Starting phenix.real_space_refine on Thu Jan 16 00:40:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ure_42491/01_2025/8ure_42491.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ure_42491/01_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_42491/01_2025/8ure_42491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ure_42491/01_2025/8ure_42491.map" model { file = "/net/cci-nas-00/data/ceres_data/8ure_42491/01_2025/8ure_42491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ure_42491/01_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-5571/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: 6.41, per 1000 atoms: 0.72 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: 2.88 Conformation dependent library (CDL) restraints added in 1.7 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: 1.01 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: 3.46 Time building geometry restraints manager: 3.20 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: 0.460 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.910 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.930 ------------------------------------------------------------------------------- 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 : 0.968 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0836 time to fit residues: 6.1896 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 : 0.901 ------------------------------------------------------------------------------- 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 = 0.067389 restraints weight = 25433.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.068236 restraints weight = 23281.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.068925 restraints weight = 21731.703| |-----------------------------------------------------------------------------| 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 : 0.963 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0858 time to fit residues: 6.6082 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 : 0.908 ------------------------------------------------------------------------------- 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: 10.0000 chunk 150 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 125 optimal weight: 0.4980 chunk 23 optimal weight: 8.9990 chunk 90 optimal weight: 0.0980 chunk 170 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 172 optimal weight: 9.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- 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 = 0.098057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.068717 restraints weight = 25704.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.069599 restraints weight = 23518.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.070311 restraints weight = 21916.524| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.018 8888 Z= 0.368 Angle : 0.501 4.067 12392 Z= 0.390 Chirality : 0.034 0.111 1728 Planarity : 0.003 0.015 1784 Dihedral : 4.640 26.192 1784 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 0.98 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: 1.58 (0.18), residues: 1776 helix: 1.56 (0.12), residues: 1428 sheet: -1.13 (0.38), residues: 152 loop : -0.54 (0.44), 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 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 : 0.898 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0785 time to fit residues: 5.9956 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 : 0.906 ------------------------------------------------------------------------------- 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: 0.8980 chunk 91 optimal weight: 9.9990 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: 7.9990 chunk 161 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 overall best weight: 6.1788 ------------------------------------------------------------------------------- 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 = 0.3382 r_free = 0.3382 target = 0.092776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.064706 restraints weight = 25808.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.065476 restraints weight = 23599.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.066113 restraints weight = 22063.659| |-----------------------------------------------------------------------------| r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.030 8888 Z= 0.572 Angle : 0.698 5.390 12392 Z= 0.552 Chirality : 0.034 0.127 1728 Planarity : 0.005 0.022 1784 Dihedral : 5.736 33.644 1784 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % 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: -0.79 (0.18), residues: 1776 helix: -0.07 (0.12), residues: 1412 sheet: -1.17 (0.39), residues: 136 loop : -2.04 (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 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 : 0.984 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0854 time to fit residues: 6.6910 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 : 1.155 ------------------------------------------------------------------------------- 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: 9.9990 chunk 98 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 97 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 = 0.3363 r_free = 0.3363 target = 0.091793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.063949 restraints weight = 26008.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.064745 restraints weight = 23909.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.065382 restraints weight = 22373.580| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.5395 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= 0.584 Angle : 0.706 5.154 12392 Z= 0.559 Chirality : 0.034 0.131 1728 Planarity : 0.006 0.021 1784 Dihedral : 5.794 31.185 1784 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % 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: -1.90 (0.18), residues: 1776 helix: -0.83 (0.12), residues: 1404 sheet: -1.65 (0.39), residues: 136 loop : -2.48 (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 *********************** 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 : 0.979 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0823 time to fit residues: 6.4262 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 : 0.953 ------------------------------------------------------------------------------- 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: 10.0000 chunk 2 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.097825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.068284 restraints weight = 25472.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.069191 restraints weight = 23164.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.069958 restraints weight = 21506.969| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 8888 Z= 0.285 Angle : 0.425 3.714 12392 Z= 0.327 Chirality : 0.034 0.124 1728 Planarity : 0.003 0.017 1784 Dihedral : 4.390 23.780 1784 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 0.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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: 0.64 (0.19), residues: 1776 helix: 1.09 (0.13), residues: 1424 sheet: -1.61 (0.39), residues: 136 loop : -2.29 (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 : 0.887 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0786 time to fit residues: 6.0297 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 : 0.929 ------------------------------------------------------------------------------- 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: 3.9990 chunk 3 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.092966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.064270 restraints weight = 25663.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.065024 restraints weight = 23443.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.065521 restraints weight = 21928.326| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.5502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.025 8888 Z= 0.518 Angle : 0.638 4.657 12392 Z= 0.505 Chirality : 0.034 0.125 1728 Planarity : 0.005 0.023 1784 Dihedral : 5.313 26.939 1784 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % 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: -0.85 (0.18), residues: 1776 helix: 0.05 (0.12), residues: 1412 sheet: -1.86 (0.39), residues: 136 loop : -2.83 (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 : 0.931 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0776 time to fit residues: 6.0774 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 : 0.930 ------------------------------------------------------------------------------- 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: 0.9990 chunk 40 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 138 optimal weight: 0.3980 overall best weight: 2.6788 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.098367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.068376 restraints weight = 25777.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.069354 restraints weight = 23305.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.070167 restraints weight = 21539.737| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 8888 Z= 0.253 Angle : 0.396 3.563 12392 Z= 0.302 Chirality : 0.034 0.121 1728 Planarity : 0.002 0.018 1784 Dihedral : 4.156 23.364 1784 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 0.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % 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: 1.38 (0.20), residues: 1776 helix: 1.70 (0.13), residues: 1436 sheet: -1.73 (0.39), residues: 136 loop : -2.73 (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 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 : 0.976 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0807 time to fit residues: 6.3031 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 : 0.973 ------------------------------------------------------------------------------- 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: 9.9990 chunk 42 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 67 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 overall best weight: 6.5588 ------------------------------------------------------------------------------- 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 = 0.3359 r_free = 0.3359 target = 0.091401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.063218 restraints weight = 26040.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.064082 restraints weight = 23717.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.064779 restraints weight = 22041.892| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.5771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.030 8888 Z= 0.603 Angle : 0.719 5.065 12392 Z= 0.572 Chirality : 0.035 0.123 1728 Planarity : 0.006 0.025 1784 Dihedral : 5.570 27.577 1784 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % 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: -1.25 (0.18), residues: 1776 helix: -0.23 (0.12), residues: 1416 sheet: -2.30 (0.38), residues: 144 loop : -2.72 (0.41), 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 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 : 0.929 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0812 time to fit residues: 6.2982 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 : 0.920 ------------------------------------------------------------------------------- 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: 4.9990 chunk 109 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 164 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.101241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.070180 restraints weight = 24445.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.071226 restraints weight = 22062.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.072084 restraints weight = 20317.709| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.5436 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= 0.140 Angle : 0.318 2.452 12392 Z= 0.231 Chirality : 0.034 0.116 1728 Planarity : 0.002 0.009 1784 Dihedral : 3.678 18.959 1784 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 0.60 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 (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: 2.68 (0.20), residues: 1776 helix: 2.71 (0.13), residues: 1432 sheet: -2.25 (0.38), residues: 152 loop : -2.29 (0.46), residues: 192 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 : 0.920 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0838 time to fit residues: 6.3745 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 : 0.908 ------------------------------------------------------------------------------- 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: 10.0000 chunk 142 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 overall best weight: 6.9588 ------------------------------------------------------------------------------- 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 = 0.3345 r_free = 0.3345 target = 0.090577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.062424 restraints weight = 26204.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.063261 restraints weight = 23933.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.063948 restraints weight = 22305.587| |-----------------------------------------------------------------------------| r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.5892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.030 8888 Z= 0.637 Angle : 0.752 5.080 12392 Z= 0.599 Chirality : 0.035 0.123 1728 Planarity : 0.006 0.025 1784 Dihedral : 5.575 27.234 1784 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % 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: -1.13 (0.18), residues: 1776 helix: -0.13 (0.12), residues: 1416 sheet: -2.31 (0.39), residues: 144 loop : -2.82 (0.41), 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1832.87 seconds wall clock time: 33 minutes 29.29 seconds (2009.29 seconds total)