Starting phenix.real_space_refine on Sat May 10 12:30:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uo0_42423/05_2025/8uo0_42423.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uo0_42423/05_2025/8uo0_42423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uo0_42423/05_2025/8uo0_42423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uo0_42423/05_2025/8uo0_42423.map" model { file = "/net/cci-nas-00/data/ceres_data/8uo0_42423/05_2025/8uo0_42423.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uo0_42423/05_2025/8uo0_42423.cif" } resolution = 3.5 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= -0.000 sd= 0.019 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 30 5.16 5 C 4018 2.51 5 N 1076 2.21 5 O 1095 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6222 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1595 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 229, 1583 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 336 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 219 Conformer: "B" Number of residues, atoms: 229, 1583 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 336 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 17, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 219 bond proxies already assigned to first conformer: 1597 Chain: "B" Number of atoms: 2290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2290 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 337 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 6, 'ARG:plan': 10, 'ASN:plan1': 6, 'ASP:plan': 24} Unresolved non-hydrogen planarities: 196 Chain: "G" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 327 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "R" Number of atoms: 1963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 1963 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 344 Unresolved non-hydrogen angles: 431 Unresolved non-hydrogen dihedrals: 279 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 192 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 360 " occ=0.17 ... (22 atoms not shown) pdb=" OH BTYR A 360 " occ=0.83 Time building chain proxies: 5.52, per 1000 atoms: 0.89 Number of scatterers: 6222 At special positions: 0 Unit cell: (82.4315, 134.493, 98.0501, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 3 15.00 O 1095 8.00 N 1076 7.00 C 4018 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " 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: 1.69 Conformation dependent library (CDL) restraints added in 1.2 seconds 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1712 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 47.8% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.764A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.679A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 removed outlier: 3.789A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.682A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 333 through 352 removed outlier: 3.525A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 5 through 26 removed outlier: 3.634A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.654A pdb=" N THR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.807A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.881A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 61 removed outlier: 3.590A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE R 47 " --> pdb=" O ILE R 43 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL R 48 " --> pdb=" O VAL R 44 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 97 removed outlier: 4.126A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER R 74 " --> pdb=" O TYR R 70 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.693A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix removed outlier: 3.846A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 238 Processing helix chain 'R' and resid 269 through 299 removed outlier: 3.607A pdb=" N ILE R 278 " --> pdb=" O THR R 274 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.817A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.633A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 327 Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 339 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.674A pdb=" N THR A 210 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.143A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL A 287 " --> pdb=" O ATYR A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 49 removed outlier: 6.907A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.236A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.936A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.986A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 4.048A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.812A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.811A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 351 hydrogen bonds defined for protein. 1026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1058 1.32 - 1.45: 1741 1.45 - 1.57: 3513 1.57 - 1.69: 5 1.69 - 1.81: 39 Bond restraints: 6356 Sorted by residual: bond pdb=" C ALA A 18 " pdb=" O ALA A 18 " ideal model delta sigma weight residual 1.237 1.278 -0.041 1.17e-02 7.31e+03 1.25e+01 bond pdb=" N SER A 352 " pdb=" CA SER A 352 " ideal model delta sigma weight residual 1.454 1.496 -0.043 1.23e-02 6.61e+03 1.22e+01 bond pdb=" N VAL A 301 " pdb=" CA VAL A 301 " ideal model delta sigma weight residual 1.460 1.502 -0.042 1.21e-02 6.83e+03 1.21e+01 bond pdb=" C LYS A 58 " pdb=" O LYS A 58 " ideal model delta sigma weight residual 1.236 1.272 -0.035 1.15e-02 7.56e+03 9.46e+00 bond pdb=" CA SER A 275 " pdb=" CB SER A 275 " ideal model delta sigma weight residual 1.530 1.483 0.047 1.56e-02 4.11e+03 9.00e+00 ... (remaining 6351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 8505 2.67 - 5.34: 196 5.34 - 8.01: 21 8.01 - 10.68: 9 10.68 - 13.34: 3 Bond angle restraints: 8734 Sorted by residual: angle pdb=" N PRO A 332 " pdb=" CA PRO A 332 " pdb=" C PRO A 332 " ideal model delta sigma weight residual 113.53 100.73 12.80 1.39e+00 5.18e-01 8.48e+01 angle pdb=" N ASN A 23 " pdb=" CA ASN A 23 " pdb=" C ASN A 23 " ideal model delta sigma weight residual 111.28 103.13 8.15 1.09e+00 8.42e-01 5.59e+01 angle pdb=" N LEU A 270 " pdb=" CA LEU A 270 " pdb=" C LEU A 270 " ideal model delta sigma weight residual 111.28 104.14 7.14 1.09e+00 8.42e-01 4.29e+01 angle pdb=" N GLN A 267 " pdb=" CA GLN A 267 " pdb=" C GLN A 267 " ideal model delta sigma weight residual 111.28 104.35 6.93 1.09e+00 8.42e-01 4.04e+01 angle pdb=" N PRO A 328 " pdb=" CA PRO A 328 " pdb=" C PRO A 328 " ideal model delta sigma weight residual 111.26 101.71 9.55 1.63e+00 3.76e-01 3.43e+01 ... (remaining 8729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.25: 3545 33.25 - 66.49: 70 66.49 - 99.74: 0 99.74 - 132.98: 1 132.98 - 166.23: 2 Dihedral angle restraints: 3618 sinusoidal: 985 harmonic: 2633 Sorted by residual: dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -96.96 166.23 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -48.14 152.74 1 2.00e+01 2.50e-03 4.53e+01 dihedral pdb=" O3B GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PB GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual -68.92 -172.61 103.69 1 2.00e+01 2.50e-03 2.97e+01 ... (remaining 3615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 759 0.047 - 0.094: 188 0.094 - 0.141: 82 0.141 - 0.189: 35 0.189 - 0.236: 6 Chirality restraints: 1070 Sorted by residual: chirality pdb=" CA GLU A 230 " pdb=" N GLU A 230 " pdb=" C GLU A 230 " pdb=" CB GLU A 230 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ARG A 20 " pdb=" N ARG A 20 " pdb=" C ARG A 20 " pdb=" CB ARG A 20 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA ILE G 9 " pdb=" N ILE G 9 " pdb=" C ILE G 9 " pdb=" CB ILE G 9 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1067 not shown) Planarity restraints: 1095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 333 " -0.233 9.50e-02 1.11e+02 1.05e-01 6.71e+00 pdb=" NE ARG A 333 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 333 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 333 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 333 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 28 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" C LYS A 28 " 0.043 2.00e-02 2.50e+03 pdb=" O LYS A 28 " -0.016 2.00e-02 2.50e+03 pdb=" N GLN A 29 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 29 " -0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C GLN A 29 " 0.042 2.00e-02 2.50e+03 pdb=" O GLN A 29 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU A 30 " -0.015 2.00e-02 2.50e+03 ... (remaining 1092 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1580 2.79 - 3.32: 5825 3.32 - 3.85: 9667 3.85 - 4.37: 10099 4.37 - 4.90: 18574 Nonbonded interactions: 45745 Sorted by model distance: nonbonded pdb=" OD2 ASP B 83 " pdb=" OG1 THR B 86 " model vdw 2.268 3.040 nonbonded pdb=" O LEU A 272 " pdb=" OG SER A 275 " model vdw 2.274 3.040 nonbonded pdb=" N GLN B 259 " pdb=" OE1 GLN B 259 " model vdw 2.312 3.120 nonbonded pdb=" O VAL R 34 " pdb=" N GLY R 37 " model vdw 2.327 3.120 nonbonded pdb=" O ILE B 37 " pdb=" NZ LYS B 301 " model vdw 2.338 3.120 ... (remaining 45740 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=0.17 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: 2.400 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.190 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 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 : 0.006 0.054 6357 Z= 0.405 Angle : 0.928 13.344 8736 Z= 0.633 Chirality : 0.057 0.236 1070 Planarity : 0.005 0.105 1095 Dihedral : 13.945 166.231 1903 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.21 % Allowed : 0.62 % Favored : 99.18 % 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: 1.21 (0.29), residues: 885 helix: 2.48 (0.27), residues: 373 sheet: 0.36 (0.39), residues: 184 loop : -0.93 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 332 HIS 0.009 0.001 HIS R 296 PHE 0.011 0.001 PHE R 104 TYR 0.034 0.002 TYR R 185 ARG 0.004 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.20514 ( 351) hydrogen bonds : angle 6.78233 ( 1026) SS BOND : bond 0.00127 ( 1) SS BOND : angle 0.22981 ( 2) covalent geometry : bond 0.00586 ( 6356) covalent geometry : angle 0.92770 ( 8734) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.668 Fit side-chains REVERT: A 267 GLN cc_start: 0.8654 (tp-100) cc_final: 0.8269 (tp40) REVERT: B 110 ASN cc_start: 0.9283 (m-40) cc_final: 0.8919 (m110) REVERT: R 161 SER cc_start: 0.8939 (t) cc_final: 0.8470 (p) outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.1712 time to fit residues: 23.5130 Evaluate side-chains 76 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 44 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.125032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.097251 restraints weight = 35491.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.101395 restraints weight = 11291.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.104221 restraints weight = 5998.358| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6357 Z= 0.163 Angle : 0.523 6.518 8736 Z= 0.288 Chirality : 0.041 0.137 1070 Planarity : 0.003 0.033 1095 Dihedral : 9.012 154.366 972 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.46 % Allowed : 10.27 % Favored : 87.27 % 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: 1.09 (0.28), residues: 885 helix: 2.34 (0.26), residues: 399 sheet: 0.18 (0.40), residues: 175 loop : -1.12 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.006 0.001 HIS A 357 PHE 0.012 0.001 PHE R 104 TYR 0.024 0.001 TYR R 185 ARG 0.003 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.05414 ( 351) hydrogen bonds : angle 4.63846 ( 1026) SS BOND : bond 0.00161 ( 1) SS BOND : angle 0.06773 ( 2) covalent geometry : bond 0.00366 ( 6356) covalent geometry : angle 0.52333 ( 8734) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.720 Fit side-chains REVERT: A 267 GLN cc_start: 0.8104 (tp-100) cc_final: 0.7866 (tp40) outliers start: 12 outliers final: 11 residues processed: 80 average time/residue: 0.1619 time to fit residues: 18.1430 Evaluate side-chains 82 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 307 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.123642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.096825 restraints weight = 43238.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.100069 restraints weight = 15973.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.102608 restraints weight = 6970.198| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6357 Z= 0.127 Angle : 0.466 6.498 8736 Z= 0.259 Chirality : 0.040 0.134 1070 Planarity : 0.003 0.031 1095 Dihedral : 8.603 149.209 972 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.85 % Allowed : 13.55 % Favored : 84.60 % 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: 1.31 (0.29), residues: 885 helix: 2.76 (0.26), residues: 391 sheet: 0.06 (0.39), residues: 183 loop : -1.15 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 PHE 0.010 0.001 PHE B 199 TYR 0.023 0.001 TYR R 185 ARG 0.004 0.000 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.04782 ( 351) hydrogen bonds : angle 4.19844 ( 1026) SS BOND : bond 0.00106 ( 1) SS BOND : angle 0.17842 ( 2) covalent geometry : bond 0.00277 ( 6356) covalent geometry : angle 0.46608 ( 8734) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.702 Fit side-chains REVERT: A 267 GLN cc_start: 0.8139 (tp-100) cc_final: 0.7865 (tp40) REVERT: B 58 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8515 (pt) outliers start: 9 outliers final: 8 residues processed: 77 average time/residue: 0.1506 time to fit residues: 16.4362 Evaluate side-chains 84 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 307 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 19 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.126739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.099845 restraints weight = 44099.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.104095 restraints weight = 14275.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.107335 restraints weight = 6352.807| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6357 Z= 0.110 Angle : 0.443 6.094 8736 Z= 0.245 Chirality : 0.039 0.132 1070 Planarity : 0.003 0.030 1095 Dihedral : 8.176 147.017 972 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.29 % Allowed : 13.76 % Favored : 82.96 % 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: 1.49 (0.29), residues: 885 helix: 2.97 (0.26), residues: 392 sheet: 0.03 (0.38), residues: 182 loop : -1.09 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.006 0.001 HIS A 357 PHE 0.010 0.001 PHE B 199 TYR 0.026 0.001 TYR R 185 ARG 0.003 0.000 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.04200 ( 351) hydrogen bonds : angle 3.90061 ( 1026) SS BOND : bond 0.00112 ( 1) SS BOND : angle 0.23329 ( 2) covalent geometry : bond 0.00236 ( 6356) covalent geometry : angle 0.44275 ( 8734) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.648 Fit side-chains REVERT: A 211 LYS cc_start: 0.8255 (ttmm) cc_final: 0.7667 (mmtt) outliers start: 16 outliers final: 14 residues processed: 86 average time/residue: 0.1566 time to fit residues: 18.5627 Evaluate side-chains 87 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 171 MET Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 307 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 52 optimal weight: 0.0470 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 81 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 225 HIS ** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.128065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.100601 restraints weight = 38938.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.105012 restraints weight = 13210.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.108483 restraints weight = 6029.792| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6357 Z= 0.098 Angle : 0.429 5.960 8736 Z= 0.236 Chirality : 0.039 0.139 1070 Planarity : 0.003 0.029 1095 Dihedral : 7.827 144.813 972 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.49 % Allowed : 15.20 % Favored : 81.31 % 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: 1.63 (0.29), residues: 885 helix: 2.97 (0.26), residues: 398 sheet: 0.18 (0.38), residues: 185 loop : -0.97 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 277 HIS 0.005 0.001 HIS A 357 PHE 0.009 0.001 PHE B 199 TYR 0.035 0.001 TYR R 185 ARG 0.005 0.000 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 351) hydrogen bonds : angle 3.77424 ( 1026) SS BOND : bond 0.00145 ( 1) SS BOND : angle 0.28435 ( 2) covalent geometry : bond 0.00198 ( 6356) covalent geometry : angle 0.42869 ( 8734) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.714 Fit side-chains REVERT: A 211 LYS cc_start: 0.8294 (ttmm) cc_final: 0.7774 (mmtt) REVERT: B 58 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8620 (pt) REVERT: B 234 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8610 (m-80) outliers start: 17 outliers final: 11 residues processed: 85 average time/residue: 0.1504 time to fit residues: 17.9935 Evaluate side-chains 88 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 307 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 6 optimal weight: 5.9990 chunk 57 optimal weight: 0.0050 chunk 28 optimal weight: 2.9990 chunk 64 optimal weight: 0.0270 chunk 7 optimal weight: 0.0670 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 overall best weight: 0.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.131585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.103621 restraints weight = 33256.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.107954 restraints weight = 10863.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.110857 restraints weight = 5806.183| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6357 Z= 0.082 Angle : 0.407 5.669 8736 Z= 0.223 Chirality : 0.039 0.154 1070 Planarity : 0.002 0.028 1095 Dihedral : 7.290 140.388 972 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.49 % Allowed : 15.61 % Favored : 80.90 % 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: 1.79 (0.29), residues: 885 helix: 3.07 (0.26), residues: 397 sheet: 0.34 (0.38), residues: 178 loop : -0.87 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 277 HIS 0.004 0.001 HIS A 357 PHE 0.008 0.001 PHE R 104 TYR 0.010 0.001 TYR R 185 ARG 0.005 0.000 ARG A 231 Details of bonding type rmsd hydrogen bonds : bond 0.02991 ( 351) hydrogen bonds : angle 3.52464 ( 1026) SS BOND : bond 0.00194 ( 1) SS BOND : angle 0.34715 ( 2) covalent geometry : bond 0.00157 ( 6356) covalent geometry : angle 0.40729 ( 8734) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.764 Fit side-chains REVERT: A 211 LYS cc_start: 0.8283 (ttmm) cc_final: 0.7908 (mmtt) REVERT: B 234 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8654 (m-80) REVERT: R 185 TYR cc_start: 0.7234 (m-80) cc_final: 0.6978 (m-80) outliers start: 17 outliers final: 13 residues processed: 93 average time/residue: 0.1527 time to fit residues: 20.3367 Evaluate side-chains 92 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 332 TRP Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 171 MET Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 55 optimal weight: 8.9990 chunk 87 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 50 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.128246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.100781 restraints weight = 51294.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.104800 restraints weight = 15452.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.108341 restraints weight = 6747.174| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6357 Z= 0.103 Angle : 0.430 5.754 8736 Z= 0.235 Chirality : 0.039 0.155 1070 Planarity : 0.002 0.029 1095 Dihedral : 7.156 137.417 972 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.67 % Allowed : 17.45 % Favored : 79.88 % 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: 1.74 (0.29), residues: 885 helix: 3.09 (0.26), residues: 399 sheet: 0.14 (0.38), residues: 182 loop : -0.92 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 277 HIS 0.006 0.001 HIS A 357 PHE 0.010 0.001 PHE B 199 TYR 0.006 0.001 TYR R 199 ARG 0.001 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.03601 ( 351) hydrogen bonds : angle 3.59980 ( 1026) SS BOND : bond 0.00083 ( 1) SS BOND : angle 0.22139 ( 2) covalent geometry : bond 0.00224 ( 6356) covalent geometry : angle 0.42969 ( 8734) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.657 Fit side-chains REVERT: A 211 LYS cc_start: 0.8304 (ttmm) cc_final: 0.7741 (mmtt) REVERT: R 185 TYR cc_start: 0.7292 (m-80) cc_final: 0.6952 (m-80) outliers start: 13 outliers final: 12 residues processed: 86 average time/residue: 0.1441 time to fit residues: 17.7292 Evaluate side-chains 88 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 332 TRP Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 0.0980 chunk 82 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.125684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.097749 restraints weight = 38136.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.102027 restraints weight = 11645.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.104900 restraints weight = 6093.743| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6357 Z= 0.126 Angle : 0.458 5.771 8736 Z= 0.252 Chirality : 0.040 0.156 1070 Planarity : 0.003 0.030 1095 Dihedral : 7.113 133.340 972 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.90 % Allowed : 16.63 % Favored : 79.47 % 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: 1.70 (0.29), residues: 885 helix: 3.09 (0.26), residues: 398 sheet: 0.21 (0.37), residues: 189 loop : -1.06 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 277 HIS 0.009 0.001 HIS A 357 PHE 0.011 0.001 PHE B 199 TYR 0.008 0.001 TYR R 199 ARG 0.002 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 351) hydrogen bonds : angle 3.78800 ( 1026) SS BOND : bond 0.00029 ( 1) SS BOND : angle 0.12009 ( 2) covalent geometry : bond 0.00284 ( 6356) covalent geometry : angle 0.45774 ( 8734) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.746 Fit side-chains REVERT: A 211 LYS cc_start: 0.8299 (ttmm) cc_final: 0.7721 (mmtt) REVERT: B 58 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8670 (pt) REVERT: B 234 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8613 (m-80) REVERT: R 185 TYR cc_start: 0.7427 (m-80) cc_final: 0.6862 (m-80) outliers start: 19 outliers final: 16 residues processed: 89 average time/residue: 0.1310 time to fit residues: 16.8199 Evaluate side-chains 93 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 332 TRP Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 48 optimal weight: 0.0000 chunk 63 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.127503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.099610 restraints weight = 40420.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.104350 restraints weight = 12029.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.106529 restraints weight = 6300.529| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6357 Z= 0.096 Angle : 0.424 5.665 8736 Z= 0.234 Chirality : 0.039 0.157 1070 Planarity : 0.003 0.029 1095 Dihedral : 6.938 129.517 972 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.49 % Allowed : 17.66 % Favored : 78.85 % 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: 1.77 (0.29), residues: 885 helix: 3.15 (0.26), residues: 397 sheet: 0.20 (0.37), residues: 190 loop : -0.97 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 277 HIS 0.006 0.001 HIS A 357 PHE 0.009 0.001 PHE B 199 TYR 0.015 0.001 TYR R 174 ARG 0.001 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 351) hydrogen bonds : angle 3.62350 ( 1026) SS BOND : bond 0.00122 ( 1) SS BOND : angle 0.21741 ( 2) covalent geometry : bond 0.00200 ( 6356) covalent geometry : angle 0.42446 ( 8734) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.625 Fit side-chains REVERT: A 211 LYS cc_start: 0.8345 (ttmm) cc_final: 0.7802 (mmtt) REVERT: B 234 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8587 (m-80) REVERT: R 185 TYR cc_start: 0.7204 (m-80) cc_final: 0.6853 (m-80) outliers start: 17 outliers final: 15 residues processed: 86 average time/residue: 0.1363 time to fit residues: 16.9556 Evaluate side-chains 91 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 332 TRP Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 73 optimal weight: 0.0980 chunk 13 optimal weight: 0.0010 chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.129090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.100856 restraints weight = 39215.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.105233 restraints weight = 11737.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.108210 restraints weight = 6119.446| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6357 Z= 0.088 Angle : 0.409 5.734 8736 Z= 0.225 Chirality : 0.039 0.164 1070 Planarity : 0.002 0.028 1095 Dihedral : 6.444 121.099 972 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.49 % Allowed : 18.07 % Favored : 78.44 % 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: 1.79 (0.29), residues: 885 helix: 3.17 (0.26), residues: 398 sheet: 0.18 (0.39), residues: 180 loop : -0.94 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 277 HIS 0.005 0.001 HIS A 357 PHE 0.008 0.001 PHE B 199 TYR 0.014 0.001 TYR R 174 ARG 0.002 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.03308 ( 351) hydrogen bonds : angle 3.48096 ( 1026) SS BOND : bond 0.00110 ( 1) SS BOND : angle 0.24785 ( 2) covalent geometry : bond 0.00179 ( 6356) covalent geometry : angle 0.40907 ( 8734) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.651 Fit side-chains REVERT: A 211 LYS cc_start: 0.8298 (ttmm) cc_final: 0.7911 (mmtt) REVERT: B 58 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8658 (pt) REVERT: B 234 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.8647 (m-80) REVERT: R 185 TYR cc_start: 0.7245 (m-80) cc_final: 0.6905 (m-80) outliers start: 17 outliers final: 14 residues processed: 89 average time/residue: 0.1339 time to fit residues: 17.1334 Evaluate side-chains 93 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 332 TRP Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 chunk 73 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.126460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.098107 restraints weight = 40204.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.102442 restraints weight = 11992.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.105410 restraints weight = 6240.456| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6357 Z= 0.124 Angle : 0.451 5.693 8736 Z= 0.249 Chirality : 0.040 0.161 1070 Planarity : 0.003 0.030 1095 Dihedral : 6.289 113.958 972 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.70 % Allowed : 17.45 % Favored : 78.85 % 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: 1.70 (0.29), residues: 885 helix: 3.13 (0.26), residues: 398 sheet: 0.13 (0.37), residues: 189 loop : -1.06 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 277 HIS 0.007 0.001 HIS A 357 PHE 0.011 0.001 PHE B 241 TYR 0.014 0.001 TYR R 174 ARG 0.002 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 351) hydrogen bonds : angle 3.68556 ( 1026) SS BOND : bond 0.00042 ( 1) SS BOND : angle 0.12867 ( 2) covalent geometry : bond 0.00284 ( 6356) covalent geometry : angle 0.45111 ( 8734) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2572.58 seconds wall clock time: 45 minutes 34.22 seconds (2734.22 seconds total)