Starting phenix.real_space_refine on Sat Aug 23 01:15:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ure_42491/08_2025/8ure_42491.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ure_42491/08_2025/8ure_42491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ure_42491/08_2025/8ure_42491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ure_42491/08_2025/8ure_42491.map" model { file = "/net/cci-nas-00/data/ceres_data/8ure_42491/08_2025/8ure_42491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ure_42491/08_2025/8ure_42491.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.002 sd= 0.037 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: 3 Type Number sf(0) Gaussians C 5312 2.51 5 N 1792 2.21 5 O 1792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8896 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 2094 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 346} Link IDs: {'PTRANS': 4, 'TRANS': 417} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1213 Unresolved non-hydrogen angles: 1518 Unresolved non-hydrogen dihedrals: 957 Unresolved non-hydrogen chiralities: 134 Planarities with less than four sites: {'PHE:plan': 5, 'ASP:plan': 20, 'ASN:plan1': 6, 'TRP:plan': 3, 'GLU:plan': 62, 'HIS:plan': 4, 'TYR:plan': 2, 'GLN:plan1': 13, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 604 Chain: "B" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 2094 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 346} Link IDs: {'PTRANS': 4, 'TRANS': 417} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1213 Unresolved non-hydrogen angles: 1518 Unresolved non-hydrogen dihedrals: 957 Unresolved non-hydrogen chiralities: 134 Planarities with less than four sites: {'PHE:plan': 5, 'ASP:plan': 20, 'ASN:plan1': 6, 'TRP:plan': 3, 'GLU:plan': 62, 'HIS:plan': 4, 'TYR:plan': 2, 'GLN:plan1': 13, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 604 Chain: "D" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "E" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 2094 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 346} Link IDs: {'PTRANS': 4, 'TRANS': 417} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1213 Unresolved non-hydrogen angles: 1518 Unresolved non-hydrogen dihedrals: 957 Unresolved non-hydrogen chiralities: 134 Planarities with less than four sites: {'PHE:plan': 5, 'ASP:plan': 20, 'ASN:plan1': 6, 'TRP:plan': 3, 'GLU:plan': 62, 'HIS:plan': 4, 'TYR:plan': 2, 'GLN:plan1': 13, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 604 Chain: "F" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "G" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 2094 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 346} Link IDs: {'PTRANS': 4, 'TRANS': 417} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1213 Unresolved non-hydrogen angles: 1518 Unresolved non-hydrogen dihedrals: 957 Unresolved non-hydrogen chiralities: 134 Planarities with less than four sites: {'PHE:plan': 5, 'ASP:plan': 20, 'ASN:plan1': 6, 'TRP:plan': 3, 'GLU:plan': 62, 'HIS:plan': 4, 'TYR:plan': 2, 'GLN:plan1': 13, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 604 Chain: "H" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 25} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 2.17, per 1000 atoms: 0.24 Number of scatterers: 8896 At special positions: 0 Unit cell: (154.687, 155.925, 65.5875, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1792 8.00 N 1792 7.00 C 5312 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: 0.96 Conformation dependent library (CDL) restraints added in 491.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3456 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 5 sheets defined 80.5% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 removed outlier: 3.840A pdb=" N MET A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N HIS A 20 " --> pdb=" O TRP A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 68 Processing helix chain 'A' and resid 70 through 96 removed outlier: 3.663A pdb=" N ARG A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS A 95 " --> pdb=" O GLU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 115 Processing helix chain 'A' and resid 117 through 134 removed outlier: 3.906A pdb=" N LYS A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 154 Processing helix chain 'A' and resid 159 through 176 Processing helix chain 'A' and resid 178 through 195 removed outlier: 3.532A pdb=" N ALA A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 224 Processing helix chain 'A' and resid 227 through 248 removed outlier: 3.741A pdb=" N LYS A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 267 removed outlier: 4.034A pdb=" N ALA A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 290 removed outlier: 3.718A pdb=" N LYS A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 316 Processing helix chain 'A' and resid 336 through 355 removed outlier: 4.039A pdb=" N LYS A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 400 Processing helix chain 'A' and resid 403 through 421 removed outlier: 3.951A pdb=" N ARG A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 447 removed outlier: 4.356A pdb=" N GLU B 447 " --> pdb=" O LYS B 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 28 Processing helix chain 'C' and resid 49 through 68 Processing helix chain 'C' and resid 70 through 96 removed outlier: 3.693A pdb=" N ARG C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU C 94 " --> pdb=" O GLU C 90 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 115 removed outlier: 3.556A pdb=" N GLU C 114 " --> pdb=" O ARG C 110 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 134 Processing helix chain 'C' and resid 136 through 155 Processing helix chain 'C' and resid 159 through 176 removed outlier: 3.642A pdb=" N LEU C 163 " --> pdb=" O PRO C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 195 Processing helix chain 'C' and resid 197 through 224 Processing helix chain 'C' and resid 227 through 247 Processing helix chain 'C' and resid 249 through 267 removed outlier: 3.607A pdb=" N ALA C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 263 " --> pdb=" O ARG C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 289 Processing helix chain 'C' and resid 292 through 316 removed outlier: 3.983A pdb=" N LYS C 300 " --> pdb=" O ALA C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 355 Processing helix chain 'C' and resid 376 through 400 Processing helix chain 'C' and resid 403 through 422 removed outlier: 4.000A pdb=" N GLY C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 446 Processing helix chain 'E' and resid 10 through 28 Processing helix chain 'E' and resid 49 through 68 Processing helix chain 'E' and resid 70 through 93 removed outlier: 3.540A pdb=" N ARG E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 96 No H-bonds generated for 'chain 'E' and resid 94 through 96' Processing helix chain 'E' and resid 98 through 115 Processing helix chain 'E' and resid 117 through 134 Processing helix chain 'E' and resid 136 through 155 removed outlier: 3.534A pdb=" N ARG E 155 " --> pdb=" O ALA E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 176 removed outlier: 4.031A pdb=" N LEU E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 195 Processing helix chain 'E' and resid 197 through 224 removed outlier: 3.641A pdb=" N LEU E 201 " --> pdb=" O ASP E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 247 removed outlier: 3.824A pdb=" N LYS E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 267 removed outlier: 3.883A pdb=" N ALA E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 290 removed outlier: 3.520A pdb=" N LYS E 278 " --> pdb=" O SER E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 316 Processing helix chain 'E' and resid 336 through 355 removed outlier: 4.579A pdb=" N LYS E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 400 Processing helix chain 'E' and resid 403 through 421 removed outlier: 3.601A pdb=" N GLU E 419 " --> pdb=" O LEU E 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 448 removed outlier: 3.627A pdb=" N GLU F 448 " --> pdb=" O LEU F 444 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 28 removed outlier: 3.784A pdb=" N LYS G 19 " --> pdb=" O GLU G 15 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N HIS G 20 " --> pdb=" O TRP G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 68 Processing helix chain 'G' and resid 70 through 96 Processing helix chain 'G' and resid 98 through 115 removed outlier: 3.818A pdb=" N ARG G 106 " --> pdb=" O ARG G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 134 Processing helix chain 'G' and resid 136 through 155 Processing helix chain 'G' and resid 159 through 176 removed outlier: 3.793A pdb=" N LEU G 163 " --> pdb=" O PRO G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 195 Processing helix chain 'G' and resid 197 through 224 Processing helix chain 'G' and resid 227 through 248 removed outlier: 4.068A pdb=" N LYS G 235 " --> pdb=" O SER G 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 267 Processing helix chain 'G' and resid 270 through 291 removed outlier: 3.569A pdb=" N LYS G 278 " --> pdb=" O SER G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 316 Processing helix chain 'G' and resid 336 through 355 removed outlier: 4.651A pdb=" N ILE G 348 " --> pdb=" O MET G 344 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 376 through 400 Processing helix chain 'G' and resid 403 through 421 Processing helix chain 'H' and resid 424 through 446 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 removed outlier: 3.763A pdb=" N GLU A 40 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL G 358 " --> pdb=" O PHE A 36 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA G 327 " --> pdb=" O GLY G 324 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY G 324 " --> pdb=" O ALA G 327 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE G 329 " --> pdb=" O HIS G 322 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS G 322 " --> pdb=" O ILE G 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 318 through 323 removed outlier: 4.051A pdb=" N ARG A 318 " --> pdb=" O GLU A 333 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS A 322 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 329 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 358 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU C 40 " --> pdb=" O LYS C 37 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY C 39 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 319 through 321 removed outlier: 3.813A pdb=" N THR C 357 " --> pdb=" O VAL C 372 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL C 358 " --> pdb=" O PHE E 36 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU E 40 " --> pdb=" O LYS E 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 318 through 320 removed outlier: 4.173A pdb=" N ARG E 318 " --> pdb=" O GLU E 333 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA E 327 " --> pdb=" O GLY E 324 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY E 324 " --> pdb=" O ALA E 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 318 through 320 removed outlier: 4.173A pdb=" N ARG E 318 " --> pdb=" O GLU E 333 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR E 357 " --> pdb=" O VAL E 372 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL E 358 " --> pdb=" O PHE G 36 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU G 40 " --> pdb=" O LYS G 37 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLY G 39 " --> pdb=" O ASN G 8 " (cutoff:3.500A) 1258 hydrogen bonds defined for protein. 3732 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: 1.22 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 1792 1.28 - 1.35: 1784 1.35 - 1.42: 0 1.42 - 1.48: 1785 1.48 - 1.55: 3527 Bond restraints: 8888 Sorted by residual: bond pdb=" N VAL C 317 " pdb=" CA VAL C 317 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.14e-02 7.69e+03 5.55e+00 bond pdb=" N THR G 7 " pdb=" CA THR G 7 " ideal model delta sigma weight residual 1.454 1.482 -0.028 1.29e-02 6.01e+03 4.79e+00 bond pdb=" N LYS G 293 " pdb=" CA LYS G 293 " ideal model delta sigma weight residual 1.459 1.483 -0.025 1.16e-02 7.43e+03 4.52e+00 bond pdb=" N LYS E 27 " pdb=" CA LYS E 27 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.41e+00 bond pdb=" N GLY A 157 " pdb=" CA GLY A 157 " ideal model delta sigma weight residual 1.447 1.472 -0.026 1.24e-02 6.50e+03 4.26e+00 ... (remaining 8883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 8267 1.30 - 2.59: 3224 2.59 - 3.89: 770 3.89 - 5.19: 121 5.19 - 6.49: 10 Bond angle restraints: 12392 Sorted by residual: angle pdb=" CA HIS E 336 " pdb=" C HIS E 336 " pdb=" N PRO E 337 " ideal model delta sigma weight residual 118.23 122.92 -4.69 9.20e-01 1.18e+00 2.59e+01 angle pdb=" CA HIS A 336 " pdb=" C HIS A 336 " pdb=" N PRO A 337 " ideal model delta sigma weight residual 117.67 122.63 -4.96 1.01e+00 9.80e-01 2.41e+01 angle pdb=" CA HIS C 336 " pdb=" C HIS C 336 " pdb=" N PRO C 337 " ideal model delta sigma weight residual 117.67 122.14 -4.47 1.01e+00 9.80e-01 1.96e+01 angle pdb=" N ASP G 117 " pdb=" CA ASP G 117 " pdb=" C ASP G 117 " ideal model delta sigma weight residual 108.41 114.90 -6.49 1.63e+00 3.76e-01 1.58e+01 angle pdb=" N ASP E 117 " pdb=" CA ASP E 117 " pdb=" C ASP E 117 " ideal model delta sigma weight residual 108.52 114.99 -6.47 1.63e+00 3.76e-01 1.57e+01 ... (remaining 12387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.79: 4567 5.79 - 11.57: 560 11.57 - 17.36: 79 17.36 - 23.14: 27 23.14 - 28.93: 7 Dihedral angle restraints: 5240 sinusoidal: 0 harmonic: 5240 Sorted by residual: dihedral pdb=" CA TRP A 16 " pdb=" C TRP A 16 " pdb=" N ILE A 17 " pdb=" CA ILE A 17 " ideal model delta harmonic sigma weight residual 180.00 -151.07 -28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA LEU E 320 " pdb=" C LEU E 320 " pdb=" N THR E 321 " pdb=" CA THR E 321 " ideal model delta harmonic sigma weight residual -180.00 -152.37 -27.63 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA VAL G 356 " pdb=" C VAL G 356 " pdb=" N THR G 357 " pdb=" CA THR G 357 " ideal model delta harmonic sigma weight residual 180.00 152.88 27.12 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 5237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1274 0.061 - 0.123: 347 0.123 - 0.184: 74 0.184 - 0.245: 30 0.245 - 0.306: 3 Chirality restraints: 1728 Sorted by residual: chirality pdb=" CA LYS B 446 " pdb=" N LYS B 446 " pdb=" C LYS B 446 " pdb=" CB LYS B 446 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA LYS A 352 " pdb=" N LYS A 352 " pdb=" C LYS A 352 " pdb=" CB LYS A 352 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ASN G 326 " pdb=" N ASN G 326 " pdb=" C ASN G 326 " pdb=" CB ASN G 326 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1725 not shown) Planarity restraints: 1784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 138 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.76e+00 pdb=" C GLU C 138 " 0.038 2.00e-02 2.50e+03 pdb=" O GLU C 138 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL C 139 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 123 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C VAL E 123 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL E 123 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL E 124 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 210 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.48e+00 pdb=" C LYS A 210 " -0.037 2.00e-02 2.50e+03 pdb=" O LYS A 210 " 0.014 2.00e-02 2.50e+03 pdb=" N MET A 211 " 0.012 2.00e-02 2.50e+03 ... (remaining 1781 not shown) Histogram of nonbonded interaction distances: 2.63 - 3.08: 6368 3.08 - 3.54: 11874 3.54 - 3.99: 10800 3.99 - 4.45: 13633 4.45 - 4.90: 19646 Nonbonded interactions: 62321 Sorted by model distance: nonbonded pdb=" N LYS C 37 " pdb=" O LYS C 37 " model vdw 2.628 2.496 nonbonded pdb=" N HIS A 322 " pdb=" O HIS A 322 " model vdw 2.644 2.496 nonbonded pdb=" N LYS A 37 " pdb=" O LYS A 37 " model vdw 2.652 2.496 nonbonded pdb=" N HIS G 322 " pdb=" O HIS G 322 " model vdw 2.655 2.496 nonbonded pdb=" N LYS G 37 " pdb=" O LYS G 37 " model vdw 2.662 2.496 ... (remaining 62316 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.800 Find NCS groups from input model: 0.140 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: 0.000 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 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 : 0.009 0.031 8888 Z= 0.654 Angle : 1.424 6.486 12392 Z= 1.046 Chirality : 0.063 0.306 1728 Planarity : 0.010 0.022 1784 Dihedral : 6.500 28.929 1784 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -0.01 (0.17), residues: 1776 helix: 0.16 (0.11), residues: 1404 sheet: 0.77 (0.38), residues: 148 loop : -0.73 (0.37), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 22 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 11 Details of bonding type rmsd covalent geometry : bond 0.00854 ( 8888) covalent geometry : angle 1.42394 (12392) hydrogen bonds : bond 0.12330 ( 1255) hydrogen bonds : angle 6.06449 ( 3732) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.226 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0377 time to fit residues: 2.6361 Evaluate side-chains 32 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.105661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.074562 restraints weight = 25495.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.075552 restraints weight = 23026.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.076348 restraints weight = 21312.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.077004 restraints weight = 20061.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.077511 restraints weight = 19105.407| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.010 8888 Z= 0.200 Angle : 0.353 2.521 12392 Z= 0.261 Chirality : 0.034 0.117 1728 Planarity : 0.002 0.010 1784 Dihedral : 3.716 17.893 1784 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 3.95 (0.18), residues: 1776 helix: 3.15 (0.12), residues: 1432 sheet: 0.21 (0.35), residues: 160 loop : 0.17 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 22 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 11 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 8888) covalent geometry : angle 0.35323 (12392) hydrogen bonds : bond 0.03693 ( 1255) hydrogen bonds : angle 3.58069 ( 3732) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.204 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0261 time to fit residues: 1.8116 Evaluate side-chains 32 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 35 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 29 optimal weight: 0.0770 chunk 115 optimal weight: 10.0000 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.097040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.067782 restraints weight = 25443.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.068636 restraints weight = 23274.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.069327 restraints weight = 21709.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.069878 restraints weight = 20542.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.070325 restraints weight = 19675.265| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.024 8888 Z= 0.463 Angle : 0.567 4.088 12392 Z= 0.444 Chirality : 0.034 0.118 1728 Planarity : 0.004 0.017 1784 Dihedral : 4.997 29.976 1784 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 1.79 (0.18), residues: 1776 helix: 1.68 (0.12), residues: 1424 sheet: -0.82 (0.37), residues: 152 loop : -0.42 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 22 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 11 Details of bonding type rmsd covalent geometry : bond 0.00595 ( 8888) covalent geometry : angle 0.56667 (12392) hydrogen bonds : bond 0.05866 ( 1255) hydrogen bonds : angle 5.38617 ( 3732) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.243 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0307 time to fit residues: 2.2246 Evaluate side-chains 32 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 108 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.089905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.062411 restraints weight = 26577.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.063142 restraints weight = 24411.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.063749 restraints weight = 22894.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.064246 restraints weight = 21717.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.064546 restraints weight = 20815.042| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.034 8888 Z= 0.753 Angle : 0.826 5.906 12392 Z= 0.655 Chirality : 0.035 0.131 1728 Planarity : 0.007 0.032 1784 Dihedral : 6.403 42.052 1784 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -1.98 (0.17), residues: 1776 helix: -0.97 (0.11), residues: 1404 sheet: -1.33 (0.39), residues: 136 loop : -2.14 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 22 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 11 Details of bonding type rmsd covalent geometry : bond 0.00969 ( 8888) covalent geometry : angle 0.82604 (12392) hydrogen bonds : bond 0.08411 ( 1255) hydrogen bonds : angle 7.19606 ( 3732) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.227 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0342 time to fit residues: 2.3012 Evaluate side-chains 32 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 4 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.101339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.070262 restraints weight = 25165.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.071251 restraints weight = 22676.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.072057 restraints weight = 20938.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.072707 restraints weight = 19657.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.073263 restraints weight = 18696.026| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 8888 Z= 0.159 Angle : 0.330 2.354 12392 Z= 0.242 Chirality : 0.034 0.116 1728 Planarity : 0.002 0.010 1784 Dihedral : 3.835 19.594 1784 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 0.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 2.43 (0.19), residues: 1776 helix: 2.37 (0.13), residues: 1444 sheet: -1.80 (0.37), residues: 152 loop : -1.66 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 22 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 11 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 8888) covalent geometry : angle 0.33038 (12392) hydrogen bonds : bond 0.03498 ( 1255) hydrogen bonds : angle 3.85543 ( 3732) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.191 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0258 time to fit residues: 1.8049 Evaluate side-chains 32 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 114 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.093435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.064695 restraints weight = 26199.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.065499 restraints weight = 24050.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.066145 restraints weight = 22491.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.066554 restraints weight = 21349.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.067055 restraints weight = 20530.900| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.027 8888 Z= 0.577 Angle : 0.653 4.196 12392 Z= 0.520 Chirality : 0.034 0.124 1728 Planarity : 0.005 0.022 1784 Dihedral : 5.185 30.532 1784 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.00 (0.18), residues: 1776 helix: 0.65 (0.12), residues: 1416 sheet: -1.66 (0.39), residues: 136 loop : -2.55 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 22 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 11 Details of bonding type rmsd covalent geometry : bond 0.00741 ( 8888) covalent geometry : angle 0.65302 (12392) hydrogen bonds : bond 0.06542 ( 1255) hydrogen bonds : angle 5.99396 ( 3732) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.171 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0306 time to fit residues: 2.1358 Evaluate side-chains 32 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 143 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.097511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.068135 restraints weight = 25596.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.069017 restraints weight = 23345.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.069765 restraints weight = 21723.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.070366 restraints weight = 20493.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.070879 restraints weight = 19536.320| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 8888 Z= 0.347 Angle : 0.450 3.407 12392 Z= 0.351 Chirality : 0.034 0.126 1728 Planarity : 0.003 0.018 1784 Dihedral : 4.359 23.827 1784 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: 1.34 (0.19), residues: 1776 helix: 1.65 (0.13), residues: 1424 sheet: -1.98 (0.38), residues: 144 loop : -2.07 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 22 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 11 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 8888) covalent geometry : angle 0.45025 (12392) hydrogen bonds : bond 0.04733 ( 1255) hydrogen bonds : angle 4.84391 ( 3732) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.298 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0304 time to fit residues: 2.2825 Evaluate side-chains 32 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 78 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.091779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.063650 restraints weight = 26004.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.064462 restraints weight = 23807.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.065133 restraints weight = 22220.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.065548 restraints weight = 21017.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.066055 restraints weight = 20198.435| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.029 8888 Z= 0.635 Angle : 0.709 5.069 12392 Z= 0.563 Chirality : 0.035 0.128 1728 Planarity : 0.006 0.026 1784 Dihedral : 5.578 30.259 1784 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.10 (0.18), residues: 1776 helix: -0.12 (0.12), residues: 1412 sheet: -1.97 (0.39), residues: 136 loop : -2.89 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 22 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 11 Details of bonding type rmsd covalent geometry : bond 0.00817 ( 8888) covalent geometry : angle 0.70891 (12392) hydrogen bonds : bond 0.07286 ( 1255) hydrogen bonds : angle 6.50262 ( 3732) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.190 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0282 time to fit residues: 2.0612 Evaluate side-chains 32 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 103 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.095518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.066375 restraints weight = 25743.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.067179 restraints weight = 23524.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.067904 restraints weight = 21948.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.068495 restraints weight = 20742.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.068969 restraints weight = 19805.189| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.019 8888 Z= 0.423 Angle : 0.517 3.819 12392 Z= 0.406 Chirality : 0.034 0.129 1728 Planarity : 0.003 0.020 1784 Dihedral : 4.812 25.748 1784 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -0.10 (0.19), residues: 1776 helix: 0.61 (0.13), residues: 1420 sheet: -2.19 (0.38), residues: 144 loop : -2.48 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 22 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 11 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 8888) covalent geometry : angle 0.51713 (12392) hydrogen bonds : bond 0.05505 ( 1255) hydrogen bonds : angle 5.45169 ( 3732) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.175 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0280 time to fit residues: 1.9118 Evaluate side-chains 32 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 120 optimal weight: 9.9990 chunk 159 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 overall best weight: 6.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.090738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.063023 restraints weight = 26109.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.063818 restraints weight = 23942.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.064478 restraints weight = 22384.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.065006 restraints weight = 21191.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.065308 restraints weight = 20277.932| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.5840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.031 8888 Z= 0.671 Angle : 0.738 5.649 12392 Z= 0.587 Chirality : 0.035 0.129 1728 Planarity : 0.006 0.024 1784 Dihedral : 5.831 33.019 1784 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.97 (0.18), residues: 1776 helix: -0.77 (0.12), residues: 1400 sheet: -2.15 (0.40), residues: 136 loop : -2.86 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 22 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 11 Details of bonding type rmsd covalent geometry : bond 0.00863 ( 8888) covalent geometry : angle 0.73843 (12392) hydrogen bonds : bond 0.07687 ( 1255) hydrogen bonds : angle 6.83055 ( 3732) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.237 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0321 time to fit residues: 2.3607 Evaluate side-chains 32 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 164 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 173 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 144 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.094995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.066301 restraints weight = 25539.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.067107 restraints weight = 23339.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.067857 restraints weight = 21789.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.068427 restraints weight = 20589.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.068890 restraints weight = 19661.526| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.5702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.020 8888 Z= 0.422 Angle : 0.518 3.998 12392 Z= 0.405 Chirality : 0.034 0.129 1728 Planarity : 0.003 0.021 1784 Dihedral : 4.872 26.001 1784 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -0.63 (0.19), residues: 1776 helix: 0.25 (0.13), residues: 1416 sheet: -2.06 (0.40), residues: 136 loop : -2.87 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 22 PHE 0.000 0.000 PHE A 4 TRP 0.000 0.000 TRP A 11 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 8888) covalent geometry : angle 0.51766 (12392) hydrogen bonds : bond 0.05550 ( 1255) hydrogen bonds : angle 5.53388 ( 3732) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 824.11 seconds wall clock time: 14 minutes 43.23 seconds (883.23 seconds total)