Starting phenix.real_space_refine on Thu Mar 13 12:58:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ure_42491/03_2025/8ure_42491.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ure_42491/03_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_42491/03_2025/8ure_42491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ure_42491/03_2025/8ure_42491.map" model { file = "/net/cci-nas-00/data/ceres_data/8ure_42491/03_2025/8ure_42491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ure_42491/03_2025/8ure_42491.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 13, 'ARG:plan': 27, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 62, 'ASP:plan': 20} 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: {'GLN:plan1': 13, 'ARG:plan': 27, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 62, 'ASP:plan': 20} 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: {'GLN:plan1': 13, 'ARG:plan': 27, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 62, 'ASP:plan': 20} 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: {'GLN:plan1': 13, 'ARG:plan': 27, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 62, 'ASP:plan': 20} 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: 5.92, per 1000 atoms: 0.67 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: 2.55 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.11 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: 3.68 Time building geometry restraints manager: 2.95 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: 0.00 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: 0.540 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 25.940 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.080 ------------------------------------------------------------------------------- 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= 0.620 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (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 TRP 0.000 0.000 TRP A 11 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 22 *********************** 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 : 0.924 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0815 time to fit residues: 6.2535 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 : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.098266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.067385 restraints weight = 25433.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.068242 restraints weight = 23290.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.068921 restraints weight = 21735.007| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3057 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= 0.458 Angle : 0.611 4.135 12392 Z= 0.477 Chirality : 0.035 0.119 1728 Planarity : 0.004 0.016 1784 Dihedral : 5.322 30.459 1784 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 1.20 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 : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.18), residues: 1776 helix: 0.87 (0.12), residues: 1424 sheet: -0.51 (0.36), residues: 152 loop : -0.32 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 11 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 22 *********************** 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 : 0.917 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0809 time to fit residues: 6.2597 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 : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 114 optimal weight: 9.9990 chunk 150 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 172 optimal weight: 10.0000 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 = 0.3463 r_free = 0.3463 target = 0.097502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.068304 restraints weight = 25598.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.069169 restraints weight = 23426.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.069860 restraints weight = 21889.363| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4042 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= 0.391 Angle : 0.527 4.372 12392 Z= 0.413 Chirality : 0.034 0.114 1728 Planarity : 0.004 0.017 1784 Dihedral : 4.819 27.094 1784 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.18), residues: 1776 helix: 1.28 (0.12), residues: 1428 sheet: -0.95 (0.38), residues: 144 loop : -0.92 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 11 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 22 *********************** 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 : 1.010 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0849 time to fit residues: 6.5349 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 : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 159 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- 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 = 0.3341 r_free = 0.3341 target = 0.090462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.063010 restraints weight = 26306.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.063776 restraints weight = 24056.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.064364 restraints weight = 22539.802| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.033 8888 Z= 0.665 Angle : 0.792 6.110 12392 Z= 0.627 Chirality : 0.035 0.126 1728 Planarity : 0.006 0.031 1784 Dihedral : 6.196 41.139 1784 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % 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 : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.17), residues: 1776 helix: -0.84 (0.12), residues: 1408 sheet: -1.31 (0.39), residues: 136 loop : -2.35 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 11 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 22 *********************** 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 : 0.875 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0793 time to fit residues: 6.0618 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 : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 154 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 158 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.095788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.066782 restraints weight = 25636.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.067645 restraints weight = 23445.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.068343 restraints weight = 21856.675| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4983 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= 0.394 Angle : 0.525 4.344 12392 Z= 0.410 Chirality : 0.034 0.128 1728 Planarity : 0.003 0.020 1784 Dihedral : 4.940 26.047 1784 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.18), residues: 1776 helix: 0.23 (0.12), residues: 1416 sheet: -1.50 (0.39), residues: 136 loop : -2.48 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 11 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 22 *********************** 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 : 0.934 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0805 time to fit residues: 6.2947 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 : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 76 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 chunk 170 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 = 0.3460 r_free = 0.3460 target = 0.097151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.067794 restraints weight = 25451.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.068693 restraints weight = 23176.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.069293 restraints weight = 21543.105| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.017 8888 Z= 0.333 Angle : 0.462 4.037 12392 Z= 0.359 Chirality : 0.034 0.125 1728 Planarity : 0.003 0.017 1784 Dihedral : 4.472 24.143 1784 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.19), residues: 1776 helix: 1.24 (0.13), residues: 1424 sheet: -1.60 (0.39), residues: 136 loop : -2.22 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 11 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 22 *********************** 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 : 0.849 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0782 time to fit residues: 5.9621 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 : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 144 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.3381 r_free = 0.3381 target = 0.092666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.064420 restraints weight = 25781.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.065229 restraints weight = 23644.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.065893 restraints weight = 22087.751| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.5505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.026 8888 Z= 0.537 Angle : 0.658 4.820 12392 Z= 0.521 Chirality : 0.034 0.129 1728 Planarity : 0.005 0.022 1784 Dihedral : 5.435 27.782 1784 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.18), residues: 1776 helix: -0.04 (0.12), residues: 1412 sheet: -1.80 (0.39), residues: 136 loop : -2.79 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 11 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 22 *********************** 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 : 0.934 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0808 time to fit residues: 6.2701 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 : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 102 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 5 optimal weight: 0.4980 chunk 135 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 169 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 138 optimal weight: 0.4980 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.099825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.069804 restraints weight = 25696.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.070817 restraints weight = 23171.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.071678 restraints weight = 21375.972| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 8888 Z= 0.177 Angle : 0.340 2.792 12392 Z= 0.252 Chirality : 0.034 0.122 1728 Planarity : 0.002 0.016 1784 Dihedral : 3.871 20.106 1784 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 0.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.20), residues: 1776 helix: 2.28 (0.13), residues: 1436 sheet: -1.88 (0.39), residues: 144 loop : -2.23 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 11 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 22 *********************** 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 : 1.153 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0819 time to fit residues: 6.2509 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 : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 144 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- 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 = 0.3301 r_free = 0.3301 target = 0.088225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.060489 restraints weight = 26498.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.061277 restraints weight = 24190.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.061922 restraints weight = 22561.859| |-----------------------------------------------------------------------------| r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.040 8888 Z= 0.781 Angle : 0.896 6.421 12392 Z= 0.713 Chirality : 0.036 0.127 1728 Planarity : 0.008 0.038 1784 Dihedral : 6.394 33.640 1784 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.17), residues: 1776 helix: -1.17 (0.12), residues: 1400 sheet: -2.32 (0.39), residues: 144 loop : -2.73 (0.39), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 11 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 22 *********************** 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 : 0.868 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0801 time to fit residues: 6.1407 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 : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 78 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 164 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.098605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.068852 restraints weight = 25096.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.069890 restraints weight = 22501.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.070744 restraints weight = 20685.777| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 8888 Z= 0.196 Angle : 0.361 2.740 12392 Z= 0.268 Chirality : 0.034 0.120 1728 Planarity : 0.002 0.018 1784 Dihedral : 4.049 21.532 1784 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 0.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.19), residues: 1776 helix: 1.75 (0.13), residues: 1436 sheet: -1.84 (0.39), residues: 136 loop : -2.80 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 11 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 22 ********************** 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 : 0.842 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0781 time to fit residues: 5.9579 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 : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 77 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 = 0.3339 r_free = 0.3339 target = 0.090171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.061937 restraints weight = 26434.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.062704 restraints weight = 24182.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.063337 restraints weight = 22629.926| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.6004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.034 8888 Z= 0.673 Angle : 0.788 6.045 12392 Z= 0.627 Chirality : 0.035 0.127 1728 Planarity : 0.007 0.030 1784 Dihedral : 5.881 27.576 1784 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.18), residues: 1776 helix: -0.70 (0.12), residues: 1396 sheet: -2.37 (0.38), residues: 144 loop : -2.65 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 11 PHE 0.000 0.000 PHE A 4 TYR 0.000 0.000 TYR A 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1809.88 seconds wall clock time: 32 minutes 5.15 seconds (1925.15 seconds total)