Starting phenix.real_space_refine on Fri Mar 15 09:28:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgx_10187/03_2024/6sgx_10187.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgx_10187/03_2024/6sgx_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_10187/03_2024/6sgx_10187.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgx_10187/03_2024/6sgx_10187.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgx_10187/03_2024/6sgx_10187.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgx_10187/03_2024/6sgx_10187.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.25, per 1000 atoms: 0.56 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: 3.93 Conformation dependent library (CDL) restraints added in 2.0 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: 1.12 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: 3.20 Time building geometry restraints manager: 4.33 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: 3.670 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: 15.590 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 31.650 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.790 ------------------------------------------------------------------------------- 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 % Allowed : 11.63 % Favored : 88.11 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 231 HIS 0.007 0.001 HIS F 118 PHE 0.023 0.002 PHE G 48 TYR 0.013 0.002 TYR F 104 ARG 0.003 0.000 ARG G 108 *********************** 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 : 1.206 Fit side-chains REVERT: A 59 MET cc_start: 0.8103 (mmm) cc_final: 0.7901 (tpp) REVERT: B 97 GLN cc_start: 0.7997 (mt0) cc_final: 0.7761 (mt0) REVERT: B 118 ILE cc_start: 0.9143 (mm) cc_final: 0.8831 (mt) REVERT: B 443 MET cc_start: 0.6726 (mtt) cc_final: 0.6235 (mtm) REVERT: C 184 ARG cc_start: 0.6290 (ttp80) cc_final: 0.5518 (mmm-85) REVERT: C 278 LEU cc_start: 0.9038 (mt) cc_final: 0.8835 (mt) REVERT: C 443 MET cc_start: 0.6863 (mmm) cc_final: 0.6440 (mmm) REVERT: C 471 LEU cc_start: 0.7870 (mt) cc_final: 0.7572 (mt) REVERT: F 151 ARG cc_start: 0.8170 (mtm110) cc_final: 0.7905 (mtm110) REVERT: F 337 VAL cc_start: 0.9078 (t) cc_final: 0.8874 (t) REVERT: G 26 GLN cc_start: 0.6384 (mm-40) cc_final: 0.6144 (mp10) outliers start: 3 outliers final: 0 residues processed: 249 average time/residue: 0.2463 time to fit residues: 84.4975 Evaluate side-chains 187 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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: 2.9990 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 97 GLN 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 11436 Z= 0.189 Angle : 0.636 9.299 15655 Z= 0.319 Chirality : 0.041 0.186 1951 Planarity : 0.006 0.060 1974 Dihedral : 5.378 36.533 1620 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 2.60 % Allowed : 16.75 % Favored : 80.64 % 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: -2.72 (0.20), residues: 1464 helix: -0.86 (0.17), residues: 814 sheet: -1.78 (0.38), residues: 151 loop : -3.32 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 231 HIS 0.007 0.001 HIS B 330 PHE 0.019 0.001 PHE A 88 TYR 0.012 0.001 TYR B 361 ARG 0.007 0.000 ARG B 66 *********************** 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 226 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 196 time to evaluate : 0.981 Fit side-chains REVERT: B 97 GLN cc_start: 0.8048 (mt0) cc_final: 0.7790 (mt0) REVERT: B 118 ILE cc_start: 0.9164 (mm) cc_final: 0.8858 (mt) REVERT: B 443 MET cc_start: 0.6678 (mtt) cc_final: 0.6383 (mtm) REVERT: C 184 ARG cc_start: 0.6330 (ttp80) cc_final: 0.5510 (mmm-85) REVERT: C 278 LEU cc_start: 0.9019 (mt) cc_final: 0.8795 (mt) REVERT: C 443 MET cc_start: 0.6896 (mmm) cc_final: 0.6441 (mmm) REVERT: C 471 LEU cc_start: 0.7931 (mt) cc_final: 0.7687 (mt) REVERT: G 4 ARG cc_start: 0.6499 (mmt180) cc_final: 0.4896 (mmt180) REVERT: G 26 GLN cc_start: 0.6242 (mm-40) cc_final: 0.5893 (mp10) outliers start: 30 outliers final: 20 residues processed: 211 average time/residue: 0.2197 time to fit residues: 66.6155 Evaluate side-chains 197 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 177 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 199 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 146 optimal weight: 0.1980 chunk 120 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11436 Z= 0.227 Angle : 0.636 9.096 15655 Z= 0.314 Chirality : 0.042 0.194 1951 Planarity : 0.005 0.061 1974 Dihedral : 5.090 37.924 1620 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 3.30 % Allowed : 19.01 % Favored : 77.69 % 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: -1.81 (0.22), residues: 1464 helix: 0.02 (0.19), residues: 808 sheet: -1.59 (0.41), residues: 146 loop : -3.06 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 231 HIS 0.005 0.001 HIS F 163 PHE 0.008 0.001 PHE G 226 TYR 0.013 0.001 TYR F 104 ARG 0.006 0.000 ARG C 325 *********************** 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 233 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 195 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: B 97 GLN cc_start: 0.8171 (mt0) cc_final: 0.7908 (mt0) REVERT: B 118 ILE cc_start: 0.9160 (mm) cc_final: 0.8904 (mt) REVERT: B 443 MET cc_start: 0.6588 (mtt) cc_final: 0.6383 (mtm) REVERT: C 72 ILE cc_start: 0.8460 (mm) cc_final: 0.8121 (mm) REVERT: C 121 GLU cc_start: 0.7832 (tp30) cc_final: 0.7597 (tt0) REVERT: C 184 ARG cc_start: 0.6424 (ttp80) cc_final: 0.5579 (mmm-85) REVERT: C 278 LEU cc_start: 0.9100 (mt) cc_final: 0.8815 (mt) REVERT: C 443 MET cc_start: 0.6956 (mmm) cc_final: 0.6438 (mmm) REVERT: G 4 ARG cc_start: 0.6718 (mmt180) cc_final: 0.5143 (mmt180) REVERT: G 26 GLN cc_start: 0.6252 (mm-40) cc_final: 0.5888 (mp10) REVERT: G 47 MET cc_start: 0.6645 (ttp) cc_final: 0.6426 (ttp) REVERT: G 123 SER cc_start: 0.9041 (m) cc_final: 0.8631 (t) outliers start: 38 outliers final: 30 residues processed: 217 average time/residue: 0.2135 time to fit residues: 66.2528 Evaluate side-chains 214 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 184 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 271 ASN Chi-restraints excluded: chain G residue 281 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 133 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 91 optimal weight: 0.4980 chunk 136 optimal weight: 0.0770 chunk 144 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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: 0.7875 moved from start: 0.1943 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= 0.185 Angle : 0.605 9.059 15655 Z= 0.298 Chirality : 0.041 0.205 1951 Planarity : 0.005 0.059 1974 Dihedral : 4.834 37.422 1620 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 4.08 % Allowed : 19.18 % Favored : 76.74 % 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: -1.35 (0.22), residues: 1464 helix: 0.46 (0.19), residues: 805 sheet: -1.41 (0.42), residues: 146 loop : -2.98 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 231 HIS 0.004 0.001 HIS B 389 PHE 0.006 0.001 PHE G 226 TYR 0.010 0.001 TYR F 104 ARG 0.004 0.000 ARG C 325 *********************** 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 243 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 196 time to evaluate : 1.248 Fit side-chains revert: symmetry clash REVERT: B 97 GLN cc_start: 0.8230 (mt0) cc_final: 0.7964 (mt0) REVERT: B 118 ILE cc_start: 0.9079 (mm) cc_final: 0.8794 (mt) REVERT: B 443 MET cc_start: 0.6720 (mtt) cc_final: 0.6513 (mtm) REVERT: C 72 ILE cc_start: 0.8387 (mm) cc_final: 0.8031 (mm) REVERT: C 184 ARG cc_start: 0.6406 (ttp80) cc_final: 0.5609 (mmm-85) REVERT: C 278 LEU cc_start: 0.9064 (mt) cc_final: 0.8805 (mt) REVERT: C 443 MET cc_start: 0.6913 (mmm) cc_final: 0.6378 (mmm) REVERT: G 4 ARG cc_start: 0.6742 (mmt180) cc_final: 0.5242 (mmt180) REVERT: G 26 GLN cc_start: 0.6414 (mm-40) cc_final: 0.5780 (mp10) REVERT: G 40 LEU cc_start: 0.8509 (mm) cc_final: 0.8157 (mm) REVERT: G 123 SER cc_start: 0.9004 (m) cc_final: 0.8597 (t) outliers start: 47 outliers final: 34 residues processed: 226 average time/residue: 0.2161 time to fit residues: 70.4716 Evaluate side-chains 215 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 181 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 271 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 0.0060 chunk 81 optimal weight: 0.0670 chunk 2 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 129 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.6936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 430 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11436 Z= 0.216 Angle : 0.623 8.683 15655 Z= 0.306 Chirality : 0.042 0.217 1951 Planarity : 0.005 0.057 1974 Dihedral : 4.802 38.007 1620 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 4.77 % Allowed : 19.79 % Favored : 75.43 % 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: -1.06 (0.23), residues: 1464 helix: 0.69 (0.19), residues: 800 sheet: -1.16 (0.43), residues: 143 loop : -2.86 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 231 HIS 0.004 0.001 HIS F 163 PHE 0.009 0.001 PHE A 88 TYR 0.012 0.001 TYR F 104 ARG 0.005 0.000 ARG C 325 *********************** 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 245 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 190 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: B 118 ILE cc_start: 0.8991 (mm) cc_final: 0.8784 (mt) REVERT: B 156 VAL cc_start: 0.7963 (m) cc_final: 0.7726 (t) REVERT: B 443 MET cc_start: 0.6707 (mtt) cc_final: 0.6486 (mtm) REVERT: B 446 MET cc_start: 0.5888 (tmm) cc_final: 0.5277 (tmm) REVERT: C 27 MET cc_start: 0.8305 (ptp) cc_final: 0.8101 (mtp) REVERT: C 72 ILE cc_start: 0.8374 (mm) cc_final: 0.8007 (mm) REVERT: C 184 ARG cc_start: 0.6387 (ttp80) cc_final: 0.5654 (mmm-85) REVERT: C 278 LEU cc_start: 0.9075 (mt) cc_final: 0.8805 (mt) REVERT: C 443 MET cc_start: 0.6946 (mmm) cc_final: 0.6400 (mmm) REVERT: G 4 ARG cc_start: 0.6699 (mmt180) cc_final: 0.5397 (mmt180) REVERT: G 26 GLN cc_start: 0.6449 (mm-40) cc_final: 0.5690 (mp10) REVERT: G 40 LEU cc_start: 0.8531 (mm) cc_final: 0.8306 (mm) REVERT: G 123 SER cc_start: 0.9025 (m) cc_final: 0.8625 (t) outliers start: 55 outliers final: 46 residues processed: 226 average time/residue: 0.2372 time to fit residues: 79.2920 Evaluate side-chains 224 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 178 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 281 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 119 optimal weight: 0.0970 chunk 66 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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: 0.7889 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11436 Z= 0.201 Angle : 0.615 9.035 15655 Z= 0.302 Chirality : 0.042 0.231 1951 Planarity : 0.005 0.057 1974 Dihedral : 4.745 37.645 1620 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 4.77 % Allowed : 20.66 % Favored : 74.57 % 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: -0.92 (0.23), residues: 1464 helix: 0.77 (0.19), residues: 807 sheet: -1.04 (0.43), residues: 143 loop : -2.79 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 231 HIS 0.004 0.001 HIS B 330 PHE 0.007 0.001 PHE G 226 TYR 0.011 0.001 TYR F 104 ARG 0.008 0.000 ARG F 116 *********************** 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 238 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 183 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: B 97 GLN cc_start: 0.7932 (mt0) cc_final: 0.7615 (mt0) REVERT: B 118 ILE cc_start: 0.8935 (mm) cc_final: 0.8734 (mt) REVERT: B 156 VAL cc_start: 0.7962 (m) cc_final: 0.7724 (t) REVERT: B 443 MET cc_start: 0.6682 (mtt) cc_final: 0.6472 (mtm) REVERT: B 446 MET cc_start: 0.5883 (tmm) cc_final: 0.5275 (tmm) REVERT: C 72 ILE cc_start: 0.8328 (mm) cc_final: 0.7952 (mm) REVERT: C 184 ARG cc_start: 0.6379 (ttp80) cc_final: 0.5644 (mmm-85) REVERT: C 278 LEU cc_start: 0.9074 (mt) cc_final: 0.8817 (mt) REVERT: C 443 MET cc_start: 0.6927 (mmm) cc_final: 0.6423 (mmm) REVERT: F 92 MET cc_start: 0.7812 (tpp) cc_final: 0.7559 (ttt) REVERT: G 4 ARG cc_start: 0.6713 (mmt180) cc_final: 0.5386 (mmt180) REVERT: G 40 LEU cc_start: 0.8499 (mm) cc_final: 0.8284 (mm) REVERT: G 123 SER cc_start: 0.9018 (m) cc_final: 0.8613 (t) outliers start: 55 outliers final: 48 residues processed: 217 average time/residue: 0.2002 time to fit residues: 63.9323 Evaluate side-chains 227 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 179 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 281 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 138 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 105 optimal weight: 0.0020 chunk 81 optimal weight: 0.5980 chunk 121 optimal weight: 0.3980 chunk 80 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 430 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11436 Z= 0.178 Angle : 0.601 8.947 15655 Z= 0.294 Chirality : 0.042 0.245 1951 Planarity : 0.005 0.054 1974 Dihedral : 4.642 37.789 1620 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 5.03 % Allowed : 20.92 % Favored : 74.05 % 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: -0.71 (0.23), residues: 1464 helix: 0.95 (0.19), residues: 810 sheet: -1.02 (0.43), residues: 148 loop : -2.72 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 264 HIS 0.004 0.001 HIS B 389 PHE 0.012 0.001 PHE A 88 TYR 0.010 0.001 TYR F 104 ARG 0.003 0.000 ARG C 325 *********************** 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 252 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 194 time to evaluate : 1.142 Fit side-chains REVERT: B 97 GLN cc_start: 0.7920 (mt0) cc_final: 0.7583 (mt0) REVERT: B 156 VAL cc_start: 0.7859 (m) cc_final: 0.7608 (t) REVERT: B 446 MET cc_start: 0.5869 (tmm) cc_final: 0.5235 (tmm) REVERT: C 72 ILE cc_start: 0.8345 (mm) cc_final: 0.7895 (mm) REVERT: C 184 ARG cc_start: 0.6313 (ttp80) cc_final: 0.5645 (mmm-85) REVERT: C 278 LEU cc_start: 0.9015 (mt) cc_final: 0.8761 (mt) REVERT: C 443 MET cc_start: 0.7031 (mmm) cc_final: 0.6480 (mmm) REVERT: F 92 MET cc_start: 0.7920 (tpp) cc_final: 0.7714 (ttt) REVERT: G 4 ARG cc_start: 0.6665 (mmt180) cc_final: 0.5364 (mmt180) REVERT: G 40 LEU cc_start: 0.8472 (mm) cc_final: 0.8248 (mm) REVERT: G 123 SER cc_start: 0.9004 (m) cc_final: 0.8573 (t) outliers start: 58 outliers final: 51 residues processed: 228 average time/residue: 0.1902 time to fit residues: 64.0439 Evaluate side-chains 232 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 181 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 281 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 88 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11436 Z= 0.241 Angle : 0.634 8.938 15655 Z= 0.312 Chirality : 0.043 0.256 1951 Planarity : 0.005 0.054 1974 Dihedral : 4.728 38.044 1620 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 5.38 % Allowed : 21.79 % Favored : 72.83 % 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: -0.69 (0.23), residues: 1464 helix: 0.95 (0.19), residues: 804 sheet: -0.95 (0.44), residues: 146 loop : -2.66 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 231 HIS 0.004 0.001 HIS F 163 PHE 0.008 0.001 PHE G 226 TYR 0.012 0.001 TYR F 104 ARG 0.003 0.000 ARG C 325 *********************** 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 239 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 177 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: B 97 GLN cc_start: 0.7937 (mt0) cc_final: 0.7587 (mt0) REVERT: C 72 ILE cc_start: 0.8387 (mm) cc_final: 0.7975 (mm) REVERT: C 184 ARG cc_start: 0.6367 (ttp80) cc_final: 0.5679 (mmm-85) REVERT: C 278 LEU cc_start: 0.9047 (mt) cc_final: 0.8778 (mt) REVERT: C 443 MET cc_start: 0.7024 (mmm) cc_final: 0.6496 (mmm) REVERT: G 4 ARG cc_start: 0.6705 (mmt180) cc_final: 0.5311 (mmt180) REVERT: G 40 LEU cc_start: 0.8491 (mm) cc_final: 0.8230 (mm) REVERT: G 79 VAL cc_start: 0.9071 (OUTLIER) cc_final: 0.8852 (p) REVERT: G 123 SER cc_start: 0.9049 (m) cc_final: 0.8563 (t) outliers start: 62 outliers final: 54 residues processed: 218 average time/residue: 0.2015 time to fit residues: 65.2512 Evaluate side-chains 231 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 176 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 281 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 130 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 133 optimal weight: 0.0870 chunk 80 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 GLN B 430 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2443 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= 0.198 Angle : 0.612 8.956 15655 Z= 0.301 Chirality : 0.042 0.261 1951 Planarity : 0.005 0.053 1974 Dihedral : 4.632 37.903 1620 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 5.21 % Allowed : 22.57 % Favored : 72.22 % 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: -0.55 (0.23), residues: 1464 helix: 1.08 (0.19), residues: 807 sheet: -0.86 (0.44), residues: 146 loop : -2.64 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 264 HIS 0.004 0.001 HIS B 389 PHE 0.024 0.001 PHE A 88 TYR 0.010 0.001 TYR F 104 ARG 0.003 0.000 ARG C 325 *********************** 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 241 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 181 time to evaluate : 1.278 Fit side-chains REVERT: B 97 GLN cc_start: 0.7909 (mt0) cc_final: 0.7610 (mt0) REVERT: C 72 ILE cc_start: 0.8309 (mm) cc_final: 0.7922 (mm) REVERT: C 184 ARG cc_start: 0.6289 (ttp80) cc_final: 0.5667 (mmm-85) REVERT: C 278 LEU cc_start: 0.9010 (mt) cc_final: 0.8750 (mt) REVERT: C 443 MET cc_start: 0.7017 (mmm) cc_final: 0.6422 (mmm) REVERT: G 4 ARG cc_start: 0.6634 (mmt180) cc_final: 0.5385 (mmt180) REVERT: G 79 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8836 (p) REVERT: G 123 SER cc_start: 0.9024 (m) cc_final: 0.8536 (t) outliers start: 60 outliers final: 54 residues processed: 220 average time/residue: 0.1932 time to fit residues: 63.3447 Evaluate side-chains 230 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 175 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 271 ASN Chi-restraints excluded: chain G residue 281 THR 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: 0.7980 chunk 67 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 12 optimal weight: 0.0370 chunk 91 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 93 optimal weight: 0.0970 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 GLN B 430 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 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 0.045 11436 Z= 0.192 Angle : 0.615 9.009 15655 Z= 0.301 Chirality : 0.042 0.268 1951 Planarity : 0.005 0.052 1974 Dihedral : 4.613 38.069 1620 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 5.03 % Allowed : 22.92 % Favored : 72.05 % 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: -0.46 (0.23), residues: 1464 helix: 1.16 (0.19), residues: 808 sheet: -0.84 (0.44), residues: 146 loop : -2.62 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 264 HIS 0.004 0.001 HIS B 389 PHE 0.015 0.001 PHE A 88 TYR 0.011 0.001 TYR F 104 ARG 0.003 0.000 ARG C 325 ********************** 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 236 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 178 time to evaluate : 1.171 Fit side-chains REVERT: B 97 GLN cc_start: 0.7906 (mt0) cc_final: 0.7605 (mt0) REVERT: C 72 ILE cc_start: 0.8318 (mm) cc_final: 0.7929 (mm) REVERT: C 184 ARG cc_start: 0.6266 (ttp80) cc_final: 0.5687 (mmm-85) REVERT: C 278 LEU cc_start: 0.9002 (mt) cc_final: 0.8747 (mt) REVERT: C 443 MET cc_start: 0.7016 (mmm) cc_final: 0.6419 (mmm) REVERT: G 4 ARG cc_start: 0.6621 (mmt180) cc_final: 0.5355 (mmt180) REVERT: G 79 VAL cc_start: 0.9050 (OUTLIER) cc_final: 0.8840 (p) REVERT: G 123 SER cc_start: 0.9016 (m) cc_final: 0.8522 (t) outliers start: 58 outliers final: 54 residues processed: 215 average time/residue: 0.2065 time to fit residues: 65.5574 Evaluate side-chains 229 residues out of total 1152 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 174 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 243 MET Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 344 THR Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 197 TYR Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 271 ASN Chi-restraints excluded: chain G residue 281 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 5.9990 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: 0.9990 chunk 49 optimal weight: 2.9990 chunk 121 optimal weight: 0.2980 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.132467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.116836 restraints weight = 16769.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.118298 restraints weight = 12958.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.119583 restraints weight = 10772.391| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11436 Z= 0.281 Angle : 0.668 8.749 15655 Z= 0.328 Chirality : 0.044 0.265 1951 Planarity : 0.005 0.054 1974 Dihedral : 4.844 38.379 1620 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 5.03 % Allowed : 23.09 % Favored : 71.88 % 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: -0.57 (0.23), residues: 1464 helix: 1.06 (0.19), residues: 809 sheet: -0.77 (0.46), residues: 134 loop : -2.67 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 264 HIS 0.005 0.001 HIS F 163 PHE 0.014 0.001 PHE A 88 TYR 0.013 0.002 TYR F 104 ARG 0.003 0.000 ARG C 325 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2394.00 seconds wall clock time: 43 minutes 30.05 seconds (2610.05 seconds total)