Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 02:40:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgx_10187/04_2023/6sgx_10187.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgx_10187/04_2023/6sgx_10187.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgx_10187/04_2023/6sgx_10187.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgx_10187/04_2023/6sgx_10187.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgx_10187/04_2023/6sgx_10187.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgx_10187/04_2023/6sgx_10187.pdb" } resolution = 3.7 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 7202 2.51 5 N 2016 2.21 5 O 1981 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 16": "NH1" <-> "NH2" Residue "A ARG 30": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B GLU 26": "OE1" <-> "OE2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ASP 114": "OD1" <-> "OD2" Residue "B GLU 121": "OE1" <-> "OE2" Residue "B ARG 239": "NH1" <-> "NH2" Residue "B ARG 406": "NH1" <-> "NH2" Residue "C ARG 36": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 269": "OD1" <-> "OD2" Residue "C ARG 312": "NH1" <-> "NH2" Residue "C ARG 406": "NH1" <-> "NH2" Residue "C ASP 455": "OD1" <-> "OD2" Residue "F ARG 10": "NH1" <-> "NH2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F ASP 154": "OD1" <-> "OD2" Residue "F ARG 159": "NH1" <-> "NH2" Residue "F ARG 162": "NH1" <-> "NH2" Residue "F ASP 175": "OD1" <-> "OD2" Residue "F ASP 195": "OD1" <-> "OD2" Residue "F ASP 202": "OD1" <-> "OD2" Residue "F ARG 280": "NH1" <-> "NH2" Residue "F ASP 327": "OD1" <-> "OD2" Residue "F ARG 369": "NH1" <-> "NH2" Residue "F ASP 380": "OD1" <-> "OD2" Residue "F ASP 383": "OD1" <-> "OD2" Residue "G ARG 4": "NH1" <-> "NH2" Residue "G ARG 61": "NH1" <-> "NH2" Residue "G ARG 64": "NH1" <-> "NH2" Residue "G ARG 112": "NH1" <-> "NH2" Residue "G ARG 118": "NH1" <-> "NH2" Residue "G ASP 130": "OD1" <-> "OD2" Residue "G ARG 160": "NH1" <-> "NH2" Residue "G ASP 173": "OD1" <-> "OD2" Residue "G GLU 225": "OE1" <-> "OE2" Residue "G ARG 242": "NH1" <-> "NH2" Residue "G ARG 264": "NH1" <-> "NH2" Residue "G GLU 276": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 11227 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 548 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain breaks: 1 Chain: "B" Number of atoms: 3042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3042 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 22, 'TRANS': 403} Chain breaks: 3 Chain: "C" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3135 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 27, 'TRANS': 410} Chain breaks: 4 Chain: "F" Number of atoms: 2673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2673 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 29, 'TRANS': 307} Chain breaks: 4 Chain: "G" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1829 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 15, 'TRANS': 225} Chain breaks: 7 Time building chain proxies: 6.14, per 1000 atoms: 0.55 Number of scatterers: 11227 At special positions: 0 Unit cell: (130.811, 105.287, 141.446, 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 28 16.00 O 1981 8.00 N 2016 7.00 C 7202 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: 4.63 Conformation dependent library (CDL) restraints added in 1.7 seconds 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2816 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 7 sheets defined 54.8% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.649A pdb=" N VAL A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 87 removed outlier: 3.704A pdb=" N THR A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 46 Processing helix chain 'B' and resid 111 through 119 Processing helix chain 'B' and resid 127 through 156 removed outlier: 3.730A pdb=" N HIS B 131 " --> pdb=" O TRP B 127 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ALA B 133 " --> pdb=" O PRO B 129 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 180 removed outlier: 3.561A pdb=" N PHE B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.732A pdb=" N ALA B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 234 removed outlier: 4.260A pdb=" N LEU B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 263 removed outlier: 3.933A pdb=" N ALA B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 285 removed outlier: 4.350A pdb=" N CYS B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.511A pdb=" N LEU B 289 " --> pdb=" O GLN B 285 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA B 294 " --> pdb=" O SER B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 351 removed outlier: 3.680A pdb=" N ARG B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG B 325 " --> pdb=" O PRO B 321 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 373 removed outlier: 3.923A pdb=" N VAL B 364 " --> pdb=" O TRP B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 377 removed outlier: 3.640A pdb=" N TRP B 377 " --> pdb=" O ALA B 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 374 through 377' Processing helix chain 'B' and resid 379 through 404 removed outlier: 3.785A pdb=" N LYS B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N SER B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 430 removed outlier: 3.893A pdb=" N ASN B 430 " --> pdb=" O VAL B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 466 removed outlier: 4.280A pdb=" N LEU B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ILE B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) Proline residue: B 460 - end of helix removed outlier: 3.574A pdb=" N ALA B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 47 removed outlier: 3.778A pdb=" N ILE C 38 " --> pdb=" O PRO C 34 " (cutoff:3.500A) Proline residue: C 40 - end of helix Processing helix chain 'C' and resid 82 through 87 removed outlier: 3.520A pdb=" N VAL C 86 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 82 through 87' Processing helix chain 'C' and resid 115 through 124 removed outlier: 3.556A pdb=" N PHE C 119 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 157 removed outlier: 3.778A pdb=" N ALA C 133 " --> pdb=" O PRO C 129 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG C 134 " --> pdb=" O THR C 130 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG C 155 " --> pdb=" O SER C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 181 removed outlier: 3.638A pdb=" N PHE C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE C 166 " --> pdb=" O LEU C 162 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 196 through 204 removed outlier: 3.511A pdb=" N ALA C 201 " --> pdb=" O LEU C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 231 Processing helix chain 'C' and resid 241 through 263 removed outlier: 3.692A pdb=" N THR C 245 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 285 removed outlier: 3.638A pdb=" N ILE C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS C 273 " --> pdb=" O ASP C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 294 Processing helix chain 'C' and resid 313 through 318 Processing helix chain 'C' and resid 319 through 345 removed outlier: 3.783A pdb=" N ARG C 325 " --> pdb=" O PRO C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 removed outlier: 4.308A pdb=" N VAL C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 373 removed outlier: 4.136A pdb=" N VAL C 364 " --> pdb=" O TRP C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 376 No H-bonds generated for 'chain 'C' and resid 374 through 376' Processing helix chain 'C' and resid 379 through 404 removed outlier: 3.683A pdb=" N HIS C 389 " --> pdb=" O TRP C 385 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N SER C 390 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 430 removed outlier: 3.748A pdb=" N TRP C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C 427 " --> pdb=" O VAL C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 467 removed outlier: 4.252A pdb=" N ASP C 455 " --> pdb=" O ALA C 451 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ILE C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) Proline residue: C 460 - end of helix removed outlier: 3.600A pdb=" N VAL C 466 " --> pdb=" O MET C 462 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY C 467 " --> pdb=" O ALA C 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 43 Processing helix chain 'F' and resid 93 through 130 removed outlier: 3.879A pdb=" N VAL F 97 " --> pdb=" O ARG F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 138 removed outlier: 3.630A pdb=" N ALA F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 197 removed outlier: 3.973A pdb=" N LEU F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP F 195 " --> pdb=" O ARG F 191 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL F 196 " --> pdb=" O GLY F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 212 No H-bonds generated for 'chain 'F' and resid 210 through 212' Processing helix chain 'F' and resid 224 through 239 removed outlier: 3.658A pdb=" N TRP F 238 " --> pdb=" O GLN F 234 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 263 removed outlier: 3.569A pdb=" N LEU F 261 " --> pdb=" O TRP F 258 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TRP F 263 " --> pdb=" O TRP F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 293 Processing helix chain 'F' and resid 386 through 396 removed outlier: 3.560A pdb=" N ALA F 390 " --> pdb=" O SER F 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 17 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 49 through 64 Processing helix chain 'G' and resid 86 through 88 No H-bonds generated for 'chain 'G' and resid 86 through 88' Processing helix chain 'G' and resid 89 through 95 removed outlier: 3.523A pdb=" N VAL G 93 " --> pdb=" O GLN G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 131 through 136 Processing helix chain 'G' and resid 143 through 162 removed outlier: 3.587A pdb=" N VAL G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 212 Processing helix chain 'G' and resid 265 through 269 Processing sheet with id=AA1, first strand: chain 'B' and resid 67 through 71 removed outlier: 8.375A pdb=" N LEU B 94 " --> pdb=" O ARG B 11 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ALA B 13 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LEU B 96 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU B 15 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N ALA B 98 " --> pdb=" O LEU B 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.542A pdb=" N LEU C 94 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ALA C 13 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU C 96 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU C 15 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ALA C 98 " --> pdb=" O LEU C 15 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 23 through 24 Processing sheet with id=AA4, first strand: chain 'F' and resid 202 through 208 removed outlier: 4.787A pdb=" N ALA F 203 " --> pdb=" O ARG F 162 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG F 162 " --> pdb=" O ALA F 203 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR F 205 " --> pdb=" O ALA F 160 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL F 381 " --> pdb=" O ARG F 162 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 339 through 343 removed outlier: 5.908A pdb=" N ILE F 215 " --> pdb=" O HIS F 341 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR F 343 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL F 217 " --> pdb=" O THR F 343 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N LEU F 360 " --> pdb=" O ARG F 214 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N THR F 216 " --> pdb=" O LEU F 360 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL F 362 " --> pdb=" O THR F 216 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE F 218 " --> pdb=" O VAL F 362 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 282 through 283 removed outlier: 8.504A pdb=" N THR F 283 " --> pdb=" O VAL F 246 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU F 248 " --> pdb=" O THR F 283 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY F 245 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL F 317 " --> pdb=" O GLY F 245 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ALA F 247 " --> pdb=" O VAL F 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 166 through 169 removed outlier: 4.762A pdb=" N VAL G 79 " --> pdb=" O VAL G 169 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER G 120 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS G 106 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL G 237 " --> pdb=" O VAL G 199 " (cutoff:3.500A) 600 hydrogen bonds defined for protein. 1776 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: 3.21 Time building geometry restraints manager: 4.98 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: 3712 1.34 - 1.46: 2306 1.46 - 1.58: 5369 1.58 - 1.70: 1 1.70 - 1.82: 48 Bond restraints: 11436 Sorted by residual: bond pdb=" C ILE F 139 " pdb=" N PRO F 140 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.33e+00 bond pdb=" C GLN G 19 " pdb=" N PRO G 20 " ideal model delta sigma weight residual 1.334 1.382 -0.049 2.34e-02 1.83e+03 4.31e+00 bond pdb=" C SER B 435 " pdb=" N PRO B 436 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.64e+00 bond pdb=" CA LEU B 441 " pdb=" C LEU B 441 " ideal model delta sigma weight residual 1.525 1.558 -0.033 2.10e-02 2.27e+03 2.49e+00 bond pdb=" CB PRO C 199 " pdb=" CG PRO C 199 " ideal model delta sigma weight residual 1.492 1.415 0.077 5.00e-02 4.00e+02 2.39e+00 ... (remaining 11431 not shown) Histogram of bond angle deviations from ideal: 99.79 - 106.92: 479 106.92 - 114.05: 6818 114.05 - 121.18: 5352 121.18 - 128.32: 2867 128.32 - 135.45: 139 Bond angle restraints: 15655 Sorted by residual: angle pdb=" N VAL G 172 " pdb=" CA VAL G 172 " pdb=" C VAL G 172 " ideal model delta sigma weight residual 110.23 116.85 -6.62 1.04e+00 9.25e-01 4.06e+01 angle pdb=" N VAL G 129 " pdb=" CA VAL G 129 " pdb=" C VAL G 129 " ideal model delta sigma weight residual 112.96 108.12 4.84 1.00e+00 1.00e+00 2.35e+01 angle pdb=" C ASP C 319 " pdb=" N LEU C 320 " pdb=" CA LEU C 320 " ideal model delta sigma weight residual 120.09 125.76 -5.67 1.25e+00 6.40e-01 2.06e+01 angle pdb=" C ASP B 211 " pdb=" N PHE B 212 " pdb=" CA PHE B 212 " ideal model delta sigma weight residual 121.54 129.92 -8.38 1.91e+00 2.74e-01 1.93e+01 angle pdb=" C GLN G 22 " pdb=" N THR G 23 " pdb=" CA THR G 23 " ideal model delta sigma weight residual 122.08 128.41 -6.33 1.47e+00 4.63e-01 1.85e+01 ... (remaining 15650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 6158 17.57 - 35.14: 592 35.14 - 52.71: 86 52.71 - 70.27: 7 70.27 - 87.84: 7 Dihedral angle restraints: 6850 sinusoidal: 2533 harmonic: 4317 Sorted by residual: dihedral pdb=" CA VAL C 282 " pdb=" C VAL C 282 " pdb=" N THR C 283 " pdb=" CA THR C 283 " ideal model delta harmonic sigma weight residual 180.00 146.28 33.72 0 5.00e+00 4.00e-02 4.55e+01 dihedral pdb=" CA GLY G 171 " pdb=" C GLY G 171 " pdb=" N VAL G 172 " pdb=" CA VAL G 172 " ideal model delta harmonic sigma weight residual -180.00 -147.28 -32.72 0 5.00e+00 4.00e-02 4.28e+01 dihedral pdb=" CA VAL B 99 " pdb=" C VAL B 99 " pdb=" N PRO B 100 " pdb=" CA PRO B 100 " ideal model delta harmonic sigma weight residual -180.00 -148.01 -31.99 0 5.00e+00 4.00e-02 4.09e+01 ... (remaining 6847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1600 0.069 - 0.137: 282 0.137 - 0.206: 53 0.206 - 0.274: 11 0.274 - 0.343: 5 Chirality restraints: 1951 Sorted by residual: chirality pdb=" CB VAL C 282 " pdb=" CA VAL C 282 " pdb=" CG1 VAL C 282 " pdb=" CG2 VAL C 282 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CG LEU C 143 " pdb=" CB LEU C 143 " pdb=" CD1 LEU C 143 " pdb=" CD2 LEU C 143 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB ILE B 108 " pdb=" CA ILE B 108 " pdb=" CG1 ILE B 108 " pdb=" CG2 ILE B 108 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 1948 not shown) Planarity restraints: 1974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU G 90 " 0.046 5.00e-02 4.00e+02 6.88e-02 7.57e+00 pdb=" N PRO G 91 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO G 91 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 91 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 459 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PRO C 460 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 460 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 460 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 39 " -0.043 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO B 40 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 40 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 40 " -0.037 5.00e-02 4.00e+02 ... (remaining 1971 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2930 2.80 - 3.33: 10147 3.33 - 3.85: 17898 3.85 - 4.38: 19373 4.38 - 4.90: 34555 Nonbonded interactions: 84903 Sorted by model distance: nonbonded pdb=" OG SER C 228 " pdb=" O PHE C 244 " model vdw 2.280 2.440 nonbonded pdb=" O GLY B 279 " pdb=" OG1 THR B 283 " model vdw 2.281 2.440 nonbonded pdb=" O SER B 231 " pdb=" OG SER B 235 " model vdw 2.292 2.440 nonbonded pdb=" OG1 THR C 82 " pdb=" OG1 THR C 85 " model vdw 2.342 2.440 nonbonded pdb=" O ILE F 139 " pdb=" OG1 THR F 142 " model vdw 2.348 2.440 ... (remaining 84898 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 'B' and (resid 8 through 16 or resid 21 through 47 or resid 65 through 21 \ 1 or resid 214 through 436 or resid 441 through 471)) selection = (chain 'C' and (resid 8 through 294 or resid 316 through 471)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.91 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: 4.730 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: 0.010 Extract box with map and model: 16.920 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 31.430 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 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 : 0.006 0.077 11436 Z= 0.397 Angle : 1.028 10.492 15655 Z= 0.545 Chirality : 0.059 0.343 1951 Planarity : 0.008 0.069 1974 Dihedral : 13.905 87.842 4034 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.90 % Favored : 90.03 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.09 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.82 (0.16), residues: 1464 helix: -2.87 (0.12), residues: 806 sheet: -2.38 (0.36), residues: 143 loop : -3.72 (0.22), residues: 515 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 247 time to evaluate : 1.706 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 249 average time/residue: 0.2677 time to fit residues: 92.5750 Evaluate side-chains 180 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.401 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 4.9990 chunk 112 optimal weight: 0.2980 chunk 62 optimal weight: 0.0070 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 0.0770 chunk 60 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS B 285 GLN C 131 HIS C 328 GLN C 389 HIS F 122 GLN F 163 HIS F 266 HIS G 74 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.102 11436 Z= 0.188 Angle : 0.630 9.242 15655 Z= 0.315 Chirality : 0.041 0.181 1951 Planarity : 0.006 0.062 1974 Dihedral : 5.309 36.880 1620 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.20), residues: 1464 helix: -0.76 (0.17), residues: 802 sheet: -1.75 (0.39), residues: 151 loop : -3.34 (0.24), residues: 511 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 196 time to evaluate : 1.323 Fit side-chains outliers start: 33 outliers final: 19 residues processed: 214 average time/residue: 0.2223 time to fit residues: 69.2238 Evaluate side-chains 194 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 175 time to evaluate : 1.259 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1033 time to fit residues: 5.5255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 135 optimal weight: 0.0570 chunk 146 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 46 optimal weight: 0.0010 chunk 108 optimal weight: 1.9990 overall best weight: 0.9908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 11436 Z= 0.271 Angle : 0.667 9.240 15655 Z= 0.330 Chirality : 0.043 0.205 1951 Planarity : 0.006 0.063 1974 Dihedral : 5.250 38.857 1620 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.22), residues: 1464 helix: -0.06 (0.19), residues: 805 sheet: -1.62 (0.41), residues: 146 loop : -3.05 (0.26), residues: 513 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 185 time to evaluate : 1.279 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 204 average time/residue: 0.2329 time to fit residues: 68.0780 Evaluate side-chains 187 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 171 time to evaluate : 1.333 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1022 time to fit residues: 4.8905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 133 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 91 optimal weight: 0.4980 chunk 136 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 128 optimal weight: 0.0050 chunk 38 optimal weight: 0.8980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 11436 Z= 0.186 Angle : 0.614 8.921 15655 Z= 0.301 Chirality : 0.041 0.208 1951 Planarity : 0.005 0.060 1974 Dihedral : 4.928 37.425 1620 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer Outliers : 2.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.23), residues: 1464 helix: 0.41 (0.19), residues: 805 sheet: -1.33 (0.43), residues: 141 loop : -2.92 (0.26), residues: 518 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 185 time to evaluate : 1.318 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 16 residues processed: 202 average time/residue: 0.2225 time to fit residues: 65.4568 Evaluate side-chains 192 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 176 time to evaluate : 1.294 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1081 time to fit residues: 5.0255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 0.9990 chunk 81 optimal weight: 0.0030 chunk 2 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 0.0980 chunk 122 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN B 131 HIS B 430 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 11436 Z= 0.279 Angle : 0.670 8.383 15655 Z= 0.330 Chirality : 0.044 0.210 1951 Planarity : 0.005 0.060 1974 Dihedral : 5.069 38.619 1620 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.22), residues: 1464 helix: 0.50 (0.19), residues: 805 sheet: -1.27 (0.43), residues: 146 loop : -2.86 (0.26), residues: 513 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 179 time to evaluate : 1.328 Fit side-chains outliers start: 33 outliers final: 24 residues processed: 200 average time/residue: 0.2262 time to fit residues: 65.9081 Evaluate side-chains 202 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 178 time to evaluate : 1.290 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1070 time to fit residues: 6.5297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 119 optimal weight: 0.2980 chunk 66 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 11436 Z= 0.213 Angle : 0.635 9.081 15655 Z= 0.312 Chirality : 0.042 0.203 1951 Planarity : 0.005 0.057 1974 Dihedral : 4.888 37.564 1620 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.23), residues: 1464 helix: 0.73 (0.19), residues: 803 sheet: -1.13 (0.43), residues: 146 loop : -2.76 (0.26), residues: 515 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 188 time to evaluate : 1.344 Fit side-chains outliers start: 24 outliers final: 19 residues processed: 201 average time/residue: 0.2179 time to fit residues: 63.9398 Evaluate side-chains 191 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 172 time to evaluate : 1.210 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1062 time to fit residues: 5.3793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 138 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 143 optimal weight: 0.0770 chunk 89 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 11436 Z= 0.224 Angle : 0.648 8.780 15655 Z= 0.317 Chirality : 0.043 0.245 1951 Planarity : 0.005 0.057 1974 Dihedral : 4.884 38.736 1620 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.23), residues: 1464 helix: 0.81 (0.19), residues: 805 sheet: -1.07 (0.43), residues: 146 loop : -2.70 (0.27), residues: 513 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 179 time to evaluate : 1.202 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 190 average time/residue: 0.2210 time to fit residues: 61.6032 Evaluate side-chains 177 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 171 time to evaluate : 1.216 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0980 time to fit residues: 2.7474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 88 optimal weight: 0.6980 chunk 57 optimal weight: 0.0970 chunk 85 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 11436 Z= 0.214 Angle : 0.642 8.818 15655 Z= 0.315 Chirality : 0.043 0.222 1951 Planarity : 0.005 0.055 1974 Dihedral : 4.818 38.121 1620 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.23), residues: 1464 helix: 0.93 (0.19), residues: 803 sheet: -1.12 (0.43), residues: 151 loop : -2.63 (0.27), residues: 510 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 174 time to evaluate : 1.250 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 184 average time/residue: 0.2182 time to fit residues: 59.2790 Evaluate side-chains 179 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 171 time to evaluate : 1.252 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1009 time to fit residues: 3.2486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 130 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 133 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 126 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 11436 Z= 0.212 Angle : 0.645 8.789 15655 Z= 0.317 Chirality : 0.043 0.211 1951 Planarity : 0.005 0.055 1974 Dihedral : 4.772 38.430 1620 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.23), residues: 1464 helix: 1.00 (0.19), residues: 808 sheet: -1.10 (0.43), residues: 151 loop : -2.68 (0.27), residues: 505 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 181 time to evaluate : 1.388 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 187 average time/residue: 0.2161 time to fit residues: 59.5454 Evaluate side-chains 176 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 170 time to evaluate : 1.280 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1020 time to fit residues: 2.8914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 141 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 12 optimal weight: 0.0040 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 93 optimal weight: 0.0470 overall best weight: 0.4490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 11436 Z= 0.187 Angle : 0.631 9.015 15655 Z= 0.309 Chirality : 0.042 0.213 1951 Planarity : 0.005 0.054 1974 Dihedral : 4.630 37.539 1620 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.23), residues: 1464 helix: 1.20 (0.19), residues: 806 sheet: -1.07 (0.42), residues: 154 loop : -2.61 (0.27), residues: 504 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 182 time to evaluate : 1.237 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 185 average time/residue: 0.2307 time to fit residues: 62.4545 Evaluate side-chains 176 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 174 time to evaluate : 1.323 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1076 time to fit residues: 2.1944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 121 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.132918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.117485 restraints weight = 16763.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.119115 restraints weight = 12916.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.120300 restraints weight = 10665.521| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 11436 Z= 0.275 Angle : 0.682 8.455 15655 Z= 0.334 Chirality : 0.045 0.205 1951 Planarity : 0.005 0.055 1974 Dihedral : 4.825 39.516 1620 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.23), residues: 1464 helix: 1.12 (0.19), residues: 807 sheet: -1.00 (0.43), residues: 154 loop : -2.65 (0.27), residues: 503 =============================================================================== Job complete usr+sys time: 2309.55 seconds wall clock time: 42 minutes 34.31 seconds (2554.31 seconds total)