Starting phenix.real_space_refine on Wed Jan 15 19:38:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zps_60353/01_2025/8zps_60353_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zps_60353/01_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_60353/01_2025/8zps_60353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zps_60353/01_2025/8zps_60353.map" model { file = "/net/cci-nas-00/data/ceres_data/8zps_60353/01_2025/8zps_60353_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zps_60353/01_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 5.10, per 1000 atoms: 0.58 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: 2.25 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.15 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: 2.35 Time building geometry restraints manager: 2.59 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: 0.710 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.620 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:10.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.240 ------------------------------------------------------------------------------- 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 : 0.002 0.037 9036 Z= 0.156 Angle : 0.537 6.406 12267 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 *********************** 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 : 0.916 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: 1.1476 time to fit residues: 249.4836 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 : 1.022 ------------------------------------------------------------------------------- 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 = 9754.206| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 1.82 r_work: 0.3770 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 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 9036 Z= 0.268 Angle : 0.619 6.444 12267 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 *********************** 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 : 0.954 Fit side-chains REVERT: A 21 LYS cc_start: 0.7655 (mttt) cc_final: 0.7410 (mttm) REVERT: A 195 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7592 (m110) REVERT: A 208 ARG cc_start: 0.7336 (ptp-110) cc_final: 0.7021 (ttm110) REVERT: A 309 ARG cc_start: 0.5760 (mtp-110) cc_final: 0.5150 (tmm-80) REVERT: B 180 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.7033 (pp30) REVERT: B 194 SER cc_start: 0.8514 (p) cc_final: 0.7974 (t) REVERT: B 219 ARG cc_start: 0.6535 (mtm110) cc_final: 0.6248 (mpt180) REVERT: B 242 ASN cc_start: 0.6963 (t0) cc_final: 0.6691 (t0) REVERT: B 260 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7366 (mp) REVERT: B 272 ASP cc_start: 0.7498 (m-30) cc_final: 0.7211 (p0) REVERT: B 327 ASP cc_start: 0.5473 (m-30) cc_final: 0.5185 (m-30) REVERT: E 155 VAL cc_start: 0.7730 (OUTLIER) cc_final: 0.7525 (t) REVERT: G 16 VAL cc_start: 0.5788 (t) cc_final: 0.5361 (m) REVERT: G 22 GLU cc_start: 0.5534 (mt-10) cc_final: 0.5270 (mt-10) REVERT: R 247 ARG cc_start: 0.5591 (mmm-85) cc_final: 0.5108 (tpt170) REVERT: R 277 PHE cc_start: 0.5187 (m-10) cc_final: 0.4688 (t80) REVERT: R 292 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6768 (tp) REVERT: R 322 TRP cc_start: 0.6163 (t60) cc_final: 0.5826 (t60) outliers start: 32 outliers final: 11 residues processed: 156 average time/residue: 1.1816 time to fit residues: 197.1203 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 : 0.902 ------------------------------------------------------------------------------- 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: 7.9990 chunk 92 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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** G 59 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 = 0.4405 r_free = 0.4405 target = 0.202330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.165944 restraints weight = 9881.034| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 1.90 r_work: 0.3750 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9036 Z= 0.183 Angle : 0.537 8.322 12267 Z= 0.277 Chirality : 0.041 0.196 1405 Planarity : 0.004 0.035 1548 Dihedral : 4.448 57.840 1244 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.62 % Allowed : 16.49 % Favored : 79.89 % 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: 2.60 (0.26), residues: 385 sheet: 1.44 (0.32), residues: 261 loop : -0.73 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 104 HIS 0.007 0.001 HIS B 59 PHE 0.011 0.001 PHE B 156 TYR 0.012 0.001 TYR E 95 ARG 0.008 0.001 ARG A 247 *********************** 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 141 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.922 Fit side-chains REVERT: A 195 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7768 (m110) REVERT: A 309 ARG cc_start: 0.5592 (mtp-110) cc_final: 0.5217 (tmm-80) REVERT: B 168 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.6521 (p0) REVERT: B 180 GLN cc_start: 0.7397 (pp30) cc_final: 0.7075 (pp30) REVERT: B 219 ARG cc_start: 0.6368 (mtm110) cc_final: 0.6009 (mpp-170) REVERT: B 261 ARG cc_start: 0.7055 (mtm180) cc_final: 0.6837 (mpp80) REVERT: B 265 GLU cc_start: 0.6719 (tt0) cc_final: 0.6484 (mm-30) REVERT: B 272 ASP cc_start: 0.7469 (m-30) cc_final: 0.7207 (p0) REVERT: B 328 ASP cc_start: 0.7216 (OUTLIER) cc_final: 0.6818 (p0) REVERT: G 22 GLU cc_start: 0.5575 (mt-10) cc_final: 0.5206 (mt-10) REVERT: R 167 LEU cc_start: 0.5910 (OUTLIER) cc_final: 0.5601 (mt) REVERT: R 247 ARG cc_start: 0.5691 (mmm-85) cc_final: 0.5139 (tpt170) REVERT: R 277 PHE cc_start: 0.5140 (m-10) cc_final: 0.4598 (t80) REVERT: R 292 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6600 (tp) REVERT: R 322 TRP cc_start: 0.6141 (t60) cc_final: 0.5886 (t60) outliers start: 34 outliers final: 11 residues processed: 132 average time/residue: 1.1706 time to fit residues: 165.5966 Evaluate side-chains 110 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 328 ASP 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 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: 5.9990 chunk 30 optimal weight: 0.3980 chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 67 optimal weight: 0.0670 chunk 87 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.0924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 HIS R 92 HIS 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 = 0.199084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.162306 restraints weight = 9737.389| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 1.97 r_work: 0.3686 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9036 Z= 0.204 Angle : 0.549 6.809 12267 Z= 0.285 Chirality : 0.042 0.202 1405 Planarity : 0.004 0.041 1548 Dihedral : 4.147 24.662 1243 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.36 % Allowed : 17.02 % Favored : 78.62 % 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: 1.24 (0.26), residues: 1111 helix: 2.44 (0.26), residues: 385 sheet: 1.04 (0.32), residues: 270 loop : -0.77 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 104 HIS 0.009 0.001 HIS B 59 PHE 0.012 0.001 PHE B 156 TYR 0.013 0.002 TYR R 311 ARG 0.008 0.000 ARG A 250 *********************** 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 149 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 108 time to evaluate : 1.031 Fit side-chains REVERT: A 198 MET cc_start: 0.8140 (ttp) cc_final: 0.7629 (ttp) REVERT: A 309 ARG cc_start: 0.5705 (mtp-110) cc_final: 0.5286 (tmm-80) REVERT: A 355 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7366 (mp) REVERT: B 168 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.6551 (p0) REVERT: B 180 GLN cc_start: 0.7489 (pp30) cc_final: 0.7157 (pp30) REVERT: B 219 ARG cc_start: 0.6527 (mtm110) cc_final: 0.6322 (mpt180) REVERT: B 260 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7679 (mp) REVERT: B 272 ASP cc_start: 0.7497 (m-30) cc_final: 0.7225 (p0) REVERT: E 59 TYR cc_start: 0.7747 (m-10) cc_final: 0.7526 (m-10) REVERT: E 144 THR cc_start: 0.6870 (OUTLIER) cc_final: 0.6614 (m) REVERT: E 150 THR cc_start: 0.6309 (p) cc_final: 0.5957 (t) REVERT: E 155 VAL cc_start: 0.7780 (OUTLIER) cc_final: 0.7556 (p) REVERT: G 19 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6138 (pt) REVERT: G 22 GLU cc_start: 0.5638 (mt-10) cc_final: 0.5282 (mt-10) REVERT: R 92 HIS cc_start: 0.6202 (OUTLIER) cc_final: 0.5904 (m90) REVERT: R 247 ARG cc_start: 0.5785 (mmm-85) cc_final: 0.5126 (tpt170) REVERT: R 277 PHE cc_start: 0.4962 (m-10) cc_final: 0.4401 (t80) REVERT: R 292 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6655 (tp) REVERT: R 322 TRP cc_start: 0.6234 (t60) cc_final: 0.5981 (t60) outliers start: 41 outliers final: 16 residues processed: 135 average time/residue: 1.1335 time to fit residues: 164.2729 Evaluate side-chains 123 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR 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 218 VAL 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 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 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 92 HIS 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: 0.9990 chunk 94 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 79 optimal weight: 0.0050 chunk 6 optimal weight: 8.9990 chunk 30 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 92 HIS R 96 ASN R 141 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.200247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.163667 restraints weight = 9793.729| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 2.02 r_work: 0.3699 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9036 Z= 0.158 Angle : 0.513 6.385 12267 Z= 0.267 Chirality : 0.040 0.183 1405 Planarity : 0.004 0.041 1548 Dihedral : 3.914 18.185 1241 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.72 % Allowed : 19.68 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.26), residues: 1111 helix: 2.46 (0.26), residues: 386 sheet: 1.07 (0.32), residues: 270 loop : -0.77 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 104 HIS 0.010 0.001 HIS R 92 PHE 0.010 0.001 PHE A 189 TYR 0.009 0.001 TYR E 103 ARG 0.009 0.000 ARG A 250 *********************** 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 149 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.911 Fit side-chains REVERT: A 53 MET cc_start: 0.5280 (OUTLIER) cc_final: 0.4880 (mpt) REVERT: A 198 MET cc_start: 0.7921 (ttp) cc_final: 0.7459 (ttp) REVERT: A 309 ARG cc_start: 0.5645 (mtp-110) cc_final: 0.5272 (tmm-80) REVERT: A 355 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7221 (mp) REVERT: B 168 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.6515 (p0) REVERT: B 180 GLN cc_start: 0.7351 (pp30) cc_final: 0.7090 (pp30) REVERT: B 260 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7492 (mp) REVERT: B 309 ARG cc_start: 0.7722 (ttm170) cc_final: 0.7401 (ttm170) REVERT: E 144 THR cc_start: 0.6647 (OUTLIER) cc_final: 0.6407 (m) REVERT: E 150 THR cc_start: 0.6219 (p) cc_final: 0.5875 (t) REVERT: E 155 VAL cc_start: 0.7726 (OUTLIER) cc_final: 0.7494 (p) REVERT: G 19 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6214 (pt) REVERT: G 22 GLU cc_start: 0.5167 (mt-10) cc_final: 0.4791 (mt-10) REVERT: R 212 GLU cc_start: 0.5551 (OUTLIER) cc_final: 0.4271 (mp0) REVERT: R 247 ARG cc_start: 0.5593 (mmm-85) cc_final: 0.5052 (tpt170) REVERT: R 277 PHE cc_start: 0.4937 (m-10) cc_final: 0.4401 (t80) REVERT: R 292 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6599 (tp) REVERT: R 322 TRP cc_start: 0.6181 (t60) cc_final: 0.5947 (t60) outliers start: 35 outliers final: 16 residues processed: 137 average time/residue: 1.0997 time to fit residues: 161.7323 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 : 0.931 ------------------------------------------------------------------------------- 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 39 THR 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 260 LEU 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 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 162 VAL Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 289 VAL Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 318 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: 3.9990 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 92 HIS R 96 ASN R 200 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.197850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.160703 restraints weight = 9738.743| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 1.77 r_work: 0.3701 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9036 Z= 0.194 Angle : 0.541 6.050 12267 Z= 0.282 Chirality : 0.041 0.189 1405 Planarity : 0.004 0.043 1548 Dihedral : 4.087 19.182 1241 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.04 % Allowed : 20.32 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1111 helix: 2.37 (0.26), residues: 386 sheet: 1.01 (0.32), residues: 264 loop : -0.85 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 104 HIS 0.008 0.001 HIS B 59 PHE 0.011 0.001 PHE B 239 TYR 0.015 0.001 TYR A 327 ARG 0.008 0.000 ARG A 250 *********************** 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 143 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 1.029 Fit side-chains REVERT: A 53 MET cc_start: 0.5242 (OUTLIER) cc_final: 0.4833 (mpt) REVERT: A 198 MET cc_start: 0.8226 (ttp) cc_final: 0.7714 (ttp) REVERT: A 309 ARG cc_start: 0.5894 (mtp-110) cc_final: 0.5433 (tmm-80) REVERT: A 355 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7347 (mp) REVERT: B 180 GLN cc_start: 0.7509 (pp30) cc_final: 0.7157 (pp30) REVERT: B 260 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7590 (mp) REVERT: B 265 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6718 (tp30) REVERT: E 59 TYR cc_start: 0.7728 (m-10) cc_final: 0.7510 (m-10) REVERT: E 144 THR cc_start: 0.6830 (OUTLIER) cc_final: 0.6583 (m) REVERT: E 150 THR cc_start: 0.6332 (p) cc_final: 0.5964 (t) REVERT: G 19 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6310 (pt) REVERT: G 22 GLU cc_start: 0.5346 (mt-10) cc_final: 0.4982 (mt-10) REVERT: R 59 LEU cc_start: 0.4036 (mt) cc_final: 0.3760 (pp) REVERT: R 212 GLU cc_start: 0.5582 (OUTLIER) cc_final: 0.4394 (mp0) REVERT: R 247 ARG cc_start: 0.5804 (mmm-85) cc_final: 0.5181 (tpt170) REVERT: R 277 PHE cc_start: 0.4864 (m-10) cc_final: 0.4274 (t80) REVERT: R 292 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6609 (tp) REVERT: R 322 TRP cc_start: 0.6345 (t60) cc_final: 0.6099 (t60) outliers start: 38 outliers final: 18 residues processed: 131 average time/residue: 1.1384 time to fit residues: 160.2946 Evaluate side-chains 122 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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 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 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 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 162 VAL Chi-restraints excluded: chain R residue 173 LEU 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: 4.9990 chunk 53 optimal weight: 0.0970 chunk 78 optimal weight: 4.9990 chunk 81 optimal weight: 0.0670 chunk 100 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 97 optimal weight: 8.9990 chunk 47 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.200773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.165276 restraints weight = 9826.163| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 1.70 r_work: 0.3751 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9036 Z= 0.139 Angle : 0.511 5.811 12267 Z= 0.264 Chirality : 0.040 0.166 1405 Planarity : 0.003 0.042 1548 Dihedral : 3.850 17.080 1241 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.30 % Allowed : 21.81 % Favored : 74.89 % 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: 1.26 (0.26), residues: 1111 helix: 2.57 (0.26), residues: 381 sheet: 1.09 (0.33), residues: 252 loop : -0.79 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 216 HIS 0.004 0.001 HIS E 35 PHE 0.010 0.001 PHE A 189 TYR 0.013 0.001 TYR A 327 ARG 0.006 0.000 ARG A 250 *********************** 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 130 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.928 Fit side-chains REVERT: A 53 MET cc_start: 0.5104 (OUTLIER) cc_final: 0.4678 (mpt) REVERT: A 309 ARG cc_start: 0.5787 (mtp-110) cc_final: 0.5368 (tmm-80) REVERT: A 355 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7336 (mp) REVERT: B 168 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6506 (p0) REVERT: B 219 ARG cc_start: 0.6718 (mpt180) cc_final: 0.6240 (mpt180) REVERT: B 244 ASN cc_start: 0.7883 (t0) cc_final: 0.7677 (m-40) REVERT: B 260 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7435 (mp) REVERT: B 265 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6560 (mm-30) REVERT: B 269 TYR cc_start: 0.7811 (m-80) cc_final: 0.7601 (m-80) REVERT: B 309 ARG cc_start: 0.7926 (ttm170) cc_final: 0.7631 (ttm170) REVERT: E 144 THR cc_start: 0.6750 (OUTLIER) cc_final: 0.6510 (m) REVERT: G 19 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.6140 (OUTLIER) REVERT: G 22 GLU cc_start: 0.5329 (mt-10) cc_final: 0.4931 (mt-10) REVERT: R 59 LEU cc_start: 0.4211 (mt) cc_final: 0.3853 (pp) REVERT: R 212 GLU cc_start: 0.5468 (OUTLIER) cc_final: 0.4270 (mp0) REVERT: R 247 ARG cc_start: 0.5761 (mmm-85) cc_final: 0.5154 (tpt170) REVERT: R 277 PHE cc_start: 0.4872 (m-10) cc_final: 0.4324 (t80) REVERT: R 292 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6518 (tp) REVERT: R 315 LEU cc_start: 0.5959 (mm) cc_final: 0.5713 (tp) REVERT: R 322 TRP cc_start: 0.6354 (t60) cc_final: 0.6129 (t60) outliers start: 31 outliers final: 16 residues processed: 118 average time/residue: 1.2271 time to fit residues: 154.8935 Evaluate side-chains 117 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 39 THR 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 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 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 162 VAL Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 212 GLU 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: 0.0980 chunk 31 optimal weight: 3.9990 chunk 65 optimal weight: 0.0870 chunk 4 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 96 ASN R 141 GLN R 298 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.201511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.166772 restraints weight = 9946.482| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 1.71 r_work: 0.3760 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9036 Z= 0.136 Angle : 0.497 6.239 12267 Z= 0.257 Chirality : 0.040 0.151 1405 Planarity : 0.003 0.046 1548 Dihedral : 3.794 16.975 1241 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.77 % Allowed : 22.66 % Favored : 74.57 % 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: 1.27 (0.26), residues: 1111 helix: 2.57 (0.26), residues: 386 sheet: 1.05 (0.33), residues: 254 loop : -0.79 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 216 HIS 0.004 0.001 HIS E 35 PHE 0.012 0.001 PHE A 189 TYR 0.013 0.001 TYR A 327 ARG 0.006 0.000 ARG A 250 *********************** 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 125 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 1.062 Fit side-chains REVERT: A 53 MET cc_start: 0.5069 (OUTLIER) cc_final: 0.4693 (mpt) REVERT: A 309 ARG cc_start: 0.5777 (mtp-110) cc_final: 0.5359 (tmm-80) REVERT: B 168 ASP cc_start: 0.7167 (OUTLIER) cc_final: 0.6530 (p0) REVERT: B 219 ARG cc_start: 0.6596 (mpt180) cc_final: 0.6099 (mtm180) REVERT: B 260 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7401 (mp) REVERT: B 265 GLU cc_start: 0.6840 (tt0) cc_final: 0.6525 (mm-30) REVERT: B 309 ARG cc_start: 0.7890 (ttm170) cc_final: 0.7579 (ttm170) REVERT: E 144 THR cc_start: 0.6754 (OUTLIER) cc_final: 0.6505 (m) REVERT: G 19 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6104 (pt) REVERT: G 22 GLU cc_start: 0.5225 (mt-10) cc_final: 0.4886 (mt-10) REVERT: R 59 LEU cc_start: 0.4209 (mt) cc_final: 0.3854 (pp) REVERT: R 212 GLU cc_start: 0.5355 (OUTLIER) cc_final: 0.4235 (mp0) REVERT: R 247 ARG cc_start: 0.5806 (mmm-85) cc_final: 0.5142 (tpt170) REVERT: R 277 PHE cc_start: 0.4978 (m-10) cc_final: 0.4488 (t80) REVERT: R 292 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6484 (tp) REVERT: R 315 LEU cc_start: 0.5845 (mm) cc_final: 0.5611 (tp) REVERT: R 322 TRP cc_start: 0.6372 (t60) cc_final: 0.6155 (t60) outliers start: 26 outliers final: 15 residues processed: 115 average time/residue: 1.2281 time to fit residues: 151.0642 Evaluate side-chains 117 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 258 LEU Chi-restraints excluded: chain A residue 266 GLU 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 239 PHE 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 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 128 VAL Chi-restraints excluded: chain R residue 162 VAL Chi-restraints excluded: chain R residue 165 HIS Chi-restraints excluded: chain R residue 212 GLU 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: 0.5980 chunk 57 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 59 optimal weight: 0.1980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN B 244 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 = 0.4373 r_free = 0.4373 target = 0.198883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.163693 restraints weight = 9882.674| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 1.78 r_work: 0.3713 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9036 Z= 0.177 Angle : 0.532 7.226 12267 Z= 0.273 Chirality : 0.041 0.174 1405 Planarity : 0.004 0.043 1548 Dihedral : 4.000 18.658 1241 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.62 % Allowed : 22.34 % 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: 1.17 (0.26), residues: 1111 helix: 2.46 (0.26), residues: 388 sheet: 0.81 (0.32), residues: 272 loop : -0.78 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 216 HIS 0.006 0.001 HIS B 59 PHE 0.012 0.001 PHE B 239 TYR 0.011 0.001 TYR B 269 ARG 0.006 0.000 ARG B 224 *********************** 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 133 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.942 Fit side-chains REVERT: A 53 MET cc_start: 0.5094 (OUTLIER) cc_final: 0.4631 (mpt) REVERT: A 309 ARG cc_start: 0.5852 (mtp-110) cc_final: 0.5422 (tmm-80) REVERT: B 168 ASP cc_start: 0.7222 (OUTLIER) cc_final: 0.6545 (p0) REVERT: B 180 GLN cc_start: 0.7422 (pp30) cc_final: 0.7038 (pp30) REVERT: B 219 ARG cc_start: 0.6606 (mpt180) cc_final: 0.6137 (mtm180) REVERT: B 244 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.7851 (t0) REVERT: B 260 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7432 (mp) REVERT: B 265 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6691 (tp30) REVERT: B 309 ARG cc_start: 0.7954 (ttm170) cc_final: 0.7641 (ttm170) REVERT: E 144 THR cc_start: 0.6824 (OUTLIER) cc_final: 0.6591 (m) REVERT: E 150 THR cc_start: 0.6302 (p) cc_final: 0.5971 (t) REVERT: G 22 GLU cc_start: 0.5356 (mt-10) cc_final: 0.4872 (mt-10) REVERT: R 59 LEU cc_start: 0.4250 (mt) cc_final: 0.3904 (pp) REVERT: R 212 GLU cc_start: 0.5360 (OUTLIER) cc_final: 0.4246 (mp0) REVERT: R 247 ARG cc_start: 0.5818 (mmm-85) cc_final: 0.5076 (tpt170) REVERT: R 277 PHE cc_start: 0.4901 (m-10) cc_final: 0.4355 (t80) REVERT: R 292 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6598 (tp) REVERT: R 322 TRP cc_start: 0.6389 (t60) cc_final: 0.6181 (t60) REVERT: R 338 LEU cc_start: 0.4813 (OUTLIER) cc_final: 0.4447 (tt) outliers start: 34 outliers final: 16 residues processed: 121 average time/residue: 1.1386 time to fit residues: 148.0626 Evaluate side-chains 121 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 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 239 PHE Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 52 SER 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 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 162 VAL Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain R residue 319 LEU Chi-restraints excluded: chain R residue 338 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: 4.9990 chunk 66 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 78 optimal weight: 0.0870 chunk 79 optimal weight: 0.2980 chunk 51 optimal weight: 0.0980 chunk 34 optimal weight: 0.9980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 R 331 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.201263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.164489 restraints weight = 9845.523| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 1.82 r_work: 0.3744 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9036 Z= 0.141 Angle : 0.515 8.080 12267 Z= 0.264 Chirality : 0.040 0.160 1405 Planarity : 0.003 0.044 1548 Dihedral : 3.868 17.138 1241 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.77 % Allowed : 23.40 % Favored : 73.83 % 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: 1.24 (0.26), residues: 1111 helix: 2.55 (0.26), residues: 387 sheet: 0.82 (0.33), residues: 262 loop : -0.70 (0.30), residues: 462 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 330 TYR 0.019 0.001 TYR B 64 ARG 0.006 0.000 ARG B 224 ********************** 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 128 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.934 Fit side-chains REVERT: A 53 MET cc_start: 0.5016 (OUTLIER) cc_final: 0.4630 (mpt) REVERT: A 309 ARG cc_start: 0.5814 (mtp-110) cc_final: 0.5378 (tmm-80) REVERT: B 168 ASP cc_start: 0.7151 (OUTLIER) cc_final: 0.6531 (p0) REVERT: B 180 GLN cc_start: 0.7377 (pp30) cc_final: 0.6985 (pp30) REVERT: B 260 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7450 (mp) REVERT: B 267 MET cc_start: 0.6729 (tpp) cc_final: 0.6501 (mmt) REVERT: E 144 THR cc_start: 0.6743 (OUTLIER) cc_final: 0.6498 (m) REVERT: E 150 THR cc_start: 0.6350 (p) cc_final: 0.6017 (t) REVERT: G 22 GLU cc_start: 0.5342 (mt-10) cc_final: 0.4872 (mt-10) REVERT: R 59 LEU cc_start: 0.4196 (mt) cc_final: 0.3961 (pp) REVERT: R 108 LEU cc_start: 0.6347 (mt) cc_final: 0.6021 (mp) REVERT: R 212 GLU cc_start: 0.5335 (OUTLIER) cc_final: 0.4211 (mp0) REVERT: R 247 ARG cc_start: 0.5776 (mmm-85) cc_final: 0.4888 (tpt90) REVERT: R 277 PHE cc_start: 0.4821 (m-10) cc_final: 0.4317 (t80) REVERT: R 292 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6533 (tp) REVERT: R 322 TRP cc_start: 0.6400 (t60) cc_final: 0.6180 (t60) outliers start: 26 outliers final: 13 residues processed: 117 average time/residue: 1.2395 time to fit residues: 155.1597 Evaluate side-chains 118 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 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 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 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 173 LEU Chi-restraints excluded: chain R residue 212 GLU 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: 0.8980 chunk 71 optimal weight: 0.0000 chunk 88 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN B 244 ASN R 96 ASN R 331 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.200496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.165564 restraints weight = 9850.065| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 1.58 r_work: 0.3763 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9036 Z= 0.194 Angle : 0.555 8.348 12267 Z= 0.285 Chirality : 0.041 0.214 1405 Planarity : 0.004 0.044 1548 Dihedral : 4.089 18.953 1241 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.77 % Allowed : 23.62 % Favored : 73.62 % 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: 1.12 (0.26), residues: 1111 helix: 2.42 (0.26), residues: 388 sheet: 0.73 (0.32), residues: 272 loop : -0.77 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 216 HIS 0.006 0.001 HIS A 324 PHE 0.015 0.001 PHE A 330 TYR 0.015 0.001 TYR B 269 ARG 0.009 0.000 ARG B 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6790.24 seconds wall clock time: 120 minutes 40.79 seconds (7240.79 seconds total)