Starting phenix.real_space_refine on Tue Sep 24 22:07:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ure_42491/09_2024/8ure_42491.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ure_42491/09_2024/8ure_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ure_42491/09_2024/8ure_42491.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ure_42491/09_2024/8ure_42491.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ure_42491/09_2024/8ure_42491.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ure_42491/09_2024/8ure_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-5461/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: 6.81, per 1000 atoms: 0.77 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: 3.64 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: 1.30 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: 3.60 Time building geometry restraints manager: 3.89 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: 0.840 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.000 Find NCS groups from input model: 0.350 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.640 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.031 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0816 time to fit residues: 6.3169 Evaluate side-chains 32 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 fitting. 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: 0.0781 time to fit residues: 6.0995 Evaluate side-chains 32 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 158 optimal weight: 0.0270 chunk 54 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 overall best weight: 4.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.020 8888 Z= 0.412 Angle : 0.545 4.490 12392 Z= 0.427 Chirality : 0.034 0.117 1728 Planarity : 0.004 0.017 1784 Dihedral : 4.955 27.637 1784 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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: 0.93 (0.18), residues: 1776 helix: 1.09 (0.12), residues: 1428 sheet: -1.29 (0.37), residues: 152 loop : -0.62 (0.45), 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 fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.933 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0831 time to fit residues: 6.4329 Evaluate side-chains 32 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.024 8888 Z= 0.486 Angle : 0.619 4.927 12392 Z= 0.487 Chirality : 0.034 0.128 1728 Planarity : 0.004 0.018 1784 Dihedral : 5.376 28.525 1784 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % 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: -0.13 (0.18), residues: 1776 helix: 0.42 (0.12), residues: 1416 sheet: -1.12 (0.39), residues: 136 loop : -1.98 (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 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 fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.975 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0885 time to fit residues: 6.7852 Evaluate side-chains 32 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 chunk 117 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 152 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.5442 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= 0.604 Angle : 0.729 5.781 12392 Z= 0.576 Chirality : 0.035 0.133 1728 Planarity : 0.006 0.025 1784 Dihedral : 5.956 35.134 1784 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.14 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: 1400 sheet: -1.52 (0.39), residues: 136 loop : -2.49 (0.39), residues: 240 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 fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.050 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0746 time to fit residues: 5.8175 Evaluate side-chains 32 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.014 8888 Z= 0.265 Angle : 0.410 3.524 12392 Z= 0.313 Chirality : 0.034 0.122 1728 Planarity : 0.002 0.019 1784 Dihedral : 4.346 23.501 1784 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % 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: 0.90 (0.19), residues: 1776 helix: 1.26 (0.13), residues: 1424 sheet: -1.43 (0.40), residues: 136 loop : -2.17 (0.45), 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 fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.981 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0827 time to fit residues: 6.7176 Evaluate side-chains 32 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 104 optimal weight: 0.0570 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.5318 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= 0.359 Angle : 0.487 3.883 12392 Z= 0.380 Chirality : 0.034 0.124 1728 Planarity : 0.003 0.019 1784 Dihedral : 4.588 25.763 1784 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 1.28 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: 0.97 (0.19), residues: 1776 helix: 1.35 (0.13), residues: 1420 sheet: -1.57 (0.40), residues: 136 loop : -2.32 (0.43), residues: 220 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 fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.969 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0789 time to fit residues: 6.1071 Evaluate side-chains 32 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.5943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.037 8888 Z= 0.727 Angle : 0.846 6.297 12392 Z= 0.672 Chirality : 0.036 0.129 1728 Planarity : 0.007 0.036 1784 Dihedral : 6.328 40.410 1784 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % 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: -2.54 (0.17), residues: 1776 helix: -1.23 (0.12), residues: 1400 sheet: -2.18 (0.40), residues: 144 loop : -2.70 (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 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 fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.026 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0785 time to fit residues: 6.2262 Evaluate side-chains 32 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 68 optimal weight: 0.4980 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.5510 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= 0.203 Angle : 0.367 2.886 12392 Z= 0.273 Chirality : 0.034 0.120 1728 Planarity : 0.002 0.017 1784 Dihedral : 4.182 22.157 1784 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 0.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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: 1.04 (0.19), residues: 1776 helix: 1.45 (0.13), residues: 1436 sheet: -1.97 (0.39), residues: 144 loop : -2.70 (0.45), 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 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 fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.992 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0742 time to fit residues: 5.7670 Evaluate side-chains 32 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 175 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.5969 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= 0.658 Angle : 0.774 5.524 12392 Z= 0.615 Chirality : 0.035 0.128 1728 Planarity : 0.006 0.027 1784 Dihedral : 5.875 34.821 1784 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (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: -1.93 (0.18), residues: 1776 helix: -0.75 (0.12), residues: 1400 sheet: -2.23 (0.40), residues: 144 loop : -2.69 (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 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 fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.029 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0832 time to fit residues: 6.5770 Evaluate side-chains 32 residues out of total 1476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 139 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.097826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.068458 restraints weight = 25247.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.069383 restraints weight = 22910.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.070160 restraints weight = 21230.647| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.5663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 8888 Z= 0.242 Angle : 0.392 3.311 12392 Z= 0.296 Chirality : 0.034 0.122 1728 Planarity : 0.002 0.019 1784 Dihedral : 4.262 22.994 1784 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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: 0.95 (0.19), residues: 1776 helix: 1.41 (0.13), residues: 1428 sheet: -1.71 (0.41), residues: 136 loop : -2.92 (0.42), residues: 212 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: 1194.56 seconds wall clock time: 21 minutes 59.71 seconds (1319.71 seconds total)