Starting phenix.real_space_refine (version: dev) on Mon Apr 4 22:49:21 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nd4_3622/04_2022/5nd4_3622_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nd4_3622/04_2022/5nd4_3622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nd4_3622/04_2022/5nd4_3622.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nd4_3622/04_2022/5nd4_3622.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nd4_3622/04_2022/5nd4_3622_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nd4_3622/04_2022/5nd4_3622_updated.pdb" } resolution = 4.4 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= 0.002 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 9435 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2701 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 10, 'TRANS': 326} Chain breaks: 2 Chain: "A" Number of atoms: 3227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3227 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 19, 'TRANS': 392} Chain breaks: 1 Chain: "B" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3351 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 20, 'TRANS': 405} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'ALF': 1, ' MG': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GTP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'GDP': 1, 'TA1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.07, per 1000 atoms: 0.64 Number of scatterers: 9435 At special positions: 0 Unit cell: (102.51, 84.15, 113.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 57 16.00 P 7 15.00 Al 1 13.00 Mg 2 11.99 F 4 9.00 O 1806 8.00 N 1629 7.00 C 5929 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.68 Conformation dependent library (CDL) restraints added in 1.3 seconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB THR C 472 " pdb=" CB SER B 280 " Number of C-beta restraints generated: 2182 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 7 sheets defined 41.4% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 132 through 149 removed outlier: 4.361A pdb=" N LYS C 141 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS C 145 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 147 " --> pdb=" O MET C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 178 through 189 removed outlier: 3.867A pdb=" N PHE C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 364 removed outlier: 3.769A pdb=" N LYS C 363 " --> pdb=" O LYS C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 420 through 448 removed outlier: 3.548A pdb=" N GLU C 425 " --> pdb=" O ARG C 422 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG C 444 " --> pdb=" O ALA C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 459 No H-bonds generated for 'chain 'C' and resid 457 through 459' Processing helix chain 'C' and resid 462 through 471 removed outlier: 4.655A pdb=" N GLY C 469 " --> pdb=" O ARG C 465 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N PHE C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 505 removed outlier: 4.194A pdb=" N ASP C 491 " --> pdb=" O SER C 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 27 removed outlier: 3.627A pdb=" N TYR A 24 " --> pdb=" O CYS A 20 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS A 25 " --> pdb=" O TRP A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 removed outlier: 3.529A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 109 through 128 removed outlier: 4.006A pdb=" N GLU A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA A 126 " --> pdb=" O ILE A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.502A pdb=" N LEU A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 195 removed outlier: 3.756A pdb=" N THR A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.513A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.784A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 removed outlier: 3.851A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 291 No H-bonds generated for 'chain 'A' and resid 288 through 291' Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.511A pdb=" N ALA A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ALA A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.863A pdb=" N TRP A 388 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A 390 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N HIS A 393 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS A 394 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 400 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 411 removed outlier: 4.310A pdb=" N HIS A 406 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP A 407 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL A 409 " --> pdb=" O HIS A 406 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLY A 410 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.528A pdb=" N ALA A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 434 No H-bonds generated for 'chain 'A' and resid 431 through 434' Processing helix chain 'B' and resid 10 through 28 removed outlier: 3.742A pdb=" N ASP B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS B 28 " --> pdb=" O ILE B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 52 Processing helix chain 'B' and resid 72 through 78 Processing helix chain 'B' and resid 83 through 86 Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 111 through 126 removed outlier: 4.242A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL B 121 " --> pdb=" O SER B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 160 removed outlier: 3.857A pdb=" N MET B 149 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 154 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 196 removed outlier: 4.144A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 215 removed outlier: 3.563A pdb=" N TYR B 210 " --> pdb=" O ASN B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 243 removed outlier: 3.647A pdb=" N GLY B 237 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG B 243 " --> pdb=" O THR B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 325 through 338 removed outlier: 3.661A pdb=" N ASP B 329 " --> pdb=" O MET B 325 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 399 removed outlier: 5.527A pdb=" N LYS B 389 " --> pdb=" O GLU B 386 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE B 391 " --> pdb=" O PHE B 388 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B 397 " --> pdb=" O GLN B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 removed outlier: 4.461A pdb=" N GLU B 411 " --> pdb=" O TRP B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 434 removed outlier: 3.988A pdb=" N THR B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 124 through 126 removed outlier: 3.688A pdb=" N GLN C 124 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE C 70 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR C 156 " --> pdb=" O CYS C 478 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 87 through 90 removed outlier: 3.563A pdb=" N GLU C 90 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C 94 " --> pdb=" O GLU C 90 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 116 " --> pdb=" O ALA C 99 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 329 through 331 removed outlier: 3.784A pdb=" N ARG C 329 " --> pdb=" O LYS C 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N CYS C 331 " --> pdb=" O TYR C 339 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR C 339 " --> pdb=" O CYS C 331 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.353A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 167 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS A 139 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 351 through 355 removed outlier: 8.665A pdb=" N LYS A 352 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS A 315 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N GLY A 354 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU A 317 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.858A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N VAL B 5 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N PHE B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE B 7 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA B 9 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N HIS B 139 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE B 165 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N LEU B 137 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASN B 167 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N HIS B 139 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE B 169 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLU B 200 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N SER B 170 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N TYR B 202 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL B 172 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE B 204 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 351 through 356 removed outlier: 8.139A pdb=" N LYS B 352 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL B 315 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ALA B 354 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ALA B 317 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N CYS B 356 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N PHE B 319 " --> pdb=" O CYS B 356 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN B 380 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL B 315 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE B 378 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA B 317 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR B 376 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N PHE B 319 " --> pdb=" O SER B 374 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N SER B 374 " --> pdb=" O PHE B 319 " (cutoff:3.500A) 313 hydrogen bonds defined for protein. 717 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: 2.60 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1656 1.32 - 1.44: 2584 1.44 - 1.57: 5291 1.57 - 1.69: 23 1.69 - 1.82: 90 Bond restraints: 9644 Sorted by residual: bond pdb=" N9 GDP B 600 " pdb=" C8 GDP B 600 " ideal model delta sigma weight residual 1.337 1.503 -0.166 2.00e-02 2.50e+03 6.88e+01 bond pdb=" N1 GDP B 600 " pdb=" C2 GDP B 600 " ideal model delta sigma weight residual 1.337 1.487 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" NE ARG A 2 " pdb=" CZ ARG A 2 " ideal model delta sigma weight residual 1.326 1.401 -0.075 1.10e-02 8.26e+03 4.68e+01 bond pdb=" C07 TA1 B 601 " pdb=" C08 TA1 B 601 " ideal model delta sigma weight residual 1.389 1.254 0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" O3B GDP B 600 " pdb=" PB GDP B 600 " ideal model delta sigma weight residual 1.510 1.634 -0.124 2.00e-02 2.50e+03 3.86e+01 ... (remaining 9639 not shown) Histogram of bond angle deviations from ideal: 83.08 - 100.25: 13 100.25 - 117.42: 7362 117.42 - 134.60: 5710 134.60 - 151.77: 3 151.77 - 168.95: 2 Bond angle restraints: 13090 Sorted by residual: angle pdb=" F1 ALF C 603 " pdb="AL ALF C 603 " pdb=" F2 ALF C 603 " ideal model delta sigma weight residual 108.68 168.95 -60.27 3.00e+00 1.11e-01 4.04e+02 angle pdb=" F3 ALF C 603 " pdb="AL ALF C 603 " pdb=" F4 ALF C 603 " ideal model delta sigma weight residual 109.63 167.08 -57.45 3.00e+00 1.11e-01 3.67e+02 angle pdb=" C GLU C 412 " pdb=" N ARG C 413 " pdb=" CA ARG C 413 " ideal model delta sigma weight residual 121.58 141.73 -20.15 1.95e+00 2.63e-01 1.07e+02 angle pdb=" CB LYS C 165 " pdb=" CG LYS C 165 " pdb=" CD LYS C 165 " ideal model delta sigma weight residual 111.30 88.91 22.39 2.30e+00 1.89e-01 9.48e+01 angle pdb=" NE ARG A 2 " pdb=" CZ ARG A 2 " pdb=" NH2 ARG A 2 " ideal model delta sigma weight residual 119.20 111.50 7.70 9.00e-01 1.23e+00 7.31e+01 ... (remaining 13085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 5365 35.86 - 71.73: 289 71.73 - 107.59: 52 107.59 - 143.46: 4 143.46 - 179.32: 3 Dihedral angle restraints: 5713 sinusoidal: 2320 harmonic: 3393 Sorted by residual: dihedral pdb=" O2B GDP B 600 " pdb=" O3A GDP B 600 " pdb=" PB GDP B 600 " pdb=" PA GDP B 600 " ideal model delta sinusoidal sigma weight residual 180.00 0.68 179.32 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP A 500 " pdb=" C1' GTP A 500 " pdb=" N9 GTP A 500 " pdb=" O4' GTP A 500 " ideal model delta sinusoidal sigma weight residual 104.59 -61.01 165.61 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" O5' GTP A 500 " pdb=" O3A GTP A 500 " pdb=" PA GTP A 500 " pdb=" PB GTP A 500 " ideal model delta sinusoidal sigma weight residual -85.88 69.60 -155.47 1 2.00e+01 2.50e-03 4.58e+01 ... (remaining 5710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.963: 1432 0.963 - 1.927: 0 1.927 - 2.890: 0 2.890 - 3.854: 0 3.854 - 4.817: 2 Chirality restraints: 1434 Sorted by residual: chirality pdb=" CA SER B 280 " pdb=" N SER B 280 " pdb=" C SER B 280 " pdb=" CB SER B 280 " both_signs ideal model delta sigma weight residual False 2.51 -2.31 4.82 2.00e-01 2.50e+01 5.80e+02 chirality pdb=" CA THR C 472 " pdb=" N THR C 472 " pdb=" C THR C 472 " pdb=" CB THR C 472 " both_signs ideal model delta sigma weight residual False 2.53 -2.12 4.64 2.00e-01 2.50e+01 5.38e+02 chirality pdb=" CA GLN B 281 " pdb=" N GLN B 281 " pdb=" C GLN B 281 " pdb=" CB GLN B 281 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.53e+00 ... (remaining 1431 not shown) Planarity restraints: 1689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 229 " -0.056 2.00e-02 2.50e+03 4.12e-02 2.54e+01 pdb=" CG HIS B 229 " 0.061 2.00e-02 2.50e+03 pdb=" ND1 HIS B 229 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 HIS B 229 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 HIS B 229 " -0.030 2.00e-02 2.50e+03 pdb=" NE2 HIS B 229 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 99 " -0.075 5.00e-02 4.00e+02 1.15e-01 2.12e+01 pdb=" N PRO C 100 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO C 100 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO C 100 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' ADP C 601 " 0.029 2.00e-02 2.50e+03 2.31e-02 1.47e+01 pdb=" C2 ADP C 601 " -0.007 2.00e-02 2.50e+03 pdb=" C4 ADP C 601 " 0.029 2.00e-02 2.50e+03 pdb=" C5 ADP C 601 " 0.021 2.00e-02 2.50e+03 pdb=" C6 ADP C 601 " -0.018 2.00e-02 2.50e+03 pdb=" C8 ADP C 601 " -0.032 2.00e-02 2.50e+03 pdb=" N1 ADP C 601 " -0.020 2.00e-02 2.50e+03 pdb=" N3 ADP C 601 " -0.012 2.00e-02 2.50e+03 pdb=" N6 ADP C 601 " 0.037 2.00e-02 2.50e+03 pdb=" N7 ADP C 601 " -0.017 2.00e-02 2.50e+03 pdb=" N9 ADP C 601 " -0.010 2.00e-02 2.50e+03 ... (remaining 1686 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 12 2.32 - 2.97: 4890 2.97 - 3.61: 14352 3.61 - 4.26: 23143 4.26 - 4.90: 37891 Nonbonded interactions: 80288 Sorted by model distance: nonbonded pdb=" CB LYS C 165 " pdb=" CE LYS C 165 " model vdw 1.678 3.072 nonbonded pdb=" OG1 THR C 166 " pdb="MG MG C 602 " model vdw 1.681 2.170 nonbonded pdb=" O2B ADP C 601 " pdb="MG MG C 602 " model vdw 2.083 2.170 nonbonded pdb=" NE2 GLN C 375 " pdb=" O1A ADP C 601 " model vdw 2.203 2.520 nonbonded pdb=" N LYS C 165 " pdb=" O1B ADP C 601 " model vdw 2.205 2.520 ... (remaining 80283 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 7 5.49 5 Mg 2 5.21 5 S 57 5.16 5 C 5929 2.51 5 N 1629 2.21 5 O 1806 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.140 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: 1.930 Check model and map are aligned: 0.290 Convert atoms to be neutral: 0.160 Process input model: 28.490 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3716 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 : 0.010 0.166 9644 Z= 0.633 Angle : 1.685 60.267 13090 Z= 0.981 Chirality : 0.202 4.817 1434 Planarity : 0.007 0.123 1689 Dihedral : 21.692 179.321 3531 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 26.62 Ramachandran Plot: Outliers : 8.34 % Allowed : 14.53 % Favored : 77.13 % Rotamer Outliers : 15.57 % Cbeta Deviations : 1.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.90 (0.21), residues: 1163 helix: -3.16 (0.19), residues: 463 sheet: -2.04 (0.36), residues: 206 loop : -3.81 (0.23), residues: 494 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 367 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 158 outliers final: 37 residues processed: 482 average time/residue: 0.2418 time to fit residues: 153.6585 Evaluate side-chains 236 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 199 time to evaluate : 1.059 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 37 outliers final: 1 residues processed: 37 average time/residue: 0.1635 time to fit residues: 10.1687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 GLN C 326 GLN C 430 ASN C 484 ASN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN A 356 ASN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN B 133 GLN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 294 GLN B 406 HIS B 436 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4160 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 9644 Z= 0.289 Angle : 1.062 29.412 13090 Z= 0.485 Chirality : 0.051 0.299 1434 Planarity : 0.007 0.100 1689 Dihedral : 12.700 176.749 1316 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 28.34 Ramachandran Plot: Outliers : 0.95 % Allowed : 8.68 % Favored : 90.37 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.22), residues: 1163 helix: -2.15 (0.20), residues: 453 sheet: -1.37 (0.37), residues: 202 loop : -2.87 (0.26), residues: 508 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 256 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 263 average time/residue: 0.2418 time to fit residues: 85.2702 Evaluate side-chains 159 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 157 time to evaluate : 1.211 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0912 time to fit residues: 1.9221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 84 optimal weight: 30.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 326 GLN A 11 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 249 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4424 moved from start: 0.6852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 9644 Z= 0.271 Angle : 1.003 29.868 13090 Z= 0.455 Chirality : 0.048 0.271 1434 Planarity : 0.005 0.056 1689 Dihedral : 12.138 173.698 1316 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 28.72 Ramachandran Plot: Outliers : 0.69 % Allowed : 8.43 % Favored : 90.89 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.23), residues: 1163 helix: -1.56 (0.22), residues: 450 sheet: -1.10 (0.36), residues: 212 loop : -2.37 (0.26), residues: 501 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 222 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 223 average time/residue: 0.2320 time to fit residues: 70.6750 Evaluate side-chains 144 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 1.134 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0881 time to fit residues: 1.6626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 11 optimal weight: 40.0000 chunk 50 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 overall best weight: 5.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 326 GLN A 11 GLN A 107 HIS ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS A 233 GLN A 256 GLN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4640 moved from start: 0.7938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 9644 Z= 0.266 Angle : 0.980 29.531 13090 Z= 0.437 Chirality : 0.047 0.271 1434 Planarity : 0.005 0.055 1689 Dihedral : 12.108 179.902 1316 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 29.36 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.91 % Favored : 91.49 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.23), residues: 1163 helix: -1.21 (0.22), residues: 473 sheet: -0.87 (0.36), residues: 213 loop : -2.10 (0.27), residues: 477 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.2132 time to fit residues: 61.8109 Evaluate side-chains 139 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.227 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 50.0000 chunk 83 optimal weight: 30.0000 chunk 46 optimal weight: 10.0000 chunk 95 optimal weight: 0.0970 chunk 77 optimal weight: 0.0970 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 overall best weight: 2.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4557 moved from start: 0.8269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 9644 Z= 0.213 Angle : 0.930 29.630 13090 Z= 0.405 Chirality : 0.045 0.274 1434 Planarity : 0.005 0.052 1689 Dihedral : 11.792 170.850 1316 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 25.65 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.79 % Favored : 92.61 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.23), residues: 1163 helix: -0.99 (0.23), residues: 475 sheet: -0.72 (0.35), residues: 215 loop : -1.98 (0.27), residues: 473 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 199 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.2118 time to fit residues: 59.5937 Evaluate side-chains 130 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.191 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 58 optimal weight: 20.0000 chunk 108 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 GLN C 188 ASN C 335 ASN ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 ASN A 256 GLN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN B 350 ASN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4837 moved from start: 0.9091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 9644 Z= 0.269 Angle : 0.968 30.421 13090 Z= 0.430 Chirality : 0.046 0.280 1434 Planarity : 0.005 0.052 1689 Dihedral : 11.866 170.735 1316 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 31.09 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.96 % Favored : 92.52 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.23), residues: 1163 helix: -1.04 (0.22), residues: 478 sheet: -0.66 (0.35), residues: 212 loop : -2.10 (0.27), residues: 473 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 195 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 198 average time/residue: 0.1978 time to fit residues: 56.6162 Evaluate side-chains 137 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.112 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 51 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 66 optimal weight: 0.0070 overall best weight: 4.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS B 350 ASN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4821 moved from start: 0.9526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 9644 Z= 0.233 Angle : 0.948 29.898 13090 Z= 0.417 Chirality : 0.046 0.259 1434 Planarity : 0.005 0.050 1689 Dihedral : 11.691 165.679 1316 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 26.89 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.96 % Favored : 92.52 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.23), residues: 1163 helix: -0.83 (0.23), residues: 469 sheet: -0.61 (0.35), residues: 212 loop : -1.94 (0.27), residues: 482 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.1931 time to fit residues: 52.0887 Evaluate side-chains 136 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.141 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 30.0000 chunk 21 optimal weight: 20.0000 chunk 71 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 87 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 323 HIS ** C 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN A 301 GLN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS B 350 ASN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4940 moved from start: 1.0174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 9644 Z= 0.254 Angle : 0.965 30.056 13090 Z= 0.428 Chirality : 0.045 0.249 1434 Planarity : 0.005 0.051 1689 Dihedral : 11.645 163.494 1316 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 29.58 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.91 % Favored : 91.57 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.23), residues: 1163 helix: -0.75 (0.23), residues: 460 sheet: -0.54 (0.35), residues: 209 loop : -1.97 (0.26), residues: 494 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 179 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.2088 time to fit residues: 53.3720 Evaluate side-chains 134 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.207 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 81 optimal weight: 20.0000 chunk 31 optimal weight: 30.0000 chunk 94 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 GLN ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 HIS ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN A 301 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN B 309 HIS ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4946 moved from start: 1.0613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 9644 Z= 0.241 Angle : 0.958 30.127 13090 Z= 0.423 Chirality : 0.046 0.260 1434 Planarity : 0.005 0.083 1689 Dihedral : 11.585 159.756 1316 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 29.90 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.65 % Favored : 91.83 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.23), residues: 1163 helix: -0.85 (0.23), residues: 464 sheet: -0.60 (0.34), residues: 214 loop : -1.85 (0.27), residues: 485 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.2091 time to fit residues: 54.4229 Evaluate side-chains 128 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.175 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 71 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 ASN C 323 HIS ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 GLN ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN A 301 GLN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4978 moved from start: 1.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 9644 Z= 0.237 Angle : 0.953 29.998 13090 Z= 0.420 Chirality : 0.046 0.283 1434 Planarity : 0.005 0.075 1689 Dihedral : 11.453 156.587 1316 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 30.66 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.25 % Favored : 91.23 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.23), residues: 1163 helix: -0.82 (0.23), residues: 461 sheet: -0.42 (0.35), residues: 206 loop : -1.92 (0.26), residues: 496 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 177 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 179 average time/residue: 0.2090 time to fit residues: 53.3777 Evaluate side-chains 132 residues out of total 1015 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 38 optimal weight: 30.0000 chunk 94 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 66 optimal weight: 0.5980 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN A 301 GLN ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 309 HIS B 349 ASN B 350 ASN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.085114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.064475 restraints weight = 41849.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.067520 restraints weight = 25567.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.069755 restraints weight = 17747.479| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 1.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 9644 Z= 0.234 Angle : 0.957 29.935 13090 Z= 0.419 Chirality : 0.045 0.268 1434 Planarity : 0.005 0.068 1689 Dihedral : 11.313 154.472 1316 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 29.69 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.22 % Favored : 92.35 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.23), residues: 1163 helix: -0.85 (0.22), residues: 466 sheet: -0.39 (0.35), residues: 204 loop : -1.88 (0.27), residues: 493 =============================================================================== Job complete usr+sys time: 1970.17 seconds wall clock time: 36 minutes 54.02 seconds (2214.02 seconds total)