Starting phenix.real_space_refine (version: dev) on Tue Feb 21 03:46:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag5_15416/02_2023/8ag5_15416.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag5_15416/02_2023/8ag5_15416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag5_15416/02_2023/8ag5_15416.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag5_15416/02_2023/8ag5_15416.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag5_15416/02_2023/8ag5_15416.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ag5_15416/02_2023/8ag5_15416.pdb" } resolution = 3.47 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= 0.010 sd= 1.052 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 Process input model Symmetric amino acids flipped Residue "A GLU 118": "OE1" <-> "OE2" Residue "A PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A ASP 441": "OD1" <-> "OD2" Residue "A ASP 476": "OD1" <-> "OD2" Residue "B TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 428": "OE1" <-> "OE2" Residue "C TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 176": "OD1" <-> "OD2" Residue "C PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 13762 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 4054 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 27, 'TRANS': 474} Chain: "B" Number of atoms: 4302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4302 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 25, 'TRANS': 513} Chain breaks: 2 Chain: "C" Number of atoms: 2703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2703 Classifications: {'peptide': 331} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 321} Chain: "D" Number of atoms: 2703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2703 Classifications: {'peptide': 331} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 321} Time building chain proxies: 7.78, per 1000 atoms: 0.57 Number of scatterers: 13762 At special positions: 0 Unit cell: (141.95, 135.27, 113.56, 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 76 16.00 O 2623 8.00 N 2293 7.00 C 8770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.79 Conformation dependent library (CDL) restraints added in 1.6 seconds 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 19 sheets defined 29.6% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 58 through 78 Processing helix chain 'A' and resid 112 through 121 Processing helix chain 'A' and resid 123 through 135 Processing helix chain 'A' and resid 142 through 156 Processing helix chain 'A' and resid 179 through 197 Processing helix chain 'A' and resid 238 through 251 removed outlier: 3.743A pdb=" N LEU A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 330 through 337 Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 377 through 393 removed outlier: 3.640A pdb=" N LEU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 480 through 495 Processing helix chain 'A' and resid 510 through 519 Processing helix chain 'A' and resid 520 through 530 Processing helix chain 'B' and resid 29 through 48 Processing helix chain 'B' and resid 87 through 97 removed outlier: 3.522A pdb=" N LEU B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 122 removed outlier: 3.535A pdb=" N THR B 122 " --> pdb=" O ILE B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 157 Processing helix chain 'B' and resid 198 through 216 Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 232 through 233 No H-bonds generated for 'chain 'B' and resid 232 through 233' Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 285 through 289 removed outlier: 3.754A pdb=" N ASP B 288 " --> pdb=" O LYS B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 326 No H-bonds generated for 'chain 'B' and resid 324 through 326' Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 352 through 356 removed outlier: 3.555A pdb=" N PHE B 355 " --> pdb=" O GLN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 447 through 461 Processing helix chain 'B' and resid 478 through 482 removed outlier: 3.647A pdb=" N LYS B 481 " --> pdb=" O PRO B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 500 removed outlier: 4.154A pdb=" N GLN B 488 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 516 removed outlier: 3.591A pdb=" N TRP B 513 " --> pdb=" O GLN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 removed outlier: 3.710A pdb=" N THR B 523 " --> pdb=" O PRO B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 537 Processing helix chain 'C' and resid 22 through 30 Processing helix chain 'C' and resid 47 through 60 Processing helix chain 'C' and resid 223 through 229 removed outlier: 3.584A pdb=" N ASP C 228 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 242 Processing helix chain 'C' and resid 282 through 298 removed outlier: 4.102A pdb=" N LYS C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 31 Processing helix chain 'D' and resid 47 through 61 Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 234 through 243 Processing helix chain 'D' and resid 281 through 299 Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 109 removed outlier: 6.505A pdb=" N VAL A 85 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLU A 107 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU A 83 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER A 37 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N MET A 167 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE A 39 " --> pdb=" O MET A 167 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE A 169 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU A 41 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N PHE A 199 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LYS A 164 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ASP A 201 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE A 166 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 262 removed outlier: 7.989A pdb=" N VAL A 394 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA A 395 " --> pdb=" O PHE A 350 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N PHE A 350 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU A 397 " --> pdb=" O MET A 348 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LYS A 260 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU A 347 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LYS A 262 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N GLY A 349 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 299 through 303 Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 329 Processing sheet with id=AA5, first strand: chain 'A' and resid 375 through 376 Processing sheet with id=AA6, first strand: chain 'A' and resid 419 through 420 removed outlier: 6.443A pdb=" N GLU A 419 " --> pdb=" O VAL A 427 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 84 removed outlier: 6.292A pdb=" N LEU B 56 " --> pdb=" O HIS B 80 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N HIS B 82 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE B 54 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA B 9 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N GLU B 133 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL B 11 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N PHE B 135 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N CYS B 13 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ARG B 130 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N GLN B 162 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE B 132 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N PHE B 164 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE B 134 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N TYR B 225 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE B 163 " --> pdb=" O TYR B 225 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 247 through 252 removed outlier: 6.644A pdb=" N VAL B 361 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N GLN B 360 " --> pdb=" O GLN B 423 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLN B 423 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ALA B 366 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N GLU B 417 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL B 405 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N MET B 389 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL B 390 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE B 345 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE B 392 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N PHE B 340 " --> pdb=" O PRO B 248 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ARG B 250 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL B 342 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N THR B 252 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLY B 344 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 313 through 315 Processing sheet with id=AB1, first strand: chain 'B' and resid 464 through 466 Processing sheet with id=AB2, first strand: chain 'C' and resid 2 through 4 removed outlier: 7.055A pdb=" N ILE C 3 " --> pdb=" O THR C 11 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N THR C 11 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP C 130 " --> pdb=" O PHE C 15 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N THR C 150 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS C 149 " --> pdb=" O TYR C 78 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 2 through 4 removed outlier: 7.055A pdb=" N ILE C 3 " --> pdb=" O THR C 11 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N THR C 11 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP C 130 " --> pdb=" O PHE C 15 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N THR C 150 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS C 66 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 85 through 86 removed outlier: 3.737A pdb=" N PHE C 139 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP C 138 " --> pdb=" O TYR C 119 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ASN C 124 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LYS D 126 " --> pdb=" O ASN C 124 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS C 126 " --> pdb=" O ASN D 124 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN D 124 " --> pdb=" O LYS C 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 165 through 167 Processing sheet with id=AB6, first strand: chain 'C' and resid 231 through 232 removed outlier: 5.698A pdb=" N LEU C 216 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILE C 207 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN C 218 " --> pdb=" O GLY C 205 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 2 through 4 removed outlier: 7.216A pdb=" N ILE D 3 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N THR D 11 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP D 130 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR D 150 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASP D 155 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR D 72 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 2 through 4 removed outlier: 7.216A pdb=" N ILE D 3 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N THR D 11 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP D 130 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR D 150 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 164 through 168 Processing sheet with id=AC1, first strand: chain 'D' and resid 231 through 232 removed outlier: 6.682A pdb=" N GLY D 205 " --> pdb=" O VAL D 217 " (cutoff:3.500A) 598 hydrogen bonds defined for protein. 1647 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: 4.33 Time building geometry restraints manager: 5.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4489 1.34 - 1.46: 2813 1.46 - 1.58: 6610 1.58 - 1.69: 0 1.69 - 1.81: 121 Bond restraints: 14033 Sorted by residual: bond pdb=" CB ASP B 65 " pdb=" CG ASP B 65 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.13e+00 bond pdb=" CB ASP C 5 " pdb=" CG ASP C 5 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 9.75e-01 bond pdb=" CB PHE B 142 " pdb=" CG PHE B 142 " ideal model delta sigma weight residual 1.502 1.519 -0.017 2.30e-02 1.89e+03 5.60e-01 bond pdb=" CB LYS A 516 " pdb=" CG LYS A 516 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.48e-01 bond pdb=" C ILE C 175 " pdb=" O ILE C 175 " ideal model delta sigma weight residual 1.229 1.236 -0.008 1.03e-02 9.43e+03 5.36e-01 ... (remaining 14028 not shown) Histogram of bond angle deviations from ideal: 99.09 - 106.09: 287 106.09 - 113.08: 7689 113.08 - 120.07: 4780 120.07 - 127.06: 6068 127.06 - 134.06: 124 Bond angle restraints: 18948 Sorted by residual: angle pdb=" C LYS D 85 " pdb=" N ARG D 86 " pdb=" CA ARG D 86 " ideal model delta sigma weight residual 121.54 126.77 -5.23 1.91e+00 2.74e-01 7.49e+00 angle pdb=" N ARG A 218 " pdb=" CA ARG A 218 " pdb=" C ARG A 218 " ideal model delta sigma weight residual 113.72 109.66 4.06 1.52e+00 4.33e-01 7.14e+00 angle pdb=" C ARG D 86 " pdb=" N THR D 87 " pdb=" CA THR D 87 " ideal model delta sigma weight residual 121.54 126.26 -4.72 1.91e+00 2.74e-01 6.11e+00 angle pdb=" CA ILE D 49 " pdb=" CB ILE D 49 " pdb=" CG1 ILE D 49 " ideal model delta sigma weight residual 110.40 114.18 -3.78 1.70e+00 3.46e-01 4.95e+00 angle pdb=" CA ARG A 218 " pdb=" C ARG A 218 " pdb=" N ASP A 219 " ideal model delta sigma weight residual 118.87 116.33 2.54 1.18e+00 7.18e-01 4.62e+00 ... (remaining 18943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 7262 17.44 - 34.89: 947 34.89 - 52.33: 294 52.33 - 69.77: 74 69.77 - 87.21: 21 Dihedral angle restraints: 8598 sinusoidal: 3580 harmonic: 5018 Sorted by residual: dihedral pdb=" CG ARG A 488 " pdb=" CD ARG A 488 " pdb=" NE ARG A 488 " pdb=" CZ ARG A 488 " ideal model delta sinusoidal sigma weight residual -90.00 -36.49 -53.51 2 1.50e+01 4.44e-03 1.38e+01 dihedral pdb=" CA ASP D 20 " pdb=" CB ASP D 20 " pdb=" CG ASP D 20 " pdb=" OD1 ASP D 20 " ideal model delta sinusoidal sigma weight residual -30.00 -88.14 58.14 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA PRO D 121 " pdb=" C PRO D 121 " pdb=" N THR D 122 " pdb=" CA THR D 122 " ideal model delta harmonic sigma weight residual 180.00 163.23 16.77 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 8595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1325 0.030 - 0.060: 525 0.060 - 0.090: 147 0.090 - 0.120: 120 0.120 - 0.151: 14 Chirality restraints: 2131 Sorted by residual: chirality pdb=" CA ILE D 73 " pdb=" N ILE D 73 " pdb=" C ILE D 73 " pdb=" CB ILE D 73 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA ILE D 12 " pdb=" N ILE D 12 " pdb=" C ILE D 12 " pdb=" CB ILE D 12 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA ILE A 166 " pdb=" N ILE A 166 " pdb=" C ILE A 166 " pdb=" CB ILE A 166 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 2128 not shown) Planarity restraints: 2432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 65 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.71e+00 pdb=" C ASP B 65 " -0.033 2.00e-02 2.50e+03 pdb=" O ASP B 65 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN B 66 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 120 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO C 121 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 121 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 121 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 369 " 0.028 5.00e-02 4.00e+02 4.30e-02 2.95e+00 pdb=" N PRO A 370 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " 0.024 5.00e-02 4.00e+02 ... (remaining 2429 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 837 2.74 - 3.28: 12553 3.28 - 3.82: 21616 3.82 - 4.36: 26188 4.36 - 4.90: 45209 Nonbonded interactions: 106403 Sorted by model distance: nonbonded pdb=" OG SER B 378 " pdb=" OE2 GLU B 417 " model vdw 2.194 2.440 nonbonded pdb=" O GLN C 10 " pdb=" OH TYR C 101 " model vdw 2.199 2.440 nonbonded pdb=" OG1 THR C 281 " pdb=" OD1 ASP C 283 " model vdw 2.226 2.440 nonbonded pdb=" OG1 THR C 312 " pdb=" O PRO C 314 " model vdw 2.231 2.440 nonbonded pdb=" OE1 GLU D 28 " pdb=" NZ LYS D 31 " model vdw 2.236 2.520 ... (remaining 106398 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 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 76 5.16 5 C 8770 2.51 5 N 2293 2.21 5 O 2623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 6.920 Check model and map are aligned: 0.200 Process input model: 35.450 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 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 : 0.003 0.027 14033 Z= 0.175 Angle : 0.487 6.284 18948 Z= 0.261 Chirality : 0.041 0.151 2131 Planarity : 0.004 0.047 2432 Dihedral : 17.817 87.212 5338 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.35 (0.21), residues: 1691 helix: 1.86 (0.26), residues: 445 sheet: 0.71 (0.27), residues: 379 loop : -0.88 (0.21), residues: 867 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 336 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 337 average time/residue: 0.3226 time to fit residues: 147.5017 Evaluate side-chains 332 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 330 time to evaluate : 1.581 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1319 time to fit residues: 2.7678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 GLN B 119 GLN C 10 GLN C 120 HIS D 52 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.0718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.046 14033 Z= 0.428 Angle : 0.566 7.364 18948 Z= 0.302 Chirality : 0.045 0.148 2131 Planarity : 0.004 0.048 2432 Dihedral : 4.557 20.065 1837 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.16 (0.20), residues: 1691 helix: 1.65 (0.25), residues: 455 sheet: 0.62 (0.26), residues: 371 loop : -1.01 (0.21), residues: 865 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 345 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 24 residues processed: 362 average time/residue: 0.3276 time to fit residues: 162.4449 Evaluate side-chains 366 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 342 time to evaluate : 1.837 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1518 time to fit residues: 8.6950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 153 optimal weight: 0.0980 chunk 166 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 GLN B 119 GLN C 17 ASN C 120 HIS C 178 HIS C 262 ASN D 10 GLN D 52 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.0698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 14033 Z= 0.177 Angle : 0.469 5.674 18948 Z= 0.252 Chirality : 0.041 0.150 2131 Planarity : 0.003 0.046 2432 Dihedral : 4.277 19.237 1837 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.37 (0.21), residues: 1691 helix: 1.92 (0.25), residues: 455 sheet: 0.70 (0.27), residues: 377 loop : -0.92 (0.21), residues: 859 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 343 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 357 average time/residue: 0.3248 time to fit residues: 158.0976 Evaluate side-chains 350 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 340 time to evaluate : 1.618 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1719 time to fit residues: 5.1703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 154 optimal weight: 0.6980 chunk 163 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 44 optimal weight: 0.0870 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 GLN B 269 GLN C 10 GLN C 120 HIS C 262 ASN D 52 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.0747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 14033 Z= 0.184 Angle : 0.464 5.783 18948 Z= 0.249 Chirality : 0.041 0.148 2131 Planarity : 0.003 0.046 2432 Dihedral : 4.203 19.123 1837 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.45 (0.21), residues: 1691 helix: 2.05 (0.25), residues: 455 sheet: 0.75 (0.27), residues: 377 loop : -0.90 (0.21), residues: 859 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 361 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 369 average time/residue: 0.3263 time to fit residues: 164.9191 Evaluate side-chains 362 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 350 time to evaluate : 1.674 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1768 time to fit residues: 5.8177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 67 optimal weight: 30.0000 chunk 139 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN B 119 GLN B 269 GLN C 10 GLN C 17 ASN C 120 HIS D 10 GLN D 52 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.057 14033 Z= 0.503 Angle : 0.598 7.152 18948 Z= 0.317 Chirality : 0.047 0.155 2131 Planarity : 0.004 0.051 2432 Dihedral : 4.701 19.706 1837 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.17 (0.20), residues: 1691 helix: 1.75 (0.25), residues: 449 sheet: 0.65 (0.26), residues: 375 loop : -1.05 (0.20), residues: 867 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 361 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 25 residues processed: 378 average time/residue: 0.3156 time to fit residues: 162.2789 Evaluate side-chains 379 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 354 time to evaluate : 1.694 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1379 time to fit residues: 8.5789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN B 119 GLN C 120 HIS D 52 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 14033 Z= 0.199 Angle : 0.488 5.474 18948 Z= 0.262 Chirality : 0.042 0.161 2131 Planarity : 0.004 0.047 2432 Dihedral : 4.370 19.168 1837 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.38 (0.21), residues: 1691 helix: 2.01 (0.25), residues: 455 sheet: 0.69 (0.27), residues: 376 loop : -0.94 (0.21), residues: 860 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 364 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 14 residues processed: 370 average time/residue: 0.3289 time to fit residues: 164.4484 Evaluate side-chains 374 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 360 time to evaluate : 1.609 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1704 time to fit residues: 6.2497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 100 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: A 68 GLN A 278 GLN B 269 GLN C 120 HIS C 262 ASN D 10 GLN D 52 ASN D 90 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 14033 Z= 0.257 Angle : 0.508 7.615 18948 Z= 0.270 Chirality : 0.043 0.174 2131 Planarity : 0.004 0.048 2432 Dihedral : 4.383 19.308 1837 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.36 (0.21), residues: 1691 helix: 2.06 (0.25), residues: 449 sheet: 0.66 (0.27), residues: 371 loop : -0.96 (0.21), residues: 871 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 362 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 368 average time/residue: 0.3245 time to fit residues: 161.9131 Evaluate side-chains 363 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 356 time to evaluate : 1.763 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1391 time to fit residues: 4.1579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 0.0000 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 80 optimal weight: 0.0040 chunk 15 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 278 GLN B 269 GLN C 120 HIS D 10 GLN D 52 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 14033 Z= 0.199 Angle : 0.488 7.928 18948 Z= 0.260 Chirality : 0.042 0.175 2131 Planarity : 0.004 0.047 2432 Dihedral : 4.300 19.182 1837 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.44 (0.21), residues: 1691 helix: 2.15 (0.25), residues: 449 sheet: 0.69 (0.27), residues: 371 loop : -0.93 (0.21), residues: 871 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 358 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 364 average time/residue: 0.3278 time to fit residues: 161.5241 Evaluate side-chains 366 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 356 time to evaluate : 1.670 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2018 time to fit residues: 5.5158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 137 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 278 GLN C 120 HIS C 262 ASN D 10 GLN D 52 ASN D 90 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 14033 Z= 0.226 Angle : 0.506 7.948 18948 Z= 0.269 Chirality : 0.042 0.176 2131 Planarity : 0.004 0.048 2432 Dihedral : 4.325 19.195 1837 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.41 (0.21), residues: 1691 helix: 2.11 (0.25), residues: 449 sheet: 0.70 (0.27), residues: 371 loop : -0.94 (0.21), residues: 871 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 356 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 357 average time/residue: 0.3371 time to fit residues: 162.9168 Evaluate side-chains 354 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 352 time to evaluate : 1.644 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1224 time to fit residues: 2.8439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 chunk 111 optimal weight: 0.1980 chunk 168 optimal weight: 0.7980 chunk 154 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 HIS D 10 GLN D 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 14033 Z= 0.226 Angle : 0.503 7.405 18948 Z= 0.267 Chirality : 0.042 0.176 2131 Planarity : 0.004 0.047 2432 Dihedral : 4.329 19.150 1837 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.43 (0.21), residues: 1691 helix: 2.14 (0.25), residues: 449 sheet: 0.71 (0.27), residues: 372 loop : -0.94 (0.21), residues: 870 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3382 Ramachandran restraints generated. 1691 Oldfield, 0 Emsley, 1691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 358 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 360 average time/residue: 0.3367 time to fit residues: 164.4788 Evaluate side-chains 359 residues out of total 1567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 356 time to evaluate : 1.801 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1438 time to fit residues: 3.3186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 19 optimal weight: 0.0470 chunk 37 optimal weight: 0.1980 chunk 134 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 chunk 7 optimal weight: 0.1980 overall best weight: 0.4080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 HIS C 262 ASN D 10 GLN D 52 ASN D 90 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.134980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.106046 restraints weight = 19782.081| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.16 r_work: 0.3011 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 14033 Z= 0.146 Angle : 0.486 10.493 18948 Z= 0.256 Chirality : 0.042 0.177 2131 Planarity : 0.004 0.051 2432 Dihedral : 4.164 18.744 1837 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.53 (0.21), residues: 1691 helix: 2.25 (0.25), residues: 449 sheet: 0.77 (0.27), residues: 370 loop : -0.89 (0.21), residues: 872 =============================================================================== Job complete usr+sys time: 3720.02 seconds wall clock time: 74 minutes 28.12 seconds (4468.12 seconds total)