Starting phenix.real_space_refine on Wed Jul 30 18:52:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vo6_43365/07_2025/8vo6_43365.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vo6_43365/07_2025/8vo6_43365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vo6_43365/07_2025/8vo6_43365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vo6_43365/07_2025/8vo6_43365.map" model { file = "/net/cci-nas-00/data/ceres_data/8vo6_43365/07_2025/8vo6_43365.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vo6_43365/07_2025/8vo6_43365.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 3 5.21 5 S 77 5.16 5 C 7936 2.51 5 N 2166 2.21 5 O 2436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12624 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3789 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 469} Chain: "E" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.67, per 1000 atoms: 0.77 Number of scatterers: 12624 At special positions: 0 Unit cell: (140.08, 93.73, 135.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 77 16.00 P 6 15.00 Mg 3 11.99 O 2436 8.00 N 2166 7.00 C 7936 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.7 seconds 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2964 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 35 sheets defined 36.5% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.584A pdb=" N SER A 175 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 removed outlier: 4.109A pdb=" N TYR A 335 " --> pdb=" O ALA A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 removed outlier: 4.008A pdb=" N GLY A 476 " --> pdb=" O ASP A 473 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 477 " --> pdb=" O HIS A 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 473 through 477' Processing helix chain 'A' and resid 486 through 490 removed outlier: 3.581A pdb=" N LEU A 490 " --> pdb=" O PRO A 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.600A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.887A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.566A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.570A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 262 removed outlier: 3.579A pdb=" N LEU E 261 " --> pdb=" O PRO E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 296 removed outlier: 4.015A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.578A pdb=" N THR E 304 " --> pdb=" O GLY E 301 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.557A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 368 through 374 removed outlier: 4.205A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 59 removed outlier: 3.611A pdb=" N GLN F 59 " --> pdb=" O GLY F 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 55 through 59' Processing helix chain 'F' and resid 61 through 63 No H-bonds generated for 'chain 'F' and resid 61 through 63' Processing helix chain 'F' and resid 78 through 92 Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.611A pdb=" N GLU F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.818A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 194 through 196 No H-bonds generated for 'chain 'F' and resid 194 through 196' Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 222 through 231 removed outlier: 3.607A pdb=" N GLU F 226 " --> pdb=" O ASP F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 286 through 296 removed outlier: 4.102A pdb=" N ASP F 292 " --> pdb=" O ASP F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 305 removed outlier: 3.539A pdb=" N THR F 304 " --> pdb=" O GLY F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 347 Processing helix chain 'F' and resid 348 through 356 removed outlier: 6.341A pdb=" N THR F 351 " --> pdb=" O SER F 348 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE F 352 " --> pdb=" O LEU F 349 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN F 353 " --> pdb=" O SER F 350 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP F 356 " --> pdb=" O GLN F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.084A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 61 removed outlier: 3.515A pdb=" N GLN G 59 " --> pdb=" O GLY G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 91 Processing helix chain 'G' and resid 97 through 101 removed outlier: 3.840A pdb=" N GLU G 100 " --> pdb=" O ALA G 97 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS G 101 " --> pdb=" O PRO G 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 97 through 101' Processing helix chain 'G' and resid 112 through 126 removed outlier: 3.905A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 172 through 175 removed outlier: 3.571A pdb=" N ILE G 175 " --> pdb=" O PRO G 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 172 through 175' Processing helix chain 'G' and resid 181 through 193 Processing helix chain 'G' and resid 194 through 197 Processing helix chain 'G' and resid 202 through 217 Processing helix chain 'G' and resid 222 through 231 Processing helix chain 'G' and resid 252 through 257 removed outlier: 3.749A pdb=" N CYS G 257 " --> pdb=" O GLU G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 262 Processing helix chain 'G' and resid 273 through 284 Processing helix chain 'G' and resid 286 through 296 removed outlier: 4.108A pdb=" N ASP G 292 " --> pdb=" O ASP G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 305 Processing helix chain 'G' and resid 308 through 321 Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 337 through 348 Processing helix chain 'G' and resid 351 through 355 removed outlier: 4.074A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 369 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 63 Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 removed outlier: 6.285A pdb=" N THR A 25 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA A 35 " --> pdb=" O THR A 25 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 95 removed outlier: 4.598A pdb=" N LEU A 103 " --> pdb=" O PHE A 112 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 163 through 167 removed outlier: 4.240A pdb=" N ASP A 166 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR A 152 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 151 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ILE A 144 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 9.630A pdb=" N LEU A 155 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 14.363A pdb=" N VAL A 142 " --> pdb=" O LEU A 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 163 through 167 removed outlier: 4.240A pdb=" N ASP A 166 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR A 152 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG A 151 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ILE A 144 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 9.630A pdb=" N LEU A 155 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 14.363A pdb=" N VAL A 142 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG A 217 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 231 through 234 Processing sheet with id=AA8, first strand: chain 'A' and resid 305 through 308 removed outlier: 4.478A pdb=" N ALA A 261 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 272 through 274 removed outlier: 6.640A pdb=" N ASN A 272 " --> pdb=" O ASN A 284 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN A 284 " --> pdb=" O ASN A 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 314 through 317 removed outlier: 5.402A pdb=" N TYR A 314 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A 326 " --> pdb=" O TYR A 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 337 through 340 Processing sheet with id=AB3, first strand: chain 'A' and resid 354 through 357 removed outlier: 6.683A pdb=" N PHE A 354 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER A 366 " --> pdb=" O PHE A 354 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 385 through 386 Processing sheet with id=AB5, first strand: chain 'A' and resid 394 through 397 removed outlier: 5.230A pdb=" N PHE A 394 " --> pdb=" O ASN A 407 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN A 407 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 432 through 435 removed outlier: 6.428A pdb=" N TYR A 432 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER A 444 " --> pdb=" O TYR A 432 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 452 through 455 removed outlier: 5.596A pdb=" N ILE A 463 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LYS A 471 " --> pdb=" O ALA A 480 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ALA A 480 " --> pdb=" O LYS A 471 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 452 through 455 Processing sheet with id=AB9, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.795A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC2, first strand: chain 'E' and resid 41 through 42 removed outlier: 4.404A pdb=" N GLN E 41 " --> pdb=" O ALA F 170 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 41 through 42 removed outlier: 4.404A pdb=" N GLN E 41 " --> pdb=" O ALA F 170 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AC6, first strand: chain 'E' and resid 169 through 170 removed outlier: 5.939A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AC8, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.796A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD2, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AD3, first strand: chain 'G' and resid 29 through 32 removed outlier: 4.109A pdb=" N THR G 106 " --> pdb=" O CYS G 10 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ASN G 12 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AD5, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AD6, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AD7, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.563A pdb=" N ASN G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 238 through 241 529 hydrogen bonds defined for protein. 1356 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: 4.38 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4156 1.34 - 1.46: 2337 1.46 - 1.57: 6267 1.57 - 1.69: 9 1.69 - 1.81: 128 Bond restraints: 12897 Sorted by residual: bond pdb=" CE1 HIC F 73 " pdb=" NE2 HIC F 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.68e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.48e+00 bond pdb=" CE1 HIC G 73 " pdb=" NE2 HIC G 73 " ideal model delta sigma weight residual 1.347 1.400 -0.053 2.00e-02 2.50e+03 7.12e+00 bond pdb=" CG HIC F 73 " pdb=" CD2 HIC F 73 " ideal model delta sigma weight residual 1.369 1.410 -0.041 2.00e-02 2.50e+03 4.13e+00 bond pdb=" CG HIC G 73 " pdb=" CD2 HIC G 73 " ideal model delta sigma weight residual 1.369 1.409 -0.040 2.00e-02 2.50e+03 4.07e+00 ... (remaining 12892 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 17074 1.83 - 3.66: 343 3.66 - 5.49: 55 5.49 - 7.32: 12 7.32 - 9.15: 3 Bond angle restraints: 17487 Sorted by residual: angle pdb=" N HIC G 73 " pdb=" CA HIC G 73 " pdb=" CB HIC G 73 " ideal model delta sigma weight residual 110.50 115.99 -5.49 1.70e+00 3.46e-01 1.04e+01 angle pdb=" CB MET E 190 " pdb=" CG MET E 190 " pdb=" SD MET E 190 " ideal model delta sigma weight residual 112.70 103.55 9.15 3.00e+00 1.11e-01 9.30e+00 angle pdb=" N THR E 148 " pdb=" CA THR E 148 " pdb=" C THR E 148 " ideal model delta sigma weight residual 114.56 110.76 3.80 1.27e+00 6.20e-01 8.94e+00 angle pdb=" N CYS A 121 " pdb=" CA CYS A 121 " pdb=" C CYS A 121 " ideal model delta sigma weight residual 112.25 108.28 3.97 1.36e+00 5.41e-01 8.52e+00 angle pdb=" N HIC F 73 " pdb=" CA HIC F 73 " pdb=" CB HIC F 73 " ideal model delta sigma weight residual 110.50 115.37 -4.87 1.70e+00 3.46e-01 8.22e+00 ... (remaining 17482 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.92: 7267 23.92 - 47.85: 404 47.85 - 71.77: 38 71.77 - 95.70: 18 95.70 - 119.62: 3 Dihedral angle restraints: 7730 sinusoidal: 3102 harmonic: 4628 Sorted by residual: dihedral pdb=" O1B ADP G 401 " pdb=" O3A ADP G 401 " pdb=" PB ADP G 401 " pdb=" PA ADP G 401 " ideal model delta sinusoidal sigma weight residual -60.00 -179.63 119.62 1 2.00e+01 2.50e-03 3.59e+01 dihedral pdb=" O1B ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PB ADP F 401 " pdb=" PA ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 -178.91 118.91 1 2.00e+01 2.50e-03 3.56e+01 dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 -176.46 116.46 1 2.00e+01 2.50e-03 3.47e+01 ... (remaining 7727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1282 0.042 - 0.085: 468 0.085 - 0.127: 158 0.127 - 0.170: 12 0.170 - 0.212: 2 Chirality restraints: 1922 Sorted by residual: chirality pdb=" CB ILE F 151 " pdb=" CA ILE F 151 " pdb=" CG1 ILE F 151 " pdb=" CG2 ILE F 151 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB ILE G 151 " pdb=" CA ILE G 151 " pdb=" CG1 ILE G 151 " pdb=" CG2 ILE G 151 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CB ILE A 163 " pdb=" CA ILE A 163 " pdb=" CG1 ILE A 163 " pdb=" CG2 ILE A 163 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 1919 not shown) Planarity restraints: 2258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO F 332 " -0.078 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO F 333 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO F 333 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO F 333 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 163 " -0.042 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO F 164 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO F 164 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 164 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 163 " -0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO E 164 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO E 164 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 164 " -0.026 5.00e-02 4.00e+02 ... (remaining 2255 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1693 2.75 - 3.29: 11933 3.29 - 3.83: 20310 3.83 - 4.36: 25114 4.36 - 4.90: 44401 Nonbonded interactions: 103451 Sorted by model distance: nonbonded pdb=" OD1 ASP F 157 " pdb=" O3' ADP F 401 " model vdw 2.214 3.040 nonbonded pdb=" O GLY E 156 " pdb=" OG1 THR E 303 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR G 69 " pdb=" OE2 GLU G 207 " model vdw 2.227 3.040 nonbonded pdb=" OG SER G 155 " pdb=" OG1 THR G 303 " model vdw 2.228 3.040 nonbonded pdb=" OD2 ASP F 56 " pdb=" NE2 HIS F 88 " model vdw 2.258 3.120 ... (remaining 103446 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 4.910 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 33.960 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 : 0.005 0.061 12897 Z= 0.208 Angle : 0.668 9.147 17487 Z= 0.350 Chirality : 0.047 0.212 1922 Planarity : 0.005 0.117 2258 Dihedral : 14.606 119.625 4766 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: -0.31 (0.21), residues: 1587 helix: -0.29 (0.23), residues: 486 sheet: 0.03 (0.29), residues: 336 loop : -0.08 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 433 HIS 0.005 0.001 HIS F 101 PHE 0.013 0.001 PHE A 31 TYR 0.014 0.002 TYR F 143 ARG 0.005 0.001 ARG A 110 Details of bonding type rmsd hydrogen bonds : bond 0.15473 ( 514) hydrogen bonds : angle 7.25031 ( 1356) covalent geometry : bond 0.00486 (12897) covalent geometry : angle 0.66797 (17487) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.505 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.5952 (ptt-90) cc_final: 0.5391 (ptt-90) REVERT: E 132 MET cc_start: 0.7286 (ppp) cc_final: 0.7081 (ppp) REVERT: G 260 THR cc_start: 0.8823 (p) cc_final: 0.8404 (p) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2284 time to fit residues: 53.0154 Evaluate side-chains 130 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 41 optimal weight: 0.0040 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 144 optimal weight: 0.0980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN G 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.141018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.118972 restraints weight = 17008.290| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.41 r_work: 0.3355 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12897 Z= 0.147 Angle : 0.596 9.266 17487 Z= 0.300 Chirality : 0.046 0.166 1922 Planarity : 0.005 0.080 2258 Dihedral : 7.817 106.713 1791 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.60 % Allowed : 5.95 % Favored : 93.45 % 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: 0.06 (0.21), residues: 1587 helix: 0.29 (0.25), residues: 486 sheet: -0.01 (0.28), residues: 332 loop : 0.06 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 433 HIS 0.004 0.001 HIS F 161 PHE 0.019 0.001 PHE A 216 TYR 0.013 0.001 TYR F 143 ARG 0.004 0.000 ARG F 335 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 514) hydrogen bonds : angle 5.39970 ( 1356) covalent geometry : bond 0.00350 (12897) covalent geometry : angle 0.59603 (17487) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 1.420 Fit side-chains REVERT: A 82 ARG cc_start: 0.6613 (ttp80) cc_final: 0.6229 (ttp80) REVERT: A 493 TYR cc_start: 0.6797 (p90) cc_final: 0.6494 (p90) REVERT: E 12 ASN cc_start: 0.8423 (p0) cc_final: 0.8164 (p0) REVERT: E 82 MET cc_start: 0.8290 (mmt) cc_final: 0.8013 (tpt) REVERT: F 325 MET cc_start: 0.8055 (mmt) cc_final: 0.7786 (mmt) outliers start: 8 outliers final: 6 residues processed: 150 average time/residue: 0.2282 time to fit residues: 50.9730 Evaluate side-chains 137 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 288 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 78 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 56 optimal weight: 0.3980 chunk 29 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 360 GLN G 87 HIS G 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.142003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.119231 restraints weight = 17215.777| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.41 r_work: 0.3351 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12897 Z= 0.141 Angle : 0.575 9.793 17487 Z= 0.287 Chirality : 0.045 0.169 1922 Planarity : 0.004 0.068 2258 Dihedral : 7.696 104.459 1791 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.04 % Allowed : 8.71 % Favored : 90.25 % 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: 0.11 (0.21), residues: 1587 helix: 0.40 (0.25), residues: 486 sheet: -0.04 (0.28), residues: 334 loop : 0.08 (0.23), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 433 HIS 0.007 0.001 HIS G 87 PHE 0.010 0.001 PHE G 31 TYR 0.014 0.001 TYR A 111 ARG 0.003 0.000 ARG A 90 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 514) hydrogen bonds : angle 5.15554 ( 1356) covalent geometry : bond 0.00338 (12897) covalent geometry : angle 0.57475 (17487) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 1.356 Fit side-chains REVERT: A 82 ARG cc_start: 0.6718 (ttp80) cc_final: 0.6448 (ttp-170) REVERT: A 493 TYR cc_start: 0.6790 (p90) cc_final: 0.6483 (p90) REVERT: E 82 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.8044 (tpt) REVERT: E 192 ILE cc_start: 0.8472 (tt) cc_final: 0.8260 (pt) REVERT: F 325 MET cc_start: 0.8017 (mmt) cc_final: 0.7688 (mmt) outliers start: 14 outliers final: 8 residues processed: 134 average time/residue: 0.2197 time to fit residues: 45.0514 Evaluate side-chains 134 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 288 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 75 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 HIS G 246 GLN G 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.137904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.115267 restraints weight = 16984.138| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.39 r_work: 0.3303 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 12897 Z= 0.239 Angle : 0.652 11.374 17487 Z= 0.327 Chirality : 0.049 0.207 1922 Planarity : 0.005 0.062 2258 Dihedral : 8.018 105.526 1791 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.49 % Allowed : 10.79 % Favored : 87.72 % 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: -0.23 (0.21), residues: 1587 helix: 0.13 (0.24), residues: 486 sheet: -0.14 (0.29), residues: 326 loop : -0.19 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 340 HIS 0.008 0.001 HIS G 87 PHE 0.018 0.002 PHE A 216 TYR 0.014 0.002 TYR G 143 ARG 0.006 0.001 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.04632 ( 514) hydrogen bonds : angle 5.28123 ( 1356) covalent geometry : bond 0.00590 (12897) covalent geometry : angle 0.65229 (17487) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 1.902 Fit side-chains REVERT: A 32 LYS cc_start: 0.7098 (mmmm) cc_final: 0.6431 (tptp) REVERT: A 479 LYS cc_start: 0.6686 (ptpt) cc_final: 0.6339 (pttp) REVERT: A 493 TYR cc_start: 0.6931 (p90) cc_final: 0.6566 (p90) REVERT: E 82 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8078 (tpt) REVERT: F 325 MET cc_start: 0.8189 (mmt) cc_final: 0.7809 (mmt) REVERT: G 72 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: G 260 THR cc_start: 0.8967 (p) cc_final: 0.8571 (p) outliers start: 20 outliers final: 13 residues processed: 141 average time/residue: 0.2818 time to fit residues: 61.5104 Evaluate side-chains 139 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 288 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 69 optimal weight: 0.5980 chunk 152 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 HIS G 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.140749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.118499 restraints weight = 16921.582| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.40 r_work: 0.3347 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12897 Z= 0.133 Angle : 0.574 11.213 17487 Z= 0.285 Chirality : 0.045 0.159 1922 Planarity : 0.004 0.058 2258 Dihedral : 7.715 103.787 1791 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.41 % Allowed : 12.05 % Favored : 86.53 % 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: -0.04 (0.21), residues: 1587 helix: 0.37 (0.24), residues: 486 sheet: -0.04 (0.29), residues: 324 loop : -0.14 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 340 HIS 0.007 0.001 HIS G 87 PHE 0.015 0.001 PHE A 216 TYR 0.011 0.001 TYR F 143 ARG 0.004 0.000 ARG A 82 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 514) hydrogen bonds : angle 5.04812 ( 1356) covalent geometry : bond 0.00319 (12897) covalent geometry : angle 0.57402 (17487) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 1.290 Fit side-chains REVERT: A 32 LYS cc_start: 0.7099 (mmmm) cc_final: 0.6449 (tptp) REVERT: A 479 LYS cc_start: 0.6599 (ptpt) cc_final: 0.6228 (pttp) REVERT: A 493 TYR cc_start: 0.6819 (p90) cc_final: 0.6499 (p90) REVERT: E 82 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.8049 (tpt) REVERT: E 305 MET cc_start: 0.8248 (mmt) cc_final: 0.7983 (mmt) REVERT: F 325 MET cc_start: 0.8143 (mmt) cc_final: 0.7741 (mmt) REVERT: G 72 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8054 (tt0) outliers start: 19 outliers final: 8 residues processed: 140 average time/residue: 0.2227 time to fit residues: 47.1929 Evaluate side-chains 130 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 288 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 123 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 108 optimal weight: 0.1980 chunk 62 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 52 optimal weight: 0.0980 chunk 33 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 246 GLN G 87 HIS G 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.142138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.119869 restraints weight = 17103.562| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.42 r_work: 0.3365 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12897 Z= 0.116 Angle : 0.553 10.079 17487 Z= 0.272 Chirality : 0.044 0.157 1922 Planarity : 0.004 0.056 2258 Dihedral : 7.456 100.257 1791 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.64 % Allowed : 12.65 % Favored : 85.71 % 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: 0.13 (0.21), residues: 1587 helix: 0.52 (0.24), residues: 486 sheet: 0.08 (0.29), residues: 321 loop : -0.04 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 340 HIS 0.008 0.001 HIS G 87 PHE 0.016 0.001 PHE A 216 TYR 0.010 0.001 TYR F 143 ARG 0.004 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.03272 ( 514) hydrogen bonds : angle 4.90625 ( 1356) covalent geometry : bond 0.00276 (12897) covalent geometry : angle 0.55274 (17487) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 1.484 Fit side-chains REVERT: A 32 LYS cc_start: 0.7138 (mmmm) cc_final: 0.6446 (tptp) REVERT: A 479 LYS cc_start: 0.6761 (ptpt) cc_final: 0.6377 (pttp) REVERT: A 493 TYR cc_start: 0.6739 (p90) cc_final: 0.6433 (p90) REVERT: E 82 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.8002 (tpt) REVERT: E 305 MET cc_start: 0.8196 (mmt) cc_final: 0.7988 (mmt) REVERT: F 325 MET cc_start: 0.8071 (mmt) cc_final: 0.7726 (mmt) REVERT: G 72 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8080 (tt0) outliers start: 22 outliers final: 13 residues processed: 142 average time/residue: 0.2884 time to fit residues: 61.8885 Evaluate side-chains 136 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 288 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 99 optimal weight: 0.1980 chunk 89 optimal weight: 0.0270 chunk 104 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 12 ASN G 87 HIS G 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.144728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.122311 restraints weight = 16853.104| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.42 r_work: 0.3405 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12897 Z= 0.098 Angle : 0.534 8.582 17487 Z= 0.260 Chirality : 0.044 0.153 1922 Planarity : 0.004 0.054 2258 Dihedral : 7.216 96.602 1791 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.49 % Allowed : 12.95 % Favored : 85.57 % 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: 0.32 (0.21), residues: 1587 helix: 0.67 (0.25), residues: 486 sheet: 0.20 (0.29), residues: 321 loop : 0.07 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 433 HIS 0.008 0.001 HIS G 87 PHE 0.008 0.001 PHE A 112 TYR 0.009 0.001 TYR F 143 ARG 0.003 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.02949 ( 514) hydrogen bonds : angle 4.76504 ( 1356) covalent geometry : bond 0.00227 (12897) covalent geometry : angle 0.53356 (17487) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 1.908 Fit side-chains REVERT: A 32 LYS cc_start: 0.7088 (mmmm) cc_final: 0.6439 (tptp) REVERT: A 479 LYS cc_start: 0.6585 (ptpt) cc_final: 0.6249 (pttp) REVERT: E 82 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7976 (tpt) REVERT: F 107 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6932 (tm-30) REVERT: F 325 MET cc_start: 0.7987 (mmt) cc_final: 0.7624 (mmt) REVERT: G 72 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8038 (tt0) outliers start: 20 outliers final: 13 residues processed: 145 average time/residue: 0.2455 time to fit residues: 53.4442 Evaluate side-chains 140 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 288 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 82 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 99 optimal weight: 0.3980 chunk 115 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 111 optimal weight: 0.0570 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN A 324 GLN G 87 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.144024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.122042 restraints weight = 16978.950| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.38 r_work: 0.3396 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12897 Z= 0.102 Angle : 0.547 8.274 17487 Z= 0.267 Chirality : 0.044 0.152 1922 Planarity : 0.004 0.053 2258 Dihedral : 7.081 93.649 1791 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.64 % Allowed : 13.62 % Favored : 84.75 % 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: 0.37 (0.21), residues: 1587 helix: 0.72 (0.25), residues: 486 sheet: 0.20 (0.30), residues: 311 loop : 0.11 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 433 HIS 0.008 0.001 HIS G 87 PHE 0.021 0.001 PHE A 216 TYR 0.009 0.001 TYR F 143 ARG 0.005 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.02970 ( 514) hydrogen bonds : angle 4.71131 ( 1356) covalent geometry : bond 0.00237 (12897) covalent geometry : angle 0.54683 (17487) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 1.500 Fit side-chains REVERT: A 32 LYS cc_start: 0.7119 (mmmm) cc_final: 0.6494 (tptp) REVERT: F 107 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6969 (tm-30) REVERT: F 325 MET cc_start: 0.8013 (mmt) cc_final: 0.7656 (mmt) REVERT: G 72 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8071 (tt0) outliers start: 22 outliers final: 17 residues processed: 140 average time/residue: 0.2280 time to fit residues: 47.9293 Evaluate side-chains 138 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 288 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 147 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN G 87 HIS G 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.141845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.119707 restraints weight = 16993.747| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.40 r_work: 0.3364 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12897 Z= 0.141 Angle : 0.573 9.090 17487 Z= 0.280 Chirality : 0.045 0.154 1922 Planarity : 0.004 0.052 2258 Dihedral : 7.222 93.216 1791 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.86 % Allowed : 13.76 % Favored : 84.38 % 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: 0.28 (0.21), residues: 1587 helix: 0.62 (0.24), residues: 486 sheet: 0.17 (0.30), residues: 311 loop : 0.06 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 340 HIS 0.008 0.001 HIS G 87 PHE 0.011 0.001 PHE G 31 TYR 0.010 0.001 TYR G 69 ARG 0.008 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 514) hydrogen bonds : angle 4.78378 ( 1356) covalent geometry : bond 0.00340 (12897) covalent geometry : angle 0.57274 (17487) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 1.394 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.7211 (mmmm) cc_final: 0.6570 (tptp) REVERT: F 107 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7117 (tm-30) REVERT: F 325 MET cc_start: 0.8070 (mmt) cc_final: 0.7708 (mmt) REVERT: G 72 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8046 (tt0) outliers start: 25 outliers final: 19 residues processed: 144 average time/residue: 0.2384 time to fit residues: 51.5367 Evaluate side-chains 143 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 288 ASP Chi-restraints excluded: chain G residue 327 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 0.0670 chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 87 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.140851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.118568 restraints weight = 16965.018| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.40 r_work: 0.3350 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12897 Z= 0.155 Angle : 0.590 11.377 17487 Z= 0.290 Chirality : 0.046 0.155 1922 Planarity : 0.004 0.052 2258 Dihedral : 7.401 95.599 1791 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.71 % Allowed : 13.84 % Favored : 84.45 % 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: 0.20 (0.21), residues: 1587 helix: 0.56 (0.24), residues: 486 sheet: 0.13 (0.30), residues: 311 loop : 0.00 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 340 HIS 0.008 0.001 HIS G 87 PHE 0.012 0.001 PHE G 31 TYR 0.011 0.001 TYR G 143 ARG 0.008 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 514) hydrogen bonds : angle 4.87079 ( 1356) covalent geometry : bond 0.00379 (12897) covalent geometry : angle 0.58953 (17487) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 1.503 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.7252 (mmmm) cc_final: 0.6619 (tptp) REVERT: A 82 ARG cc_start: 0.6609 (ttp-170) cc_final: 0.6342 (ttp80) REVERT: F 107 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7285 (tm-30) REVERT: F 325 MET cc_start: 0.8125 (mmt) cc_final: 0.7759 (mmt) REVERT: G 72 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8054 (tt0) outliers start: 23 outliers final: 18 residues processed: 141 average time/residue: 0.2231 time to fit residues: 47.5561 Evaluate side-chains 140 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 72 GLU Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 288 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 75 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 144 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 87 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.140002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.117730 restraints weight = 17009.514| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.40 r_work: 0.3337 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12897 Z= 0.171 Angle : 0.600 10.871 17487 Z= 0.296 Chirality : 0.046 0.154 1922 Planarity : 0.004 0.052 2258 Dihedral : 7.530 99.130 1791 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.71 % Allowed : 13.99 % Favored : 84.30 % 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: 0.07 (0.21), residues: 1587 helix: 0.48 (0.24), residues: 486 sheet: -0.06 (0.29), residues: 311 loop : -0.04 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 340 HIS 0.008 0.001 HIS G 87 PHE 0.013 0.001 PHE G 31 TYR 0.012 0.001 TYR G 143 ARG 0.010 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 514) hydrogen bonds : angle 4.91660 ( 1356) covalent geometry : bond 0.00418 (12897) covalent geometry : angle 0.60032 (17487) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7221.74 seconds wall clock time: 127 minutes 35.67 seconds (7655.67 seconds total)