance : 1.563 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 15.32 % Favored : 84.63 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 4.73 % Twisted General : 0.79 % 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: -5.50 (0.10), residues: 4164 helix: -3.38 (0.10), residues: 1226 sheet: -3.90 (0.18), residues: 478 loop : -3.92 (0.10), residues: 2460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 602 time to evaluate : 4.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 12 residues processed: 638 average time/residue: 0.4335 time to fit residues: 440.3659 Evaluate side-chains 371 residues out of total 3694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 359 time to evaluate : 3.685 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2612 time to fit residues: 10.7218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 352 optimal weight: 9.9990 chunk 316 optimal weight: 1.9990 chunk 175 optimal weight: 40.0000 chunk 107 optimal weight: 3.9990 chunk 213 optimal weight: 0.9990 chunk 168 optimal weight: 9.9990 chunk 326 optimal weight: 0.6980 chunk 126 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 243 optimal weight: 0.1980 chunk 378 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN A 214 GLN B 128 HIS ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 GLN ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 281 ASN G 347 GLN H 317 GLN H 347 GLN H 455 ASN I 72 ASN I 192 HIS I 214 HIS ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 359 ASN I 409 HIS J 72 ASN J 105 HIS J 118 ASN ** J 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 279 ASN ** J 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 598 HIS K 132 GLN P 184 HIS P 231 ASN P 329 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 33144 Z= 0.224 Angle : 0.812 11.260 44903 Z= 0.420 Chirality : 0.050 0.261 5282 Planarity : 0.006 0.096 5753 Dihedral : 8.061 40.943 4557 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.01 % Favored : 87.92 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 2.37 % Twisted General : 0.27 % 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: -4.60 (0.11), residues: 4164 helix: -2.23 (0.12), residues: 1295 sheet: -3.61 (0.19), residues: 453 loop : -3.58 (0.11), residues: 2416 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 3694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 482 time to evaluate : 3.789 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 outliers start: 16 outliers final: 6 residues processed: 490 average time/residue: 0.4148 time to fit residues: 331.9092 Evaluate side-chains 359 residues out of total 3694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 353 time to evaluate : 4.024 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2877 time to fit residues: 8.8903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 210 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 chunk 315 optimal weight: 0.7980 chunk 257 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 379 optimal weight: 0.8980 chunk 409 optimal weight: 6.9990 chunk 337 optimal weight: 1.9990 chunk 376 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 304 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN B 128 HIS ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 255 GLN ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 222 ASN P 173 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 33144 Z= 0.194 Angle : 0.748 10.847 44903 Z= 0.381 Chirality : 0.049 0.250 5282 Planarity : 0.005 0.087 5753 Dihedral : 7.241 41.874 4557 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.67 % Favored : 88.30 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 2.96 % Twisted General : 0.17 % 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: -4.08 (0.12), residues: 4164 helix: -1.55 (0.13), residues: 1305 sheet: -3.42 (0.20), residues: 454 loop : -3.39 (0.11), residues: 2405 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 477 time to evaluate : 3.812 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 outliers start: 6 outliers final: 3 residues processed: 483 average time/residue: 0.4141 time to fit residues: 332.1764 Evaluate side-chains 368 residues out of total 3694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 365 time to evaluate : 3.982 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3006 time to fit residues: 7.2387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 374 optimal weight: 10.0000 chunk 285 optimal weight: 0.9980 chunk 196 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 181 optimal weight: 10.0000 chunk 254 optimal weight: 0.2980 chunk 380 optimal weight: 0.0270 chunk 403 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 360 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 overall best weight: 1.4642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN B 48 ASN B 128 HIS ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 HIS ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN D 188 HIS ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 479 HIS ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 598 HIS K 10 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 33144 Z= 0.214 Angle : 0.747 10.016 44903 Z= 0.379 Chirality : 0.049 0.252 5282 Planarity : 0.005 0.077 5753 Dihedral : 6.913 39.771 4557 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.01 % Favored : 87.99 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 2.37 % Twisted General : 0.12 % 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: -3.80 (0.12), residues: 4164 helix: -1.22 (0.14), residues: 1289 sheet: -3.17 (0.20), residues: 467 loop : -3.29 (0.11), residues: 2408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 460 time to evaluate : 3.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 462 average time/residue: 0.4194 time to fit residues: 322.2260 Evaluate side-chains 356 residues out of total 3694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 353 time to evaluate : 3.945 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3150 time to fit residues: 7.3900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 335 optimal weight: 0.0470 chunk 228 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 300 optimal weight: 0.2980 chunk 166 optimal weight: 0.2980 chunk 343 optimal weight: 10.0000 chunk 278 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 361 optimal weight: 0.0060 chunk 101 optimal weight: 5.9990 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN B 48 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 ASN ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS D 327 ASN ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 411 ASN H 455 ASN H 479 HIS ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 267 GLN J 376 ASN J 398 GLN J 598 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6224 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 33144 Z= 0.170 Angle : 0.712 11.067 44903 Z= 0.358 Chirality : 0.048 0.203 5282 Planarity : 0.005 0.073 5753 Dihedral : 6.428 39.669 4557 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 2.37 % Twisted General : 0.12 % 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: -3.43 (0.12), residues: 4164 helix: -0.92 (0.14), residues: 1304 sheet: -2.91 (0.22), residues: 444 loop : -3.08 (0.12), residues: 2416 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 493 time to evaluate : 3.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 496 average time/residue: 0.4020 time to fit residues: 327.9341 Evaluate side-chains 351 residues out of total 3694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 350 time to evaluate : 3.711 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3725 time to fit residues: 5.7861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 135 optimal weight: 5.9990 chunk 362 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 99 optimal weight: 0.2980 chunk 403 optimal weight: 4.9990 chunk 334 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 133 optimal weight: 0.2980 chunk 211 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN B 48 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 HIS F 190 HIS ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 478 ASN H 479 HIS ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 ASN ** J 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 33144 Z= 0.242 Angle : 0.761 9.725 44903 Z= 0.384 Chirality : 0.049 0.249 5282 Planarity : 0.005 0.069 5753 Dihedral : 6.519 38.091 4557 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.01 % Favored : 87.99 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 2.37 % Twisted General : 0.10 % 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: -3.36 (0.12), residues: 4164 helix: -0.85 (0.14), residues: 1292 sheet: -2.79 (0.21), residues: 484 loop : -3.05 (0.12), residues: 2388 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 451 time to evaluate : 4.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 453 average time/residue: 0.3882 time to fit residues: 295.8598 Evaluate side-chains 350 residues out of total 3694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 349 time to evaluate : 3.675 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3115 time to fit residues: 5.4914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 388 optimal weight: 0.5980 chunk 45 optimal weight: 0.3980 chunk 229 optimal weight: 1.9990 chunk 294 optimal weight: 7.9990 chunk 228 optimal weight: 1.9990 chunk 339 optimal weight: 0.9990 chunk 225 optimal weight: 4.9990 chunk 401 optimal weight: 3.9990 chunk 251 optimal weight: 4.9990 chunk 245 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 243 GLN B 48 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 ASN ** J 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 85 ASN ** P 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 33144 Z= 0.193 Angle : 0.733 10.360 44903 Z= 0.365 Chirality : 0.048 0.311 5282 Planarity : 0.005 0.071 5753 Dihedral : 6.312 38.400 4557 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 2.37 % Twisted General : 0.10 % 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: -3.14 (0.12), residues: 4164 helix: -0.63 (0.14), residues: 1288 sheet: -2.68 (0.22), residues: 453 loop : -2.93 (0.12), residues: 2423 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 464 time to evaluate : 4.073 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 outliers start: 2 outliers final: 1 residues processed: 464 average time/residue: 0.4062 time to fit residues: 316.4748 Evaluate side-chains 347 residues out of total 3694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 346 time to evaluate : 3.876 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3078 time to fit residues: 5.8477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 248 optimal weight: 0.9980 chunk 160 optimal weight: 9.9990 chunk 240 optimal weight: 8.9990 chunk 121 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 255 optimal weight: 2.9990 chunk 273 optimal weight: 0.6980 chunk 198 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 315 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 HIS ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 ASN J 255 GLN J 267 GLN ** P 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 33144 Z= 0.179 Angle : 0.722 11.433 44903 Z= 0.358 Chirality : 0.048 0.253 5282 Planarity : 0.005 0.076 5753 Dihedral : 6.109 37.943 4557 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 1.78 % 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: -2.96 (0.13), residues: 4164 helix: -0.49 (0.15), residues: 1286 sheet: -2.54 (0.22), residues: 465 loop : -2.82 (0.12), residues: 2413 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 467 time to evaluate : 3.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 467 average time/residue: 0.4203 time to fit residues: 331.5999 Evaluate side-chains 348 residues out of total 3694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 3.647 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 365 optimal weight: 0.9980 chunk 385 optimal weight: 10.0000 chunk 351 optimal weight: 20.0000 chunk 374 optimal weight: 8.9990 chunk 384 optimal weight: 7.9990 chunk 225 optimal weight: 1.9990 chunk 163 optimal weight: 9.9990 chunk 294 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 338 optimal weight: 8.9990 chunk 354 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS D 280 ASN ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 286 GLN ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 579 ASN K 132 GLN K 179 ASN ** P 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.132 33144 Z= 0.330 Angle : 0.834 9.957 44903 Z= 0.424 Chirality : 0.052 0.318 5282 Planarity : 0.006 0.076 5753 Dihedral : 6.651 38.789 4557 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.48 % Favored : 85.52 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 2.37 % Twisted General : 0.12 % 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: -3.29 (0.12), residues: 4164 helix: -0.83 (0.14), residues: 1279 sheet: -2.71 (0.21), residues: 482 loop : -2.98 (0.12), residues: 2403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 424 time to evaluate : 4.308 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 outliers start: 2 outliers final: 1 residues processed: 425 average time/residue: 0.4390 time to fit residues: 316.8898 Evaluate side-chains 324 residues out of total 3694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 323 time to evaluate : 3.883 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2758 time to fit residues: 5.8112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 373 optimal weight: 8.9990 chunk 245 optimal weight: 7.9990 chunk 396 optimal weight: 7.9990 chunk 241 optimal weight: 5.9990 chunk 187 optimal weight: 0.0270 chunk 275 optimal weight: 0.9980 chunk 415 optimal weight: 4.9990 chunk 382 optimal weight: 4.9990 chunk 330 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 255 optimal weight: 3.9990 overall best weight: 2.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 479 HIS ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 132 GLN ** K 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 33144 Z= 0.250 Angle : 0.789 11.068 44903 Z= 0.396 Chirality : 0.050 0.279 5282 Planarity : 0.005 0.083 5753 Dihedral : 6.539 39.332 4557 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.44 % Favored : 87.56 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 2.96 % Twisted General : 0.05 % 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: -3.17 (0.12), residues: 4164 helix: -0.71 (0.14), residues: 1273 sheet: -2.61 (0.22), residues: 460 loop : -2.92 (0.12), residues: 2431 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 3.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 410 average time/residue: 0.4094 time to fit residues: 284.4437 Evaluate side-chains 327 residues out of total 3694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 3.787 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 202 optimal weight: 0.9990 chunk 262 optimal weight: 4.9990 chunk 352 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 305 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 331 optimal weight: 2.9990 chunk 138 optimal weight: 30.0000 chunk 340 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN B 48 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN C 206 ASN ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS D 150 ASN D 154 GLN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.135307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.120341 restraints weight = 91182.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.121154 restraints weight = 70081.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.121681 restraints weight = 55124.796| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 33144 Z= 0.246 Angle : 0.786 12.502 44903 Z= 0.393 Chirality : 0.050 0.276 5282 Planarity : 0.005 0.081 5753 Dihedral : 6.476 39.320 4557 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.26 % Favored : 86.74 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 2.96 % 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: -3.12 (0.13), residues: 4164 helix: -0.69 (0.14), residues: 1276 sheet: -2.53 (0.22), residues: 470 loop : -2.89 (0.12), residues: 2418 =============================================================================== Job complete usr+sys time: 6231.00 seconds wall clock time: 115 minutes 8.77 seconds (6908.77 seconds total)