Starting phenix.real_space_refine on Sat Oct 11 07:11:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vo6_43365/10_2025/8vo6_43365.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vo6_43365/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8vo6_43365/10_2025/8vo6_43365.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vo6_43365/10_2025/8vo6_43365.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vo6_43365/10_2025/8vo6_43365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vo6_43365/10_2025/8vo6_43365.map" } resolution = 3.1 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 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 2.56, per 1000 atoms: 0.20 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: 1.10 Conformation dependent library (CDL) restraints added in 616.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.61 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: 2.37 Time building geometry restraints manager: 1.47 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: 6.010 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 12.710 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.670 ------------------------------------------------------------------------------- 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 : 8.85 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG A 110 TYR 0.014 0.002 TYR F 143 PHE 0.013 0.001 PHE A 31 TRP 0.022 0.002 TRP A 433 HIS 0.005 0.001 HIS F 101 Details of bonding type rmsd covalent geometry : bond 0.00486 (12897) covalent geometry : angle 0.66797 (17487) hydrogen bonds : bond 0.15473 ( 514) hydrogen bonds : angle 7.25031 ( 1356) *********************** 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 : 0.496 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: 0.1002 time to fit residues: 23.6023 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 : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 59 GLN G 115 ASN G 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.140949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.118837 restraints weight = 17044.422| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.42 r_work: 0.3352 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12897 Z= 0.149 Angle : 0.598 9.335 17487 Z= 0.302 Chirality : 0.046 0.165 1922 Planarity : 0.005 0.079 2258 Dihedral : 7.845 107.210 1791 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.60 % Allowed : 5.88 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.21), residues: 1587 helix: 0.28 (0.25), residues: 486 sheet: -0.02 (0.28), residues: 332 loop : 0.05 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 335 TYR 0.013 0.001 TYR F 143 PHE 0.018 0.001 PHE A 216 TRP 0.013 0.001 TRP A 433 HIS 0.004 0.001 HIS F 161 Details of bonding type rmsd covalent geometry : bond 0.00356 (12897) covalent geometry : angle 0.59814 (17487) hydrogen bonds : bond 0.04074 ( 514) hydrogen bonds : angle 5.42063 ( 1356) *********************** 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 : 0.432 Fit side-chains REVERT: A 82 ARG cc_start: 0.6680 (ttp80) cc_final: 0.6288 (ttp80) REVERT: A 493 TYR cc_start: 0.6803 (p90) cc_final: 0.6497 (p90) REVERT: E 12 ASN cc_start: 0.8420 (p0) cc_final: 0.8168 (p0) REVERT: E 82 MET cc_start: 0.8290 (mmt) cc_final: 0.8000 (tpt) REVERT: F 325 MET cc_start: 0.8063 (mmt) cc_final: 0.7801 (mmt) outliers start: 8 outliers final: 6 residues processed: 149 average time/residue: 0.1061 time to fit residues: 23.6628 Evaluate side-chains 136 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 96 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 247 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 123 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 56 optimal weight: 0.0270 chunk 57 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 59 optimal weight: 0.2980 chunk 1 optimal weight: 0.5980 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 246 GLN F 360 GLN G 87 HIS G 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.143517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.121021 restraints weight = 17207.106| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.40 r_work: 0.3378 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 : 0.003 0.033 12897 Z= 0.113 Angle : 0.552 8.948 17487 Z= 0.275 Chirality : 0.044 0.162 1922 Planarity : 0.004 0.067 2258 Dihedral : 7.554 103.413 1791 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.89 % Allowed : 8.48 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.21), residues: 1587 helix: 0.49 (0.25), residues: 486 sheet: 0.06 (0.28), residues: 331 loop : 0.15 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 90 TYR 0.011 0.001 TYR F 143 PHE 0.008 0.001 PHE G 31 TRP 0.014 0.001 TRP A 433 HIS 0.007 0.001 HIS G 87 Details of bonding type rmsd covalent geometry : bond 0.00264 (12897) covalent geometry : angle 0.55180 (17487) hydrogen bonds : bond 0.03446 ( 514) hydrogen bonds : angle 5.09432 ( 1356) *********************** 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: 12 poor density : 129 time to evaluate : 0.526 Fit side-chains REVERT: A 32 LYS cc_start: 0.6781 (mmmm) cc_final: 0.6303 (tptp) REVERT: A 82 ARG cc_start: 0.6718 (ttp80) cc_final: 0.6441 (ttp-170) REVERT: A 493 TYR cc_start: 0.6741 (p90) cc_final: 0.6445 (p90) REVERT: E 82 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.8009 (tpt) REVERT: F 107 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7098 (tm-30) REVERT: F 325 MET cc_start: 0.7998 (mmt) cc_final: 0.7676 (mmt) outliers start: 12 outliers final: 7 residues processed: 135 average time/residue: 0.1065 time to fit residues: 21.7317 Evaluate side-chains 131 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 82 MET Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 201 VAL 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 97 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 158 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 2 optimal weight: 0.0670 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 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 = 0.3776 r_free = 0.3776 target = 0.143262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.121204 restraints weight = 16998.979| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.49 r_work: 0.3366 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12897 Z= 0.115 Angle : 0.541 7.642 17487 Z= 0.268 Chirality : 0.044 0.160 1922 Planarity : 0.004 0.061 2258 Dihedral : 7.347 100.079 1791 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.26 % Allowed : 9.82 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.21), residues: 1587 helix: 0.55 (0.25), residues: 486 sheet: 0.09 (0.28), residues: 322 loop : 0.12 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 271 TYR 0.010 0.001 TYR F 143 PHE 0.018 0.001 PHE A 216 TRP 0.014 0.001 TRP A 433 HIS 0.007 0.001 HIS G 87 Details of bonding type rmsd covalent geometry : bond 0.00271 (12897) covalent geometry : angle 0.54110 (17487) hydrogen bonds : bond 0.03291 ( 514) hydrogen bonds : angle 4.93156 ( 1356) *********************** 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 154 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.532 Fit side-chains REVERT: A 32 LYS cc_start: 0.6810 (mmmm) cc_final: 0.6364 (tptp) REVERT: A 479 LYS cc_start: 0.6682 (ptpt) cc_final: 0.6357 (pttp) REVERT: A 493 TYR cc_start: 0.6756 (p90) cc_final: 0.6445 (p90) REVERT: E 82 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.8008 (tpt) REVERT: F 325 MET cc_start: 0.8036 (mmt) cc_final: 0.7750 (mmt) REVERT: G 72 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8080 (tt0) outliers start: 17 outliers final: 7 residues processed: 146 average time/residue: 0.1071 time to fit residues: 23.7887 Evaluate side-chains 139 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 82 MET Chi-restraints excluded: chain E residue 358 THR 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 288 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 131 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 99 optimal weight: 0.0770 chunk 128 optimal weight: 0.0270 chunk 74 optimal weight: 0.1980 chunk 69 optimal weight: 1.9990 chunk 122 optimal weight: 0.2980 chunk 113 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 112 optimal weight: 0.5980 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 12 ASN ** 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 = 0.3808 r_free = 0.3808 target = 0.146088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.124118 restraints weight = 17002.139| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.47 r_work: 0.3407 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1510 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= 0.089 Angle : 0.516 8.386 17487 Z= 0.254 Chirality : 0.043 0.154 1922 Planarity : 0.004 0.055 2258 Dihedral : 6.999 95.434 1791 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.04 % Allowed : 10.94 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.21), residues: 1587 helix: 0.76 (0.25), residues: 483 sheet: 0.26 (0.29), residues: 315 loop : 0.15 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 82 TYR 0.009 0.001 TYR F 143 PHE 0.008 0.001 PHE A 195 TRP 0.011 0.001 TRP A 433 HIS 0.008 0.001 HIS G 87 Details of bonding type rmsd covalent geometry : bond 0.00197 (12897) covalent geometry : angle 0.51645 (17487) hydrogen bonds : bond 0.02807 ( 514) hydrogen bonds : angle 4.75561 ( 1356) *********************** 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 153 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.520 Fit side-chains REVERT: A 32 LYS cc_start: 0.7093 (mmmm) cc_final: 0.6410 (tptp) REVERT: A 82 ARG cc_start: 0.6571 (ttp80) cc_final: 0.6324 (ttp-170) REVERT: A 284 ASN cc_start: 0.8259 (p0) cc_final: 0.8059 (p0) REVERT: A 433 TRP cc_start: 0.7532 (m-10) cc_final: 0.7274 (m-10) REVERT: A 479 LYS cc_start: 0.6739 (ptpt) cc_final: 0.6441 (pttp) REVERT: F 325 MET cc_start: 0.7925 (mmt) cc_final: 0.7657 (mmt) outliers start: 14 outliers final: 7 residues processed: 148 average time/residue: 0.1125 time to fit residues: 25.0044 Evaluate side-chains 131 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL 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 358 THR Chi-restraints excluded: chain F residue 201 VAL 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 73 optimal weight: 0.0070 chunk 89 optimal weight: 0.0670 chunk 101 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 59 GLN 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 = 0.3782 r_free = 0.3782 target = 0.143830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.121836 restraints weight = 16954.930| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.39 r_work: 0.3390 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12897 Z= 0.117 Angle : 0.541 7.696 17487 Z= 0.266 Chirality : 0.044 0.158 1922 Planarity : 0.004 0.052 2258 Dihedral : 6.944 92.066 1791 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.49 % Allowed : 12.13 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.21), residues: 1587 helix: 0.73 (0.25), residues: 486 sheet: 0.24 (0.29), residues: 315 loop : 0.13 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 90 TYR 0.010 0.001 TYR A 493 PHE 0.017 0.001 PHE A 216 TRP 0.009 0.001 TRP G 340 HIS 0.008 0.001 HIS G 87 Details of bonding type rmsd covalent geometry : bond 0.00277 (12897) covalent geometry : angle 0.54114 (17487) hydrogen bonds : bond 0.03130 ( 514) hydrogen bonds : angle 4.75988 ( 1356) *********************** 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: 20 poor density : 128 time to evaluate : 0.538 Fit side-chains REVERT: A 32 LYS cc_start: 0.7082 (mmmm) cc_final: 0.6488 (tptp) REVERT: A 433 TRP cc_start: 0.7607 (m-10) cc_final: 0.7362 (m-10) REVERT: A 479 LYS cc_start: 0.6685 (ptpt) cc_final: 0.6380 (pttp) REVERT: E 305 MET cc_start: 0.8172 (mmt) cc_final: 0.7899 (mmt) REVERT: F 107 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6945 (tm-30) REVERT: F 325 MET cc_start: 0.7966 (mmt) cc_final: 0.7672 (mmt) outliers start: 20 outliers final: 11 residues processed: 143 average time/residue: 0.1075 time to fit residues: 23.4242 Evaluate side-chains 134 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 VAL 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 65 LEU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 250 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 26 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 15 optimal weight: 0.2980 chunk 7 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.136329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.113838 restraints weight = 17190.186| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.40 r_work: 0.3276 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 12897 Z= 0.315 Angle : 0.729 13.708 17487 Z= 0.364 Chirality : 0.052 0.193 1922 Planarity : 0.005 0.055 2258 Dihedral : 7.893 103.858 1791 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.01 % Allowed : 12.50 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.21), residues: 1587 helix: 0.11 (0.23), residues: 486 sheet: -0.12 (0.28), residues: 328 loop : -0.27 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 335 TYR 0.021 0.002 TYR A 493 PHE 0.021 0.002 PHE G 31 TRP 0.017 0.002 TRP A 171 HIS 0.008 0.002 HIS G 87 Details of bonding type rmsd covalent geometry : bond 0.00779 (12897) covalent geometry : angle 0.72950 (17487) hydrogen bonds : bond 0.05234 ( 514) hydrogen bonds : angle 5.31381 ( 1356) *********************** 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: 27 poor density : 123 time to evaluate : 0.604 Fit side-chains REVERT: A 82 ARG cc_start: 0.6798 (ttp-170) cc_final: 0.6405 (ttp80) REVERT: A 479 LYS cc_start: 0.6713 (ptpt) cc_final: 0.6324 (pttp) REVERT: F 325 MET cc_start: 0.8190 (mmt) cc_final: 0.7819 (mmt) REVERT: G 72 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8139 (tt0) REVERT: G 260 THR cc_start: 0.8975 (p) cc_final: 0.8593 (p) outliers start: 27 outliers final: 16 residues processed: 144 average time/residue: 0.1119 time to fit residues: 24.6094 Evaluate side-chains 136 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 VAL 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 477 VAL 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 65 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain G residue 34 ILE 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 108 optimal weight: 0.2980 chunk 99 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 150 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 15 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.140915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.118774 restraints weight = 16814.554| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.39 r_work: 0.3350 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12897 Z= 0.127 Angle : 0.581 10.653 17487 Z= 0.286 Chirality : 0.045 0.156 1922 Planarity : 0.004 0.054 2258 Dihedral : 7.393 99.991 1791 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.34 % Allowed : 13.54 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.21), residues: 1587 helix: 0.45 (0.24), residues: 486 sheet: 0.02 (0.29), residues: 321 loop : -0.13 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 68 TYR 0.017 0.001 TYR A 493 PHE 0.009 0.001 PHE G 31 TRP 0.012 0.001 TRP E 340 HIS 0.008 0.001 HIS G 87 Details of bonding type rmsd covalent geometry : bond 0.00305 (12897) covalent geometry : angle 0.58123 (17487) hydrogen bonds : bond 0.03386 ( 514) hydrogen bonds : angle 4.96953 ( 1356) *********************** 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 142 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.564 Fit side-chains REVERT: A 32 LYS cc_start: 0.7097 (mmmm) cc_final: 0.6487 (tptp) REVERT: A 82 ARG cc_start: 0.6735 (ttp-170) cc_final: 0.6451 (ttt180) REVERT: A 479 LYS cc_start: 0.6743 (ptpt) cc_final: 0.6369 (pttp) REVERT: F 325 MET cc_start: 0.8108 (mmt) cc_final: 0.7771 (mmt) REVERT: G 72 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8054 (tt0) outliers start: 18 outliers final: 14 residues processed: 139 average time/residue: 0.1098 time to fit residues: 23.1251 Evaluate side-chains 135 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 93 ILE 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 180 LEU 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 G residue 34 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 128 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 9 optimal weight: 0.0870 chunk 63 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.141798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.119671 restraints weight = 16917.943| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.39 r_work: 0.3361 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12897 Z= 0.124 Angle : 0.569 9.561 17487 Z= 0.278 Chirality : 0.045 0.152 1922 Planarity : 0.004 0.052 2258 Dihedral : 7.248 96.196 1791 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.49 % Allowed : 13.39 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.21), residues: 1587 helix: 0.57 (0.24), residues: 486 sheet: -0.09 (0.30), residues: 301 loop : -0.03 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 68 TYR 0.018 0.001 TYR A 493 PHE 0.020 0.001 PHE A 216 TRP 0.011 0.001 TRP E 340 HIS 0.008 0.001 HIS G 87 Details of bonding type rmsd covalent geometry : bond 0.00296 (12897) covalent geometry : angle 0.56903 (17487) hydrogen bonds : bond 0.03299 ( 514) hydrogen bonds : angle 4.86922 ( 1356) *********************** 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 143 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.7140 (mmmm) cc_final: 0.6476 (tptp) REVERT: A 82 ARG cc_start: 0.6823 (ttp-170) cc_final: 0.6513 (ttt180) REVERT: F 325 MET cc_start: 0.8072 (mmt) cc_final: 0.7725 (mmt) REVERT: G 72 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8084 (tt0) outliers start: 20 outliers final: 17 residues processed: 139 average time/residue: 0.1072 time to fit residues: 22.4498 Evaluate side-chains 139 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 93 ILE 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 381 ILE 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 65 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain G residue 34 ILE 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 287 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 8 optimal weight: 10.0000 chunk 157 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.138647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.116367 restraints weight = 17024.468| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.39 r_work: 0.3316 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12897 Z= 0.210 Angle : 0.638 11.060 17487 Z= 0.314 Chirality : 0.048 0.166 1922 Planarity : 0.004 0.053 2258 Dihedral : 7.583 101.004 1791 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.71 % Allowed : 13.32 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.21), residues: 1587 helix: 0.32 (0.24), residues: 486 sheet: -0.17 (0.29), residues: 311 loop : -0.18 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 68 TYR 0.022 0.002 TYR A 493 PHE 0.015 0.001 PHE G 31 TRP 0.014 0.002 TRP G 340 HIS 0.008 0.001 HIS G 87 Details of bonding type rmsd covalent geometry : bond 0.00521 (12897) covalent geometry : angle 0.63844 (17487) hydrogen bonds : bond 0.04186 ( 514) hydrogen bonds : angle 5.05390 ( 1356) ********************** 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 141 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: A 82 ARG cc_start: 0.6908 (ttp-170) cc_final: 0.6663 (ttt180) REVERT: E 305 MET cc_start: 0.8196 (mmt) cc_final: 0.7962 (mmt) REVERT: F 325 MET cc_start: 0.8197 (mmt) cc_final: 0.7818 (mmt) REVERT: G 72 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8050 (tt0) outliers start: 23 outliers final: 19 residues processed: 138 average time/residue: 0.1044 time to fit residues: 22.0821 Evaluate side-chains 138 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 93 ILE 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 381 ILE 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 65 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain G residue 34 ILE 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 133 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 89 optimal weight: 0.0980 chunk 34 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 106 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 87 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.140075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.117785 restraints weight = 17013.024| |-----------------------------------------------------------------------------| r_work (start): 0.3448 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: 0.8193 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12897 Z= 0.155 Angle : 0.594 10.487 17487 Z= 0.291 Chirality : 0.046 0.153 1922 Planarity : 0.004 0.052 2258 Dihedral : 7.503 100.365 1791 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.64 % Allowed : 13.39 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.21), residues: 1587 helix: 0.44 (0.24), residues: 486 sheet: -0.18 (0.30), residues: 301 loop : -0.17 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 68 TYR 0.019 0.001 TYR A 493 PHE 0.012 0.001 PHE G 31 TRP 0.013 0.001 TRP E 340 HIS 0.008 0.001 HIS G 87 Details of bonding type rmsd covalent geometry : bond 0.00379 (12897) covalent geometry : angle 0.59363 (17487) hydrogen bonds : bond 0.03612 ( 514) hydrogen bonds : angle 4.95337 ( 1356) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3223.28 seconds wall clock time: 56 minutes 7.53 seconds (3367.53 seconds total)