Starting phenix.real_space_refine on Fri Nov 15 15:42:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jim_36318/11_2024/8jim_36318_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jim_36318/11_2024/8jim_36318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jim_36318/11_2024/8jim_36318.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jim_36318/11_2024/8jim_36318.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jim_36318/11_2024/8jim_36318_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jim_36318/11_2024/8jim_36318_neut.cif" } resolution = 2.98 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= 0.019 sd= 0.095 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: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 5779 2.51 5 N 1538 2.21 5 O 1665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9051 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "D" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1813 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "E" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2370 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'AW9': 1, 'CLR': 1} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 2} Time building chain proxies: 5.91, per 1000 atoms: 0.65 Number of scatterers: 9051 At special positions: 0 Unit cell: (93.5, 122.4, 137.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 1665 8.00 N 1538 7.00 C 5779 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Simple disulfide: pdb=" SG CYS E 18 " - pdb=" SG CYS E 183 " distance=2.04 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 266 " distance=2.03 Simple disulfide: pdb=" SG CYS E 100 " - pdb=" SG CYS E 177 " distance=2.03 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: 2.96 Conformation dependent library (CDL) restraints added in 1.1 seconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 33.0% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'B' and resid 1 through 25 removed outlier: 3.982A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 23 removed outlier: 3.884A pdb=" N GLN C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.607A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 removed outlier: 4.192A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'D' and resid 11 through 27 Processing helix chain 'D' and resid 45 through 54 Processing helix chain 'D' and resid 207 through 211 removed outlier: 3.692A pdb=" N LYS D 210 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 230 No H-bonds generated for 'chain 'D' and resid 228 through 230' Processing helix chain 'D' and resid 241 through 255 removed outlier: 3.766A pdb=" N ALA D 245 " --> pdb=" O ASN D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 279 removed outlier: 3.752A pdb=" N PHE D 274 " --> pdb=" O LYS D 270 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU D 275 " --> pdb=" O LYS D 271 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 286 removed outlier: 3.692A pdb=" N ILE D 285 " --> pdb=" O PRO D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 310 removed outlier: 3.598A pdb=" N ALA D 299 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU D 310 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 351 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.840A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 54 removed outlier: 3.817A pdb=" N VAL E 29 " --> pdb=" O PHE E 25 " (cutoff:3.500A) Proline residue: E 31 - end of helix removed outlier: 4.309A pdb=" N LEU E 43 " --> pdb=" O ILE E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 78 removed outlier: 3.741A pdb=" N LEU E 69 " --> pdb=" O PHE E 65 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE E 78 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 89 removed outlier: 4.025A pdb=" N LEU E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 101 removed outlier: 3.834A pdb=" N CYS E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 111 removed outlier: 3.552A pdb=" N ARG E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 120 removed outlier: 4.133A pdb=" N PHE E 117 " --> pdb=" O GLY E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 130 removed outlier: 4.672A pdb=" N TYR E 126 " --> pdb=" O ALA E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 139 removed outlier: 3.971A pdb=" N ILE E 139 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 157 Processing helix chain 'E' and resid 158 through 163 removed outlier: 5.347A pdb=" N HIS E 161 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 193 removed outlier: 4.268A pdb=" N ALA E 191 " --> pdb=" O GLN E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 214 removed outlier: 4.131A pdb=" N ILE E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 244 removed outlier: 3.650A pdb=" N ARG E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA E 229 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE E 230 " --> pdb=" O ILE E 226 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR E 231 " --> pdb=" O LYS E 227 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE E 240 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL E 241 " --> pdb=" O ALA E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 261 removed outlier: 3.590A pdb=" N VAL E 250 " --> pdb=" O PRO E 246 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 270 removed outlier: 3.607A pdb=" N VAL E 268 " --> pdb=" O ASN E 265 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG E 270 " --> pdb=" O GLU E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 280 removed outlier: 3.866A pdb=" N ILE E 278 " --> pdb=" O LEU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 289 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.851A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.950A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.155A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.545A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.509A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.575A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.709A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 185 through 191 removed outlier: 3.865A pdb=" N ALA D 220 " --> pdb=" O LYS D 35 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.613A pdb=" N VAL S 12 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.662A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR S 243 " --> pdb=" O TYR S 227 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.687A pdb=" N GLU E 12 " --> pdb=" O CYS E 18 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 169 through 170 removed outlier: 3.578A pdb=" N ILE E 169 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 1041 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.69 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: 1.18 - 1.31: 1462 1.31 - 1.44: 2571 1.44 - 1.57: 5114 1.57 - 1.70: 0 1.70 - 1.83: 100 Bond restraints: 9247 Sorted by residual: bond pdb=" CA SER S 193 " pdb=" CB SER S 193 " ideal model delta sigma weight residual 1.533 1.460 0.073 1.60e-02 3.91e+03 2.07e+01 bond pdb=" C ILE E 230 " pdb=" O ILE E 230 " ideal model delta sigma weight residual 1.237 1.285 -0.048 1.17e-02 7.31e+03 1.68e+01 bond pdb=" CA ALA E 229 " pdb=" CB ALA E 229 " ideal model delta sigma weight residual 1.528 1.465 0.064 1.66e-02 3.63e+03 1.47e+01 bond pdb=" C ARG E 228 " pdb=" O ARG E 228 " ideal model delta sigma weight residual 1.237 1.281 -0.044 1.19e-02 7.06e+03 1.40e+01 bond pdb=" C ALA E 229 " pdb=" O ALA E 229 " ideal model delta sigma weight residual 1.236 1.282 -0.046 1.26e-02 6.30e+03 1.33e+01 ... (remaining 9242 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 12241 2.60 - 5.21: 240 5.21 - 7.81: 22 7.81 - 10.42: 9 10.42 - 13.02: 1 Bond angle restraints: 12513 Sorted by residual: angle pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta sigma weight residual 122.60 109.58 13.02 1.88e+00 2.83e-01 4.80e+01 angle pdb=" N ARG S 191 " pdb=" CA ARG S 191 " pdb=" C ARG S 191 " ideal model delta sigma weight residual 108.00 99.52 8.48 1.48e+00 4.57e-01 3.28e+01 angle pdb=" N SER S 193 " pdb=" CA SER S 193 " pdb=" CB SER S 193 " ideal model delta sigma weight residual 110.61 102.05 8.56 1.51e+00 4.39e-01 3.21e+01 angle pdb=" C ASN S 194 " pdb=" CA ASN S 194 " pdb=" CB ASN S 194 " ideal model delta sigma weight residual 109.89 117.74 -7.85 1.60e+00 3.91e-01 2.41e+01 angle pdb=" N ALA E 229 " pdb=" CA ALA E 229 " pdb=" C ALA E 229 " ideal model delta sigma weight residual 111.82 106.75 5.07 1.16e+00 7.43e-01 1.91e+01 ... (remaining 12508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 4864 15.46 - 30.91: 514 30.91 - 46.37: 124 46.37 - 61.82: 21 61.82 - 77.28: 7 Dihedral angle restraints: 5530 sinusoidal: 2218 harmonic: 3312 Sorted by residual: dihedral pdb=" CB CYS E 18 " pdb=" SG CYS E 18 " pdb=" SG CYS E 183 " pdb=" CB CYS E 183 " ideal model delta sinusoidal sigma weight residual 93.00 49.73 43.27 1 1.00e+01 1.00e-02 2.61e+01 dihedral pdb=" CA ASP B 290 " pdb=" C ASP B 290 " pdb=" N ASP B 291 " pdb=" CA ASP B 291 " ideal model delta harmonic sigma weight residual 180.00 156.89 23.11 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA PHE E 52 " pdb=" C PHE E 52 " pdb=" N CYS E 53 " pdb=" CA CYS E 53 " ideal model delta harmonic sigma weight residual -180.00 -159.29 -20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 5527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 830 0.041 - 0.082: 432 0.082 - 0.123: 110 0.123 - 0.164: 29 0.164 - 0.205: 6 Chirality restraints: 1407 Sorted by residual: chirality pdb=" CA ILE E 233 " pdb=" N ILE E 233 " pdb=" C ILE E 233 " pdb=" CB ILE E 233 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA VAL E 235 " pdb=" N VAL E 235 " pdb=" C VAL E 235 " pdb=" CB VAL E 235 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.23e-01 chirality pdb=" CB VAL S 64 " pdb=" CA VAL S 64 " pdb=" CG1 VAL S 64 " pdb=" CG2 VAL S 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.97e-01 ... (remaining 1404 not shown) Planarity restraints: 1578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 227 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.46e+00 pdb=" C LYS E 227 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS E 227 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG E 228 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.025 2.00e-02 2.50e+03 1.98e-02 7.85e+00 pdb=" CG TYR B 105 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET S 192 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.80e+00 pdb=" C MET S 192 " -0.045 2.00e-02 2.50e+03 pdb=" O MET S 192 " 0.017 2.00e-02 2.50e+03 pdb=" N SER S 193 " 0.016 2.00e-02 2.50e+03 ... (remaining 1575 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1638 2.77 - 3.30: 8251 3.30 - 3.83: 13628 3.83 - 4.37: 16317 4.37 - 4.90: 29620 Nonbonded interactions: 69454 Sorted by model distance: nonbonded pdb=" O LEU S 174 " pdb=" O ARG S 191 " model vdw 2.232 3.040 nonbonded pdb=" O ILE S 100 " pdb=" OG SER S 105 " model vdw 2.234 3.040 nonbonded pdb=" O SER E 214 " pdb=" OG SER E 214 " model vdw 2.257 3.040 nonbonded pdb=" OG SER S 161 " pdb=" OG1 THR S 210 " model vdw 2.261 3.040 nonbonded pdb=" NZ LYS B 89 " pdb=" OD1 ASP D 20 " model vdw 2.287 3.120 ... (remaining 69449 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.800 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 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 : 0.007 0.073 9247 Z= 0.453 Angle : 0.905 13.021 12513 Z= 0.533 Chirality : 0.052 0.205 1407 Planarity : 0.004 0.050 1578 Dihedral : 13.511 77.278 3378 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.75 % Favored : 94.16 % Rotamer: Outliers : 0.41 % Allowed : 1.01 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.91 (0.23), residues: 1130 helix: -0.53 (0.28), residues: 329 sheet: -0.41 (0.31), residues: 271 loop : -2.23 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP S 47 HIS 0.009 0.002 HIS S 35 PHE 0.025 0.002 PHE E 52 TYR 0.049 0.003 TYR B 105 ARG 0.007 0.001 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 162 time to evaluate : 1.157 Fit side-chains REVERT: B 217 MET cc_start: 0.7942 (ptt) cc_final: 0.7734 (ptt) REVERT: C 48 ASP cc_start: 0.6571 (p0) cc_final: 0.6366 (p0) REVERT: D 24 ARG cc_start: 0.7980 (ttp-110) cc_final: 0.7729 (ttp80) REVERT: D 270 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7866 (mtmp) REVERT: S 46 GLU cc_start: 0.7826 (pm20) cc_final: 0.7585 (pm20) REVERT: E 269 TYR cc_start: 0.7639 (m-80) cc_final: 0.7306 (m-80) REVERT: E 274 LEU cc_start: 0.7943 (tp) cc_final: 0.7734 (tm) REVERT: E 282 PHE cc_start: 0.7587 (m-80) cc_final: 0.7049 (m-10) outliers start: 4 outliers final: 2 residues processed: 166 average time/residue: 1.2905 time to fit residues: 229.1022 Evaluate side-chains 135 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain E residue 231 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 268 ASN B 340 ASN S 82 GLN S 194 ASN E 161 HIS E 189 HIS E 223 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9247 Z= 0.201 Angle : 0.641 7.791 12513 Z= 0.338 Chirality : 0.044 0.151 1407 Planarity : 0.004 0.039 1578 Dihedral : 6.356 89.596 1307 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.33 % Allowed : 9.74 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.34 (0.24), residues: 1130 helix: 0.12 (0.29), residues: 341 sheet: -0.18 (0.31), residues: 278 loop : -2.01 (0.24), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP S 47 HIS 0.011 0.002 HIS E 161 PHE 0.035 0.001 PHE E 255 TYR 0.019 0.002 TYR B 105 ARG 0.004 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.057 Fit side-chains REVERT: D 24 ARG cc_start: 0.7972 (ttp-110) cc_final: 0.7695 (ttp80) REVERT: S 67 ARG cc_start: 0.7456 (mtm180) cc_final: 0.7068 (mtm180) REVERT: S 93 MET cc_start: 0.8210 (ttt) cc_final: 0.7825 (ttt) REVERT: E 269 TYR cc_start: 0.7691 (m-80) cc_final: 0.7488 (m-80) REVERT: E 282 PHE cc_start: 0.7416 (m-80) cc_final: 0.7114 (m-10) outliers start: 23 outliers final: 9 residues processed: 139 average time/residue: 1.3448 time to fit residues: 199.5878 Evaluate side-chains 132 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 257 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 340 ASN E 161 HIS E 223 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9247 Z= 0.391 Angle : 0.717 8.014 12513 Z= 0.376 Chirality : 0.047 0.171 1407 Planarity : 0.004 0.041 1578 Dihedral : 6.255 84.786 1304 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.35 % Allowed : 12.47 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.22 (0.24), residues: 1130 helix: 0.26 (0.29), residues: 339 sheet: -0.12 (0.31), residues: 281 loop : -1.96 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP S 47 HIS 0.011 0.002 HIS E 161 PHE 0.028 0.002 PHE E 255 TYR 0.039 0.002 TYR B 105 ARG 0.004 0.000 ARG E 270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 1.033 Fit side-chains REVERT: D 24 ARG cc_start: 0.8009 (ttp-110) cc_final: 0.7787 (ttm170) REVERT: D 53 MET cc_start: 0.6064 (mtp) cc_final: 0.5755 (mtp) REVERT: D 270 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8200 (mtmp) REVERT: S 60 TYR cc_start: 0.7946 (m-80) cc_final: 0.7711 (m-80) REVERT: S 67 ARG cc_start: 0.7564 (mtm180) cc_final: 0.7214 (mtm180) outliers start: 33 outliers final: 15 residues processed: 142 average time/residue: 1.2975 time to fit residues: 196.4433 Evaluate side-chains 135 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 281 SER Chi-restraints excluded: chain E residue 292 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 0.0980 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN B 340 ASN S 113 GLN E 161 HIS E 223 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9247 Z= 0.224 Angle : 0.615 7.492 12513 Z= 0.323 Chirality : 0.044 0.147 1407 Planarity : 0.004 0.037 1578 Dihedral : 5.821 79.573 1304 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.94 % Allowed : 15.72 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.24), residues: 1130 helix: 0.51 (0.30), residues: 339 sheet: -0.01 (0.31), residues: 282 loop : -1.83 (0.24), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.011 0.001 HIS E 161 PHE 0.033 0.002 PHE E 255 TYR 0.021 0.002 TYR B 105 ARG 0.003 0.000 ARG E 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.995 Fit side-chains REVERT: D 24 ARG cc_start: 0.7975 (ttp-110) cc_final: 0.7761 (ttp-110) REVERT: D 53 MET cc_start: 0.6067 (mtp) cc_final: 0.5797 (mtp) REVERT: D 188 HIS cc_start: 0.6782 (t-170) cc_final: 0.6355 (t-170) REVERT: D 195 HIS cc_start: 0.7261 (OUTLIER) cc_final: 0.6687 (t70) REVERT: E 192 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7091 (ttm) outliers start: 29 outliers final: 16 residues processed: 142 average time/residue: 1.2419 time to fit residues: 189.8008 Evaluate side-chains 140 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 274 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN E 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9247 Z= 0.321 Angle : 0.662 7.458 12513 Z= 0.347 Chirality : 0.046 0.152 1407 Planarity : 0.004 0.039 1578 Dihedral : 5.908 75.236 1304 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 4.06 % Allowed : 17.14 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.24), residues: 1130 helix: 0.54 (0.30), residues: 338 sheet: 0.07 (0.31), residues: 273 loop : -1.84 (0.24), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP S 47 HIS 0.011 0.001 HIS E 161 PHE 0.032 0.002 PHE E 38 TYR 0.034 0.002 TYR B 105 ARG 0.002 0.000 ARG S 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.991 Fit side-chains REVERT: B 258 ASP cc_start: 0.7506 (p0) cc_final: 0.7246 (p0) REVERT: C 46 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7828 (mmtm) REVERT: D 195 HIS cc_start: 0.7261 (OUTLIER) cc_final: 0.6710 (t70) REVERT: D 248 LYS cc_start: 0.8093 (tppt) cc_final: 0.7314 (mtpm) outliers start: 40 outliers final: 18 residues processed: 144 average time/residue: 1.3007 time to fit residues: 200.8253 Evaluate side-chains 140 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 292 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 104 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9247 Z= 0.170 Angle : 0.585 7.926 12513 Z= 0.306 Chirality : 0.043 0.145 1407 Planarity : 0.004 0.053 1578 Dihedral : 5.545 72.239 1304 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.94 % Allowed : 19.37 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.77 (0.25), residues: 1130 helix: 0.73 (0.30), residues: 339 sheet: 0.10 (0.32), residues: 271 loop : -1.72 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.010 0.001 HIS E 161 PHE 0.033 0.001 PHE E 38 TYR 0.014 0.001 TYR B 105 ARG 0.014 0.000 ARG D 242 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 1.035 Fit side-chains REVERT: B 258 ASP cc_start: 0.7320 (p0) cc_final: 0.7069 (p0) REVERT: D 53 MET cc_start: 0.6015 (mtp) cc_final: 0.5793 (mtp) REVERT: D 195 HIS cc_start: 0.7247 (OUTLIER) cc_final: 0.6752 (t70) REVERT: D 248 LYS cc_start: 0.8041 (tppt) cc_final: 0.7296 (mtpm) REVERT: D 270 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8297 (mtmp) REVERT: S 78 THR cc_start: 0.7921 (t) cc_final: 0.7661 (m) REVERT: E 102 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7358 (tt) outliers start: 29 outliers final: 13 residues processed: 142 average time/residue: 1.1028 time to fit residues: 168.5082 Evaluate side-chains 136 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 292 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 66 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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: 0.7620 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9247 Z= 0.257 Angle : 0.629 8.143 12513 Z= 0.327 Chirality : 0.044 0.151 1407 Planarity : 0.004 0.034 1578 Dihedral : 5.593 69.441 1304 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.75 % Allowed : 19.78 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.73 (0.25), residues: 1130 helix: 0.75 (0.30), residues: 339 sheet: 0.17 (0.31), residues: 270 loop : -1.71 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.011 0.001 HIS E 161 PHE 0.032 0.002 PHE E 38 TYR 0.023 0.002 TYR B 105 ARG 0.005 0.000 ARG D 242 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 1.085 Fit side-chains REVERT: B 46 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.6914 (ptm-80) REVERT: B 258 ASP cc_start: 0.7379 (p0) cc_final: 0.7152 (p0) REVERT: D 52 GLN cc_start: 0.7020 (OUTLIER) cc_final: 0.6682 (mt0) REVERT: D 53 MET cc_start: 0.6056 (mtp) cc_final: 0.5782 (mtp) REVERT: D 195 HIS cc_start: 0.7275 (OUTLIER) cc_final: 0.6742 (t70) REVERT: D 248 LYS cc_start: 0.8066 (tppt) cc_final: 0.7310 (mtpm) REVERT: D 270 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8353 (mtmp) REVERT: S 58 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8256 (mp) REVERT: S 78 THR cc_start: 0.7881 (t) cc_final: 0.7642 (m) REVERT: E 102 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7631 (mp) outliers start: 37 outliers final: 19 residues processed: 143 average time/residue: 1.1611 time to fit residues: 178.3433 Evaluate side-chains 144 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 223 HIS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 292 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 0.0670 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 98 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9247 Z= 0.162 Angle : 0.570 8.173 12513 Z= 0.298 Chirality : 0.042 0.146 1407 Planarity : 0.003 0.034 1578 Dihedral : 5.319 65.671 1304 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.45 % Allowed : 20.28 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.58 (0.25), residues: 1130 helix: 0.90 (0.30), residues: 339 sheet: 0.18 (0.31), residues: 277 loop : -1.61 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.011 0.001 HIS E 161 PHE 0.034 0.001 PHE E 38 TYR 0.014 0.001 TYR S 190 ARG 0.004 0.000 ARG D 242 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 1.013 Fit side-chains REVERT: B 258 ASP cc_start: 0.7185 (p0) cc_final: 0.6971 (p0) REVERT: D 52 GLN cc_start: 0.6950 (OUTLIER) cc_final: 0.6613 (mt0) REVERT: D 53 MET cc_start: 0.5989 (mtp) cc_final: 0.5747 (mtp) REVERT: D 195 HIS cc_start: 0.7262 (OUTLIER) cc_final: 0.6755 (t70) REVERT: D 248 LYS cc_start: 0.7972 (tppt) cc_final: 0.7264 (mtpm) REVERT: D 270 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8351 (mtmp) REVERT: S 78 THR cc_start: 0.7847 (t) cc_final: 0.7600 (m) outliers start: 34 outliers final: 19 residues processed: 140 average time/residue: 1.1619 time to fit residues: 174.6806 Evaluate side-chains 137 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain S residue 64 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 223 HIS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 292 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9247 Z= 0.180 Angle : 0.591 8.828 12513 Z= 0.305 Chirality : 0.043 0.146 1407 Planarity : 0.003 0.034 1578 Dihedral : 5.271 62.280 1304 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.04 % Allowed : 21.20 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.51 (0.25), residues: 1130 helix: 0.96 (0.30), residues: 341 sheet: 0.23 (0.31), residues: 276 loop : -1.58 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.011 0.001 HIS E 161 PHE 0.033 0.001 PHE E 38 TYR 0.015 0.001 TYR B 105 ARG 0.004 0.000 ARG D 242 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 1.108 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6906 (ptm-80) REVERT: B 258 ASP cc_start: 0.7311 (p0) cc_final: 0.7052 (p0) REVERT: D 52 GLN cc_start: 0.6882 (OUTLIER) cc_final: 0.6622 (mt0) REVERT: D 53 MET cc_start: 0.5976 (mtp) cc_final: 0.5687 (mtp) REVERT: D 195 HIS cc_start: 0.7255 (OUTLIER) cc_final: 0.6741 (t70) REVERT: D 248 LYS cc_start: 0.7896 (tppt) cc_final: 0.7238 (mtpm) REVERT: D 270 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8261 (mtmp) REVERT: S 78 THR cc_start: 0.7820 (t) cc_final: 0.7590 (m) REVERT: E 103 MET cc_start: 0.7500 (tmt) cc_final: 0.7143 (tmt) REVERT: E 220 MET cc_start: 0.8056 (tpp) cc_final: 0.7823 (tpp) outliers start: 30 outliers final: 17 residues processed: 139 average time/residue: 1.1781 time to fit residues: 175.7409 Evaluate side-chains 139 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 223 HIS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 292 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 0.0070 chunk 111 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 88 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9247 Z= 0.156 Angle : 0.576 9.043 12513 Z= 0.297 Chirality : 0.042 0.147 1407 Planarity : 0.003 0.034 1578 Dihedral : 5.165 59.216 1304 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.13 % Allowed : 22.21 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.43 (0.25), residues: 1130 helix: 1.03 (0.31), residues: 341 sheet: 0.33 (0.32), residues: 270 loop : -1.55 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.011 0.001 HIS E 161 PHE 0.033 0.001 PHE E 38 TYR 0.014 0.001 TYR S 190 ARG 0.004 0.000 ARG D 242 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 1.144 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.6896 (ptm-80) REVERT: B 258 ASP cc_start: 0.7273 (p0) cc_final: 0.7051 (p0) REVERT: D 52 GLN cc_start: 0.6740 (OUTLIER) cc_final: 0.6529 (mt0) REVERT: D 53 MET cc_start: 0.5952 (mtp) cc_final: 0.5706 (mtp) REVERT: D 195 HIS cc_start: 0.7224 (OUTLIER) cc_final: 0.6709 (t70) REVERT: D 270 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8272 (mtmp) REVERT: S 78 THR cc_start: 0.7782 (t) cc_final: 0.7549 (m) REVERT: E 103 MET cc_start: 0.7419 (tmt) cc_final: 0.7174 (tmt) REVERT: E 220 MET cc_start: 0.8052 (tpp) cc_final: 0.7800 (tpp) outliers start: 21 outliers final: 15 residues processed: 128 average time/residue: 1.2091 time to fit residues: 166.1500 Evaluate side-chains 130 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 223 HIS Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 292 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 91 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.145127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.105979 restraints weight = 13947.404| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.53 r_work: 0.3322 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9247 Z= 0.162 Angle : 0.579 9.316 12513 Z= 0.299 Chirality : 0.042 0.174 1407 Planarity : 0.003 0.034 1578 Dihedral : 5.032 52.786 1304 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.43 % Allowed : 22.21 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.38 (0.25), residues: 1130 helix: 1.11 (0.31), residues: 339 sheet: 0.24 (0.31), residues: 279 loop : -1.49 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.011 0.001 HIS E 161 PHE 0.033 0.001 PHE E 38 TYR 0.013 0.001 TYR S 190 ARG 0.004 0.000 ARG D 242 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3680.55 seconds wall clock time: 66 minutes 58.72 seconds (4018.72 seconds total)