Starting phenix.real_space_refine on Tue Apr 29 14:04:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zps_60353/04_2025/8zps_60353_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zps_60353/04_2025/8zps_60353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zps_60353/04_2025/8zps_60353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zps_60353/04_2025/8zps_60353.map" model { file = "/net/cci-nas-00/data/ceres_data/8zps_60353/04_2025/8zps_60353_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zps_60353/04_2025/8zps_60353_neut.cif" } resolution = 2.97 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= 0.002 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 53 5.16 5 C 5645 2.51 5 N 1561 2.21 5 O 1589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8848 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1709 Classifications: {'peptide': 208} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 205} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2537 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "E" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1698 Classifications: {'peptide': 228} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 217} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "G" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 409 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 161 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 3, 'TRANS': 16} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2333 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.28, per 1000 atoms: 0.60 Number of scatterers: 8848 At special positions: 0 Unit cell: (84.872, 119.48, 131.016, 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 53 16.00 O 1589 8.00 N 1561 7.00 C 5645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 977.8 milliseconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 13 sheets defined 37.3% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.643A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.574A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 246 through 250 removed outlier: 3.649A pdb=" N ARG A 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 268 removed outlier: 3.794A pdb=" N GLU A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.796A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 359 Processing helix chain 'B' and resid 12 through 30 Processing helix chain 'B' and resid 35 through 40 removed outlier: 4.158A pdb=" N ASN B 40 " --> pdb=" O SER B 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.200A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 19 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.663A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'L' and resid 4 through 11 removed outlier: 4.103A pdb=" N TRP L 8 " --> pdb=" O ILE L 4 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER L 11 " --> pdb=" O ALA L 7 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 88 removed outlier: 3.765A pdb=" N ILE R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL R 88 " --> pdb=" O VAL R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 92 Processing helix chain 'R' and resid 93 through 123 Proline residue: R 115 - end of helix removed outlier: 3.653A pdb=" N ALA R 119 " --> pdb=" O PRO R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 164 removed outlier: 3.819A pdb=" N LEU R 136 " --> pdb=" O GLY R 132 " (cutoff:3.500A) Proline residue: R 142 - end of helix Processing helix chain 'R' and resid 172 through 198 Proline residue: R 193 - end of helix Processing helix chain 'R' and resid 220 through 255 removed outlier: 3.984A pdb=" N LEU R 224 " --> pdb=" O ARG R 220 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU R 236 " --> pdb=" O VAL R 232 " (cutoff:3.500A) Proline residue: R 237 - end of helix Processing helix chain 'R' and resid 267 through 304 Proline residue: R 293 - end of helix removed outlier: 3.555A pdb=" N ASP R 304 " --> pdb=" O LEU R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 312 through 337 removed outlier: 3.820A pdb=" N SER R 327 " --> pdb=" O LEU R 323 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA R 328 " --> pdb=" O ALA R 324 " (cutoff:3.500A) Proline residue: R 332 - end of helix Processing helix chain 'R' and resid 339 through 351 removed outlier: 3.838A pdb=" N ARG R 343 " --> pdb=" O HIS R 339 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU R 345 " --> pdb=" O SER R 341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.449A pdb=" N HIS A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N PHE A 199 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.884A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 6.451A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.722A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 85 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS B 96 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 3.698A pdb=" N SER B 127 " --> pdb=" O CYS B 119 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N CYS B 126 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU B 143 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG B 139 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 153 through 156 removed outlier: 3.584A pdb=" N ALA B 172 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR B 183 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.925A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 208 " --> pdb=" O SER B 212 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 4.066A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 4.680A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN B 300 " --> pdb=" O ALA B 292 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY B 311 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.485A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.508A pdb=" N THR E 141 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG E 160 " --> pdb=" O THR E 141 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 194 through 195 removed outlier: 6.848A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 199 through 200 424 hydrogen bonds defined for protein. 1197 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: 2.64 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2467 1.33 - 1.45: 1566 1.45 - 1.57: 4930 1.57 - 1.69: 0 1.69 - 1.81: 73 Bond restraints: 9036 Sorted by residual: bond pdb=" N LYS A 352 " pdb=" CA LYS A 352 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.23e-02 6.61e+03 9.07e+00 bond pdb=" N VAL R 201 " pdb=" CA VAL R 201 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.88e+00 bond pdb=" N VAL R 208 " pdb=" CA VAL R 208 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.07e-02 8.73e+03 8.58e+00 bond pdb=" N GLU E 6 " pdb=" CA GLU E 6 " ideal model delta sigma weight residual 1.454 1.491 -0.036 1.27e-02 6.20e+03 8.12e+00 bond pdb=" N SER E 7 " pdb=" CA SER E 7 " ideal model delta sigma weight residual 1.455 1.489 -0.035 1.29e-02 6.01e+03 7.20e+00 ... (remaining 9031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 11889 1.28 - 2.56: 265 2.56 - 3.84: 83 3.84 - 5.12: 21 5.12 - 6.41: 9 Bond angle restraints: 12267 Sorted by residual: angle pdb=" CA VAL R 208 " pdb=" C VAL R 208 " pdb=" O VAL R 208 " ideal model delta sigma weight residual 121.09 117.17 3.92 8.20e-01 1.49e+00 2.28e+01 angle pdb=" C HIS R 206 " pdb=" N ASP R 207 " pdb=" CA ASP R 207 " ideal model delta sigma weight residual 122.42 116.19 6.23 1.33e+00 5.65e-01 2.20e+01 angle pdb=" N GLY A 359 " pdb=" CA GLY A 359 " pdb=" C GLY A 359 " ideal model delta sigma weight residual 115.30 108.89 6.41 1.39e+00 5.18e-01 2.12e+01 angle pdb=" N THR R 117 " pdb=" CA THR R 117 " pdb=" C THR R 117 " ideal model delta sigma weight residual 112.54 106.93 5.61 1.22e+00 6.72e-01 2.12e+01 angle pdb=" N MET A 353 " pdb=" CA MET A 353 " pdb=" C MET A 353 " ideal model delta sigma weight residual 111.28 106.70 4.58 1.09e+00 8.42e-01 1.77e+01 ... (remaining 12262 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.62: 4989 13.62 - 27.24: 230 27.24 - 40.87: 76 40.87 - 54.49: 23 54.49 - 68.11: 6 Dihedral angle restraints: 5324 sinusoidal: 2038 harmonic: 3286 Sorted by residual: dihedral pdb=" CA CYS R 113 " pdb=" C CYS R 113 " pdb=" N VAL R 114 " pdb=" CA VAL R 114 " ideal model delta harmonic sigma weight residual -180.00 -164.32 -15.68 0 5.00e+00 4.00e-02 9.84e+00 dihedral pdb=" N LEU A 355 " pdb=" CA LEU A 355 " pdb=" CB LEU A 355 " pdb=" CG LEU A 355 " ideal model delta sinusoidal sigma weight residual -60.00 -118.48 58.48 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N MET A 353 " pdb=" CA MET A 353 " pdb=" CB MET A 353 " pdb=" CG MET A 353 " ideal model delta sinusoidal sigma weight residual 60.00 117.77 -57.77 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 5321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1154 0.049 - 0.099: 201 0.099 - 0.148: 46 0.148 - 0.198: 2 0.198 - 0.247: 2 Chirality restraints: 1405 Sorted by residual: chirality pdb=" CA VAL R 208 " pdb=" N VAL R 208 " pdb=" C VAL R 208 " pdb=" CB VAL R 208 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA VAL E 5 " pdb=" N VAL E 5 " pdb=" C VAL E 5 " pdb=" CB VAL E 5 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA LEU A 360 " pdb=" N LEU A 360 " pdb=" C LEU A 360 " pdb=" CB LEU A 360 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.15e-01 ... (remaining 1402 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 351 " 0.026 2.00e-02 2.50e+03 5.10e-02 2.60e+01 pdb=" C ILE A 351 " -0.088 2.00e-02 2.50e+03 pdb=" O ILE A 351 " 0.033 2.00e-02 2.50e+03 pdb=" N LYS A 352 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 4 " 0.022 2.00e-02 2.50e+03 4.54e-02 2.06e+01 pdb=" C LEU E 4 " -0.079 2.00e-02 2.50e+03 pdb=" O LEU E 4 " 0.030 2.00e-02 2.50e+03 pdb=" N VAL E 5 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 208 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C VAL R 208 " -0.029 2.00e-02 2.50e+03 pdb=" O VAL R 208 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG R 209 " 0.010 2.00e-02 2.50e+03 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.38: 14 2.38 - 3.01: 4718 3.01 - 3.64: 13013 3.64 - 4.27: 19335 4.27 - 4.90: 32934 Nonbonded interactions: 70014 Sorted by model distance: nonbonded pdb=" OG SER E 7 " pdb=" OG SER E 21 " model vdw 1.744 3.040 nonbonded pdb=" O LEU B 35 " pdb=" OG1 THR B 39 " model vdw 2.272 3.040 nonbonded pdb=" OG SER B 152 " pdb=" O MET B 193 " model vdw 2.274 3.040 nonbonded pdb=" OG SER B 336 " pdb=" OD1 ASP B 338 " model vdw 2.281 3.040 nonbonded pdb=" ND2 ASN R 93 " pdb=" OD1 ASN R 96 " model vdw 2.285 3.120 ... (remaining 70009 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: 1.850 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: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.080 Find NCS groups from input model: 0.110 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:11.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 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 : 0.003 0.101 9038 Z= 0.197 Angle : 0.537 6.406 12269 Z= 0.331 Chirality : 0.040 0.247 1405 Planarity : 0.003 0.051 1548 Dihedral : 9.774 68.111 3199 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.06 % Allowed : 7.77 % Favored : 91.17 % 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 (0.26), residues: 1111 helix: 2.74 (0.26), residues: 379 sheet: 1.54 (0.33), residues: 254 loop : -0.84 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 174 HIS 0.003 0.001 HIS A 324 PHE 0.006 0.001 PHE B 204 TYR 0.006 0.001 TYR E 95 ARG 0.002 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.19171 ( 424) hydrogen bonds : angle 6.30726 ( 1197) SS BOND : bond 0.00220 ( 1) SS BOND : angle 0.36308 ( 2) covalent geometry : bond 0.00238 ( 9036) covalent geometry : angle 0.53672 (12267) Misc. bond : bond 0.10123 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 196 time to evaluate : 0.973 Fit side-chains REVERT: A 192 ASP cc_start: 0.6767 (p0) cc_final: 0.6535 (m-30) REVERT: A 198 MET cc_start: 0.8634 (ttp) cc_final: 0.8361 (ttp) REVERT: A 208 ARG cc_start: 0.6847 (ptp-110) cc_final: 0.6480 (ttm110) REVERT: A 309 ARG cc_start: 0.4397 (mtp-110) cc_final: 0.3971 (tmm-80) REVERT: A 330 PHE cc_start: 0.5931 (m-10) cc_final: 0.4135 (t80) REVERT: B 20 LYS cc_start: 0.5740 (mptm) cc_final: 0.5450 (mmtm) REVERT: B 103 SER cc_start: 0.6905 (m) cc_final: 0.6634 (p) REVERT: B 105 VAL cc_start: 0.7293 (m) cc_final: 0.6987 (p) REVERT: B 142 ARG cc_start: 0.6466 (tpp-160) cc_final: 0.6116 (tpp80) REVERT: B 219 ARG cc_start: 0.5850 (mtm110) cc_final: 0.5377 (mpt180) REVERT: B 261 ARG cc_start: 0.6994 (mtm180) cc_final: 0.6405 (mmt90) REVERT: B 272 ASP cc_start: 0.7225 (m-30) cc_final: 0.6737 (p0) REVERT: B 285 LYS cc_start: 0.7446 (tttm) cc_final: 0.7225 (tttm) REVERT: E 155 VAL cc_start: 0.7549 (p) cc_final: 0.7341 (p) REVERT: E 234 GLU cc_start: 0.6534 (mt-10) cc_final: 0.6278 (mp0) REVERT: G 16 VAL cc_start: 0.5479 (t) cc_final: 0.4962 (m) REVERT: R 277 PHE cc_start: 0.4980 (m-10) cc_final: 0.4553 (t80) REVERT: R 279 LEU cc_start: 0.6792 (tm) cc_final: 0.6210 (mt) REVERT: R 322 TRP cc_start: 0.5930 (t60) cc_final: 0.5713 (t60) outliers start: 10 outliers final: 3 residues processed: 203 average time/residue: 1.0483 time to fit residues: 228.3022 Evaluate side-chains 122 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain R residue 276 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 33 optimal weight: 0.0980 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 99 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 246 ASN B 21 ASN ** B 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS E 3 GLN E 82 GLN L 5 ASN R 96 ASN R 141 GLN R 165 HIS R 223 GLN R 331 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.203360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.167462 restraints weight = 9754.209| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 1.82 r_work: 0.3767 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9038 Z= 0.180 Angle : 0.619 6.444 12269 Z= 0.320 Chirality : 0.044 0.189 1405 Planarity : 0.005 0.044 1548 Dihedral : 4.665 58.533 1245 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.40 % Allowed : 13.19 % Favored : 83.40 % 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: 1.37 (0.26), residues: 1111 helix: 2.48 (0.26), residues: 386 sheet: 1.31 (0.31), residues: 270 loop : -0.77 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 216 HIS 0.010 0.002 HIS A 324 PHE 0.021 0.002 PHE B 239 TYR 0.015 0.002 TYR B 64 ARG 0.007 0.001 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.04297 ( 424) hydrogen bonds : angle 4.50285 ( 1197) SS BOND : bond 0.00266 ( 1) SS BOND : angle 1.01030 ( 2) covalent geometry : bond 0.00401 ( 9036) covalent geometry : angle 0.61899 (12267) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 1.037 Fit side-chains REVERT: A 21 LYS cc_start: 0.7641 (mttt) cc_final: 0.7400 (mttm) REVERT: A 195 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7592 (m110) REVERT: A 208 ARG cc_start: 0.7339 (ptp-110) cc_final: 0.7022 (ttm110) REVERT: A 309 ARG cc_start: 0.5755 (mtp-110) cc_final: 0.5146 (tmm-80) REVERT: B 180 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.7033 (pp30) REVERT: B 194 SER cc_start: 0.8513 (p) cc_final: 0.7973 (t) REVERT: B 219 ARG cc_start: 0.6529 (mtm110) cc_final: 0.6250 (mpt180) REVERT: B 242 ASN cc_start: 0.6969 (t0) cc_final: 0.6691 (t0) REVERT: B 260 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7365 (mp) REVERT: B 272 ASP cc_start: 0.7499 (m-30) cc_final: 0.7214 (p0) REVERT: B 327 ASP cc_start: 0.5476 (m-30) cc_final: 0.5187 (m-30) REVERT: E 155 VAL cc_start: 0.7728 (OUTLIER) cc_final: 0.7522 (t) REVERT: G 16 VAL cc_start: 0.5773 (t) cc_final: 0.5347 (m) REVERT: G 22 GLU cc_start: 0.5535 (mt-10) cc_final: 0.5271 (mt-10) REVERT: R 247 ARG cc_start: 0.5585 (mmm-85) cc_final: 0.5101 (tpt170) REVERT: R 277 PHE cc_start: 0.5191 (m-10) cc_final: 0.4682 (t80) REVERT: R 292 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6770 (tp) REVERT: R 322 TRP cc_start: 0.6186 (t60) cc_final: 0.5845 (t60) outliers start: 32 outliers final: 11 residues processed: 156 average time/residue: 1.1716 time to fit residues: 195.6262 Evaluate side-chains 120 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 319 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 21 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** B 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN R 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.203101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.168051 restraints weight = 9881.045| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 1.87 r_work: 0.3749 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9038 Z= 0.119 Angle : 0.532 8.567 12269 Z= 0.274 Chirality : 0.041 0.190 1405 Planarity : 0.004 0.034 1548 Dihedral : 4.401 54.334 1244 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.72 % Allowed : 16.28 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.26), residues: 1111 helix: 2.59 (0.26), residues: 387 sheet: 1.44 (0.32), residues: 261 loop : -0.73 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.006 0.001 HIS A 324 PHE 0.011 0.001 PHE A 189 TYR 0.012 0.001 TYR E 95 ARG 0.009 0.001 ARG A 250 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 424) hydrogen bonds : angle 4.18548 ( 1197) SS BOND : bond 0.00405 ( 1) SS BOND : angle 0.99843 ( 2) covalent geometry : bond 0.00259 ( 9036) covalent geometry : angle 0.53156 (12267) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 104 time to evaluate : 0.967 Fit side-chains REVERT: A 195 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7730 (m110) REVERT: A 309 ARG cc_start: 0.5566 (mtp-110) cc_final: 0.5151 (tmm-80) REVERT: B 168 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6528 (p0) REVERT: B 180 GLN cc_start: 0.7421 (pp30) cc_final: 0.7084 (pp30) REVERT: B 219 ARG cc_start: 0.6322 (mtm110) cc_final: 0.5890 (mpp-170) REVERT: B 265 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6550 (mm-30) REVERT: B 272 ASP cc_start: 0.7465 (m-30) cc_final: 0.7174 (p0) REVERT: G 22 GLU cc_start: 0.5506 (mt-10) cc_final: 0.5183 (mt-10) REVERT: R 167 LEU cc_start: 0.5885 (OUTLIER) cc_final: 0.5604 (mt) REVERT: R 247 ARG cc_start: 0.5642 (mmm-85) cc_final: 0.5116 (tpt170) REVERT: R 277 PHE cc_start: 0.5172 (m-10) cc_final: 0.4645 (t80) REVERT: R 292 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6641 (tp) REVERT: R 322 TRP cc_start: 0.6132 (t60) cc_final: 0.5869 (t60) outliers start: 35 outliers final: 12 residues processed: 129 average time/residue: 1.0703 time to fit residues: 148.5027 Evaluate side-chains 115 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 319 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 70 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 0.0670 chunk 105 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 59 HIS B 235 ASN R 96 ASN R 141 GLN R 200 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.194688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.157371 restraints weight = 9809.346| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.07 r_work: 0.3604 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9038 Z= 0.199 Angle : 0.617 6.911 12269 Z= 0.322 Chirality : 0.044 0.228 1405 Planarity : 0.005 0.039 1548 Dihedral : 4.577 27.615 1243 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.04 % Allowed : 18.09 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.26), residues: 1111 helix: 2.21 (0.26), residues: 384 sheet: 0.92 (0.31), residues: 264 loop : -0.93 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 104 HIS 0.013 0.002 HIS B 59 PHE 0.015 0.002 PHE B 239 TYR 0.015 0.002 TYR B 269 ARG 0.010 0.001 ARG A 250 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 424) hydrogen bonds : angle 4.46675 ( 1197) SS BOND : bond 0.00439 ( 1) SS BOND : angle 1.21911 ( 2) covalent geometry : bond 0.00459 ( 9036) covalent geometry : angle 0.61637 (12267) Misc. bond : bond 0.00089 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 1.108 Fit side-chains REVERT: A 309 ARG cc_start: 0.5621 (mtp-110) cc_final: 0.5191 (tmm-80) REVERT: A 336 THR cc_start: 0.6933 (OUTLIER) cc_final: 0.6683 (t) REVERT: A 355 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7210 (mp) REVERT: B 180 GLN cc_start: 0.7466 (pp30) cc_final: 0.7140 (pp30) REVERT: B 260 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7804 (mp) REVERT: E 144 THR cc_start: 0.6876 (OUTLIER) cc_final: 0.6620 (m) REVERT: E 150 THR cc_start: 0.6317 (p) cc_final: 0.5977 (t) REVERT: E 155 VAL cc_start: 0.7737 (OUTLIER) cc_final: 0.7481 (p) REVERT: G 19 LEU cc_start: 0.6906 (OUTLIER) cc_final: 0.6295 (pt) REVERT: G 22 GLU cc_start: 0.5687 (mt-10) cc_final: 0.5248 (mt-10) REVERT: R 247 ARG cc_start: 0.5686 (mmm-85) cc_final: 0.5106 (tpt170) REVERT: R 277 PHE cc_start: 0.4851 (m-10) cc_final: 0.4274 (t80) REVERT: R 292 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6753 (tp) REVERT: R 322 TRP cc_start: 0.6208 (t60) cc_final: 0.5956 (t60) outliers start: 38 outliers final: 18 residues processed: 147 average time/residue: 1.1815 time to fit residues: 186.3099 Evaluate side-chains 126 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 319 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 93 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN R 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.197526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.160950 restraints weight = 9761.924| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.94 r_work: 0.3673 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9038 Z= 0.130 Angle : 0.550 6.391 12269 Z= 0.289 Chirality : 0.042 0.207 1405 Planarity : 0.004 0.043 1548 Dihedral : 4.218 19.203 1241 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.83 % Allowed : 19.26 % Favored : 76.91 % 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: 1.01 (0.26), residues: 1111 helix: 2.31 (0.26), residues: 385 sheet: 0.94 (0.31), residues: 261 loop : -0.94 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 104 HIS 0.006 0.001 HIS B 59 PHE 0.012 0.001 PHE A 215 TYR 0.013 0.001 TYR B 269 ARG 0.010 0.000 ARG A 250 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 424) hydrogen bonds : angle 4.23687 ( 1197) SS BOND : bond 0.00363 ( 1) SS BOND : angle 1.19653 ( 2) covalent geometry : bond 0.00284 ( 9036) covalent geometry : angle 0.54956 (12267) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.5399 (OUTLIER) cc_final: 0.5107 (mpt) REVERT: A 198 MET cc_start: 0.8272 (ttp) cc_final: 0.7813 (ttp) REVERT: A 309 ARG cc_start: 0.5922 (mtp-110) cc_final: 0.5491 (tmm-80) REVERT: A 355 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7252 (mp) REVERT: B 168 ASP cc_start: 0.7187 (OUTLIER) cc_final: 0.6544 (p0) REVERT: B 180 GLN cc_start: 0.7498 (pp30) cc_final: 0.7148 (pp30) REVERT: B 260 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7732 (mp) REVERT: E 144 THR cc_start: 0.6866 (OUTLIER) cc_final: 0.6627 (m) REVERT: E 150 THR cc_start: 0.6322 (p) cc_final: 0.5939 (t) REVERT: G 19 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6408 (pt) REVERT: G 22 GLU cc_start: 0.5707 (mt-10) cc_final: 0.5335 (mt-10) REVERT: R 212 GLU cc_start: 0.5710 (OUTLIER) cc_final: 0.4421 (mp0) REVERT: R 247 ARG cc_start: 0.5809 (mmm-85) cc_final: 0.5151 (tpt170) REVERT: R 277 PHE cc_start: 0.4872 (m-10) cc_final: 0.4268 (t80) REVERT: R 292 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6661 (tp) REVERT: R 322 TRP cc_start: 0.6263 (t60) cc_final: 0.6050 (t60) outliers start: 36 outliers final: 14 residues processed: 131 average time/residue: 1.0865 time to fit residues: 153.0739 Evaluate side-chains 119 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 319 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 71 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.0000 overall best weight: 1.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN R 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.194845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.158268 restraints weight = 9738.143| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 1.97 r_work: 0.3630 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9038 Z= 0.167 Angle : 0.591 5.967 12269 Z= 0.310 Chirality : 0.043 0.222 1405 Planarity : 0.004 0.038 1548 Dihedral : 4.449 20.034 1241 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.47 % Allowed : 19.79 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.25), residues: 1111 helix: 2.20 (0.25), residues: 383 sheet: 0.68 (0.31), residues: 272 loop : -1.05 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 104 HIS 0.010 0.001 HIS B 59 PHE 0.013 0.002 PHE A 189 TYR 0.018 0.002 TYR B 269 ARG 0.008 0.001 ARG A 250 Details of bonding type rmsd hydrogen bonds : bond 0.03922 ( 424) hydrogen bonds : angle 4.34837 ( 1197) SS BOND : bond 0.00497 ( 1) SS BOND : angle 1.40438 ( 2) covalent geometry : bond 0.00378 ( 9036) covalent geometry : angle 0.59077 (12267) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 109 time to evaluate : 0.906 Fit side-chains REVERT: A 53 MET cc_start: 0.5489 (OUTLIER) cc_final: 0.5136 (mpt) REVERT: A 198 MET cc_start: 0.8384 (ttp) cc_final: 0.7852 (ttp) REVERT: A 309 ARG cc_start: 0.5960 (mtp-110) cc_final: 0.5396 (tmm-80) REVERT: A 314 ARG cc_start: 0.6689 (OUTLIER) cc_final: 0.5517 (ptt-90) REVERT: A 360 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6493 (tm) REVERT: B 80 GLN cc_start: 0.8280 (mm-40) cc_final: 0.7901 (tp40) REVERT: B 180 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7239 (pp30) REVERT: B 260 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7865 (mp) REVERT: B 265 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6535 (tp30) REVERT: E 144 THR cc_start: 0.6915 (OUTLIER) cc_final: 0.6709 (m) REVERT: E 150 THR cc_start: 0.6373 (p) cc_final: 0.6001 (t) REVERT: G 19 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6536 (pt) REVERT: G 22 GLU cc_start: 0.5816 (mt-10) cc_final: 0.5396 (mt-10) REVERT: R 59 LEU cc_start: 0.4063 (mt) cc_final: 0.3781 (pp) REVERT: R 212 GLU cc_start: 0.5602 (OUTLIER) cc_final: 0.5067 (mp0) REVERT: R 247 ARG cc_start: 0.5845 (mmm-85) cc_final: 0.5188 (tpt170) REVERT: R 277 PHE cc_start: 0.4884 (m-10) cc_final: 0.4318 (t80) REVERT: R 292 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6686 (tp) REVERT: R 322 TRP cc_start: 0.6366 (t60) cc_final: 0.6147 (t60) outliers start: 42 outliers final: 20 residues processed: 139 average time/residue: 1.1882 time to fit residues: 176.5578 Evaluate side-chains 123 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 319 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 78 optimal weight: 4.9990 chunk 81 optimal weight: 0.0770 chunk 100 optimal weight: 0.8980 chunk 80 optimal weight: 0.0980 chunk 97 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 238 ASN L 5 ASN R 96 ASN R 298 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.199177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.161855 restraints weight = 9813.130| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 1.82 r_work: 0.3709 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9038 Z= 0.108 Angle : 0.529 5.926 12269 Z= 0.276 Chirality : 0.041 0.181 1405 Planarity : 0.004 0.050 1548 Dihedral : 4.087 18.025 1241 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.62 % Allowed : 21.38 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1111 helix: 2.35 (0.26), residues: 387 sheet: 0.69 (0.32), residues: 270 loop : -0.93 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 216 HIS 0.004 0.001 HIS E 35 PHE 0.011 0.001 PHE A 189 TYR 0.012 0.001 TYR E 95 ARG 0.012 0.000 ARG A 250 Details of bonding type rmsd hydrogen bonds : bond 0.03325 ( 424) hydrogen bonds : angle 4.10024 ( 1197) SS BOND : bond 0.00271 ( 1) SS BOND : angle 1.14475 ( 2) covalent geometry : bond 0.00224 ( 9036) covalent geometry : angle 0.52925 (12267) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 105 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.5239 (OUTLIER) cc_final: 0.4944 (mpt) REVERT: A 309 ARG cc_start: 0.5713 (mtp-110) cc_final: 0.5462 (tmm-80) REVERT: B 168 ASP cc_start: 0.7141 (OUTLIER) cc_final: 0.6534 (p0) REVERT: B 180 GLN cc_start: 0.7446 (pp30) cc_final: 0.7129 (pp30) REVERT: B 260 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7622 (mp) REVERT: E 144 THR cc_start: 0.6808 (OUTLIER) cc_final: 0.6594 (m) REVERT: E 150 THR cc_start: 0.6434 (p) cc_final: 0.6031 (t) REVERT: G 22 GLU cc_start: 0.5486 (mt-10) cc_final: 0.5059 (mt-10) REVERT: R 59 LEU cc_start: 0.4229 (mt) cc_final: 0.3849 (pp) REVERT: R 277 PHE cc_start: 0.4852 (m-10) cc_final: 0.4315 (t80) REVERT: R 279 LEU cc_start: 0.7013 (tm) cc_final: 0.6438 (mt) REVERT: R 292 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6574 (tp) REVERT: R 315 LEU cc_start: 0.5947 (mm) cc_final: 0.5732 (tp) outliers start: 34 outliers final: 16 residues processed: 128 average time/residue: 1.1812 time to fit residues: 162.8719 Evaluate side-chains 121 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 173 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 319 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 7 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.0040 chunk 102 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 216 ASN R 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.198115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.160986 restraints weight = 9923.599| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 1.85 r_work: 0.3693 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9038 Z= 0.123 Angle : 0.544 7.607 12269 Z= 0.282 Chirality : 0.041 0.179 1405 Planarity : 0.004 0.043 1548 Dihedral : 4.144 18.154 1241 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.77 % Allowed : 22.77 % Favored : 74.47 % 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: 0.98 (0.26), residues: 1111 helix: 2.33 (0.26), residues: 388 sheet: 0.71 (0.32), residues: 269 loop : -0.91 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.006 0.001 HIS B 59 PHE 0.012 0.001 PHE A 189 TYR 0.016 0.001 TYR E 95 ARG 0.011 0.000 ARG A 250 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 424) hydrogen bonds : angle 4.10777 ( 1197) SS BOND : bond 0.00386 ( 1) SS BOND : angle 1.36637 ( 2) covalent geometry : bond 0.00269 ( 9036) covalent geometry : angle 0.54414 (12267) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 1.048 Fit side-chains REVERT: A 250 ARG cc_start: 0.7511 (ptp-110) cc_final: 0.7148 (ptp-170) REVERT: A 309 ARG cc_start: 0.5706 (mtp-110) cc_final: 0.5462 (ttt-90) REVERT: A 355 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7425 (mp) REVERT: B 168 ASP cc_start: 0.7154 (OUTLIER) cc_final: 0.6539 (p0) REVERT: B 180 GLN cc_start: 0.7492 (pp30) cc_final: 0.7163 (pp30) REVERT: B 260 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7634 (mp) REVERT: E 144 THR cc_start: 0.6855 (OUTLIER) cc_final: 0.6636 (m) REVERT: E 150 THR cc_start: 0.6396 (p) cc_final: 0.6002 (t) REVERT: G 22 GLU cc_start: 0.5485 (mt-10) cc_final: 0.5077 (mt-10) REVERT: R 59 LEU cc_start: 0.4240 (mt) cc_final: 0.3861 (pp) REVERT: R 212 GLU cc_start: 0.5505 (OUTLIER) cc_final: 0.5007 (mp0) REVERT: R 277 PHE cc_start: 0.4857 (m-10) cc_final: 0.4323 (t80) REVERT: R 292 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6609 (tp) outliers start: 26 outliers final: 13 residues processed: 124 average time/residue: 1.3627 time to fit residues: 181.5854 Evaluate side-chains 120 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 319 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 4 optimal weight: 0.3980 chunk 94 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN R 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.200246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.165563 restraints weight = 9812.421| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 1.58 r_work: 0.3753 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9038 Z= 0.119 Angle : 0.542 7.692 12269 Z= 0.280 Chirality : 0.041 0.182 1405 Planarity : 0.004 0.041 1548 Dihedral : 4.126 17.864 1241 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.66 % Allowed : 22.87 % Favored : 74.47 % 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: 0.96 (0.26), residues: 1111 helix: 2.35 (0.26), residues: 385 sheet: 0.69 (0.32), residues: 269 loop : -0.92 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 104 HIS 0.005 0.001 HIS B 59 PHE 0.012 0.001 PHE A 189 TYR 0.024 0.001 TYR E 95 ARG 0.010 0.000 ARG A 250 Details of bonding type rmsd hydrogen bonds : bond 0.03377 ( 424) hydrogen bonds : angle 4.07683 ( 1197) SS BOND : bond 0.00351 ( 1) SS BOND : angle 1.44779 ( 2) covalent geometry : bond 0.00259 ( 9036) covalent geometry : angle 0.54173 (12267) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.952 Fit side-chains REVERT: A 53 MET cc_start: 0.5174 (mpt) cc_final: 0.4816 (mpt) REVERT: A 250 ARG cc_start: 0.7474 (ptp-110) cc_final: 0.7118 (ptp-170) REVERT: A 355 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7432 (mp) REVERT: B 168 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6405 (p0) REVERT: B 180 GLN cc_start: 0.7492 (pp30) cc_final: 0.7204 (pp30) REVERT: B 260 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7573 (mp) REVERT: E 144 THR cc_start: 0.6787 (OUTLIER) cc_final: 0.6527 (m) REVERT: E 150 THR cc_start: 0.6333 (p) cc_final: 0.5980 (t) REVERT: G 22 GLU cc_start: 0.5462 (mt-10) cc_final: 0.5068 (mt-10) REVERT: R 59 LEU cc_start: 0.4236 (mt) cc_final: 0.3979 (pp) REVERT: R 212 GLU cc_start: 0.5413 (OUTLIER) cc_final: 0.4942 (mp0) REVERT: R 277 PHE cc_start: 0.4805 (m-10) cc_final: 0.4383 (t80) REVERT: R 292 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6557 (tp) outliers start: 25 outliers final: 12 residues processed: 118 average time/residue: 1.1954 time to fit residues: 151.4395 Evaluate side-chains 115 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 319 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 27 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 37 GLN R 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.198482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.164033 restraints weight = 9848.877| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 1.53 r_work: 0.3733 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9038 Z= 0.139 Angle : 0.572 8.683 12269 Z= 0.296 Chirality : 0.042 0.216 1405 Planarity : 0.004 0.041 1548 Dihedral : 4.289 18.978 1241 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.45 % Allowed : 23.51 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1111 helix: 2.29 (0.26), residues: 384 sheet: 0.58 (0.32), residues: 274 loop : -0.96 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 104 HIS 0.006 0.001 HIS B 59 PHE 0.014 0.001 PHE A 330 TYR 0.029 0.002 TYR E 95 ARG 0.009 0.000 ARG A 250 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 424) hydrogen bonds : angle 4.16909 ( 1197) SS BOND : bond 0.00313 ( 1) SS BOND : angle 1.70550 ( 2) covalent geometry : bond 0.00311 ( 9036) covalent geometry : angle 0.57191 (12267) Misc. bond : bond 0.00033 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 1.034 Fit side-chains REVERT: A 53 MET cc_start: 0.5320 (mpt) cc_final: 0.5076 (mpt) REVERT: A 355 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7466 (mp) REVERT: B 180 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.7208 (pp30) REVERT: B 260 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7651 (mp) REVERT: E 144 THR cc_start: 0.6907 (OUTLIER) cc_final: 0.6676 (m) REVERT: E 150 THR cc_start: 0.6307 (p) cc_final: 0.6020 (t) REVERT: G 22 GLU cc_start: 0.5466 (mt-10) cc_final: 0.5079 (mt-10) REVERT: R 59 LEU cc_start: 0.4212 (mt) cc_final: 0.3951 (pp) REVERT: R 206 HIS cc_start: 0.4183 (m-70) cc_final: 0.3547 (m170) REVERT: R 212 GLU cc_start: 0.5322 (OUTLIER) cc_final: 0.4868 (mp0) REVERT: R 277 PHE cc_start: 0.4781 (m-10) cc_final: 0.4328 (t80) REVERT: R 292 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6601 (tp) outliers start: 23 outliers final: 15 residues processed: 117 average time/residue: 1.0814 time to fit residues: 136.5448 Evaluate side-chains 115 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 319 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 12 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 37 GLN R 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.197010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.159620 restraints weight = 9809.462| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.74 r_work: 0.3704 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9038 Z= 0.152 Angle : 0.594 7.984 12269 Z= 0.306 Chirality : 0.043 0.259 1405 Planarity : 0.004 0.053 1548 Dihedral : 4.360 18.954 1241 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.66 % Allowed : 23.30 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.26), residues: 1111 helix: 2.24 (0.26), residues: 384 sheet: 0.53 (0.32), residues: 274 loop : -0.96 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 104 HIS 0.007 0.001 HIS B 59 PHE 0.017 0.002 PHE A 215 TYR 0.026 0.002 TYR E 95 ARG 0.015 0.000 ARG A 250 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 424) hydrogen bonds : angle 4.22153 ( 1197) SS BOND : bond 0.00434 ( 1) SS BOND : angle 1.52783 ( 2) covalent geometry : bond 0.00341 ( 9036) covalent geometry : angle 0.59331 (12267) Misc. bond : bond 0.00039 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7439.40 seconds wall clock time: 130 minutes 16.57 seconds (7816.57 seconds total)