Starting phenix.real_space_refine on Wed Sep 17 12:40:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zps_60353/09_2025/8zps_60353_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zps_60353/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zps_60353/09_2025/8zps_60353_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zps_60353/09_2025/8zps_60353_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zps_60353/09_2025/8zps_60353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zps_60353/09_2025/8zps_60353.map" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 4, 'ARG:plan': 2, 'GLN:plan1': 1, '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, 'ASP:plan': 2, 'ARG: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: 2.20, per 1000 atoms: 0.25 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: 0.77 Conformation dependent library (CDL) restraints added in 352.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.22 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: 1.35 Time building geometry restraints manager: 0.93 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: 1.170 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.190 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.320 ------------------------------------------------------------------------------- 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 : 7.90 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG E 67 TYR 0.006 0.001 TYR E 95 PHE 0.006 0.001 PHE B 204 TRP 0.005 0.001 TRP B 174 HIS 0.003 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9036) covalent geometry : angle 0.53672 (12267) SS BOND : bond 0.00220 ( 1) SS BOND : angle 0.36308 ( 2) hydrogen bonds : bond 0.19171 ( 424) hydrogen bonds : angle 6.30726 ( 1197) 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 : 0.279 Fit side-chains REVERT: A 192 ASP cc_start: 0.6767 (p0) cc_final: 0.6536 (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: 0.6986 (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: 0.5782 time to fit residues: 125.1750 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 : 0.345 ------------------------------------------------------------------------------- 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 108 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 59 HIS B 230 HIS E 82 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN L 5 ASN R 96 ASN R 165 HIS R 223 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.197786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.160803 restraints weight = 9781.049| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 1.93 r_work: 0.3677 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 9038 Z= 0.248 Angle : 0.717 7.543 12269 Z= 0.375 Chirality : 0.047 0.211 1405 Planarity : 0.006 0.056 1548 Dihedral : 5.219 59.522 1245 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.72 % Allowed : 13.72 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.25), residues: 1111 helix: 2.08 (0.25), residues: 386 sheet: 0.93 (0.30), residues: 277 loop : -0.84 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 247 TYR 0.019 0.003 TYR B 64 PHE 0.023 0.003 PHE B 156 TRP 0.020 0.002 TRP B 216 HIS 0.017 0.003 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00564 ( 9036) covalent geometry : angle 0.71710 (12267) SS BOND : bond 0.00502 ( 1) SS BOND : angle 1.33856 ( 2) hydrogen bonds : bond 0.04743 ( 424) hydrogen bonds : angle 4.75383 ( 1197) Misc. bond : bond 0.00004 ( 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 167 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 21 LYS cc_start: 0.7921 (mttt) cc_final: 0.7699 (mttt) REVERT: A 208 ARG cc_start: 0.7495 (ptp-110) cc_final: 0.7248 (ptp90) REVERT: A 250 ARG cc_start: 0.7557 (ptp-110) cc_final: 0.7013 (ptp-170) REVERT: A 309 ARG cc_start: 0.5918 (mtp-110) cc_final: 0.5229 (tmm-80) REVERT: A 353 MET cc_start: 0.6829 (OUTLIER) cc_final: 0.6545 (ptp) REVERT: B 180 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.7178 (pp30) REVERT: B 194 SER cc_start: 0.8620 (p) cc_final: 0.8187 (t) REVERT: B 260 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7590 (mp) REVERT: B 264 GLN cc_start: 0.7076 (mt0) cc_final: 0.6799 (mt0) REVERT: B 272 ASP cc_start: 0.7458 (m-30) cc_final: 0.7194 (p0) REVERT: E 144 THR cc_start: 0.7088 (OUTLIER) cc_final: 0.6846 (m) REVERT: E 155 VAL cc_start: 0.7698 (OUTLIER) cc_final: 0.7464 (t) REVERT: G 22 GLU cc_start: 0.5774 (mt-10) cc_final: 0.5407 (mt-10) REVERT: R 167 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5748 (mt) REVERT: R 247 ARG cc_start: 0.5731 (mmm-85) cc_final: 0.5125 (tpt170) REVERT: R 277 PHE cc_start: 0.5181 (m-10) cc_final: 0.4598 (t80) REVERT: R 292 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6762 (tp) REVERT: R 322 TRP cc_start: 0.6240 (t60) cc_final: 0.5919 (t60) outliers start: 35 outliers final: 9 residues processed: 157 average time/residue: 0.5934 time to fit residues: 99.2231 Evaluate side-chains 119 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 353 MET 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 E residue 52 SER 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 93 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN 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 = 0.4385 r_free = 0.4385 target = 0.199998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.163510 restraints weight = 9792.872| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 1.95 r_work: 0.3698 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4198 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= 0.126 Angle : 0.546 8.222 12269 Z= 0.284 Chirality : 0.041 0.202 1405 Planarity : 0.004 0.031 1548 Dihedral : 4.260 34.123 1243 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.30 % Allowed : 18.30 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.26), residues: 1111 helix: 2.33 (0.26), residues: 385 sheet: 1.14 (0.31), residues: 267 loop : -0.81 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 247 TYR 0.011 0.001 TYR E 190 PHE 0.011 0.001 PHE A 189 TRP 0.014 0.001 TRP B 104 HIS 0.005 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9036) covalent geometry : angle 0.54625 (12267) SS BOND : bond 0.00402 ( 1) SS BOND : angle 0.94089 ( 2) hydrogen bonds : bond 0.03797 ( 424) hydrogen bonds : angle 4.27356 ( 1197) Misc. bond : bond 0.00054 ( 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 140 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.369 Fit side-chains REVERT: A 208 ARG cc_start: 0.7464 (ptp-110) cc_final: 0.6991 (ptp90) REVERT: A 309 ARG cc_start: 0.5871 (mtp-110) cc_final: 0.5347 (tmm-80) REVERT: A 353 MET cc_start: 0.6678 (OUTLIER) cc_final: 0.6393 (ptp) REVERT: A 355 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7383 (mp) REVERT: B 64 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.8211 (m-80) REVERT: B 168 ASP cc_start: 0.7211 (OUTLIER) cc_final: 0.6543 (p0) REVERT: B 180 GLN cc_start: 0.7472 (pp30) cc_final: 0.7155 (pp30) REVERT: B 264 GLN cc_start: 0.6768 (mt0) cc_final: 0.6535 (mt0) REVERT: B 272 ASP cc_start: 0.7476 (m-30) cc_final: 0.7207 (p0) REVERT: G 22 GLU cc_start: 0.5690 (mt-10) cc_final: 0.5332 (mt-10) REVERT: R 247 ARG cc_start: 0.5778 (mmm-85) cc_final: 0.5149 (tpt170) REVERT: R 277 PHE cc_start: 0.5042 (m-10) cc_final: 0.4465 (t80) REVERT: R 292 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6610 (tp) REVERT: R 322 TRP cc_start: 0.6229 (t60) cc_final: 0.5964 (t60) outliers start: 31 outliers final: 14 residues processed: 130 average time/residue: 0.6393 time to fit residues: 88.3751 Evaluate side-chains 115 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 28 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 46 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 1 optimal weight: 0.4980 chunk 95 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 4 optimal weight: 0.0870 chunk 3 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.197860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.160910 restraints weight = 9797.091| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 1.87 r_work: 0.3684 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9038 Z= 0.139 Angle : 0.553 6.568 12269 Z= 0.286 Chirality : 0.042 0.204 1405 Planarity : 0.004 0.041 1548 Dihedral : 4.160 19.299 1241 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.26 % Allowed : 18.30 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.26), residues: 1111 helix: 2.36 (0.26), residues: 381 sheet: 0.89 (0.31), residues: 267 loop : -0.77 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 250 TYR 0.011 0.002 TYR E 103 PHE 0.012 0.001 PHE A 189 TRP 0.014 0.001 TRP B 104 HIS 0.008 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9036) covalent geometry : angle 0.55315 (12267) SS BOND : bond 0.00565 ( 1) SS BOND : angle 1.09797 ( 2) hydrogen bonds : bond 0.03699 ( 424) hydrogen bonds : angle 4.19831 ( 1197) Misc. bond : bond 0.00055 ( 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 153 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 113 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.5403 (mpt) cc_final: 0.5176 (mpt) REVERT: A 198 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7696 (ttp) REVERT: A 309 ARG cc_start: 0.6006 (mtp-110) cc_final: 0.5417 (tmm-80) REVERT: A 353 MET cc_start: 0.6632 (OUTLIER) cc_final: 0.6248 (ptp) REVERT: A 355 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7279 (mp) REVERT: B 168 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6580 (p0) REVERT: B 180 GLN cc_start: 0.7451 (pp30) cc_final: 0.7135 (pp30) REVERT: B 260 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7671 (mp) REVERT: B 272 ASP cc_start: 0.7405 (m-30) cc_final: 0.7195 (p0) REVERT: B 309 ARG cc_start: 0.7919 (ttm170) cc_final: 0.7654 (ttm170) REVERT: E 150 THR cc_start: 0.6276 (p) cc_final: 0.5907 (t) REVERT: E 155 VAL cc_start: 0.7762 (OUTLIER) cc_final: 0.7506 (p) REVERT: G 19 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6353 (pt) REVERT: G 22 GLU cc_start: 0.5576 (mt-10) cc_final: 0.5126 (mt-10) REVERT: R 247 ARG cc_start: 0.5799 (mmm-85) cc_final: 0.5153 (tpt170) REVERT: R 292 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6622 (tp) REVERT: R 322 TRP cc_start: 0.6283 (t60) cc_final: 0.6036 (t60) outliers start: 40 outliers final: 17 residues processed: 142 average time/residue: 0.6019 time to fit residues: 91.2704 Evaluate side-chains 124 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 353 MET 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 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 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 252 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 45 optimal weight: 0.0040 chunk 16 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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 = 0.4372 r_free = 0.4372 target = 0.199096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.162086 restraints weight = 9845.209| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 1.83 r_work: 0.3706 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9038 Z= 0.113 Angle : 0.518 6.158 12269 Z= 0.268 Chirality : 0.040 0.187 1405 Planarity : 0.004 0.040 1548 Dihedral : 4.003 18.171 1241 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.94 % Allowed : 20.85 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.26), residues: 1111 helix: 2.36 (0.26), residues: 387 sheet: 0.90 (0.31), residues: 263 loop : -0.80 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 250 TYR 0.013 0.001 TYR B 64 PHE 0.011 0.001 PHE A 189 TRP 0.013 0.001 TRP B 216 HIS 0.005 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 9036) covalent geometry : angle 0.51752 (12267) SS BOND : bond 0.00491 ( 1) SS BOND : angle 0.94170 ( 2) hydrogen bonds : bond 0.03423 ( 424) hydrogen bonds : angle 4.08770 ( 1197) Misc. bond : bond 0.00048 ( 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 143 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 0.371 Fit side-chains REVERT: A 309 ARG cc_start: 0.5943 (mtp-110) cc_final: 0.5436 (tmm-80) REVERT: A 353 MET cc_start: 0.6592 (OUTLIER) cc_final: 0.6157 (ttp) REVERT: A 355 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7283 (mp) REVERT: B 48 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7937 (mp) REVERT: B 168 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.6560 (p0) REVERT: B 180 GLN cc_start: 0.7431 (pp30) cc_final: 0.7110 (pp30) REVERT: B 244 ASN cc_start: 0.7970 (t0) cc_final: 0.7760 (m-40) REVERT: B 260 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7637 (mp) REVERT: B 265 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6612 (tp30) REVERT: B 309 ARG cc_start: 0.7924 (ttm170) cc_final: 0.7662 (ttm170) REVERT: E 150 THR cc_start: 0.6315 (p) cc_final: 0.5938 (t) REVERT: E 155 VAL cc_start: 0.7750 (OUTLIER) cc_final: 0.7506 (p) REVERT: G 22 GLU cc_start: 0.5284 (mt-10) cc_final: 0.4905 (mt-10) REVERT: R 59 LEU cc_start: 0.4149 (mt) cc_final: 0.3860 (pp) REVERT: R 247 ARG cc_start: 0.5788 (mmm-85) cc_final: 0.5116 (tpt170) REVERT: R 292 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6602 (tp) REVERT: R 322 TRP cc_start: 0.6272 (t60) cc_final: 0.6013 (t60) outliers start: 37 outliers final: 17 residues processed: 134 average time/residue: 0.6002 time to fit residues: 85.7909 Evaluate side-chains 124 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 353 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 48 ILE 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 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 155 VAL 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 162 VAL 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 42 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4330 r_free = 0.4330 target = 0.194226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.157209 restraints weight = 9899.141| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 1.83 r_work: 0.3647 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9038 Z= 0.186 Angle : 0.613 6.170 12269 Z= 0.321 Chirality : 0.044 0.221 1405 Planarity : 0.005 0.040 1548 Dihedral : 4.491 21.110 1241 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 5.00 % Allowed : 20.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.26), residues: 1111 helix: 2.16 (0.26), residues: 384 sheet: 0.56 (0.31), residues: 271 loop : -0.99 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 250 TYR 0.015 0.002 TYR B 269 PHE 0.015 0.002 PHE A 215 TRP 0.017 0.002 TRP B 104 HIS 0.009 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 9036) covalent geometry : angle 0.61305 (12267) SS BOND : bond 0.00677 ( 1) SS BOND : angle 1.33012 ( 2) hydrogen bonds : bond 0.04030 ( 424) hydrogen bonds : angle 4.39991 ( 1197) Misc. bond : bond 0.00077 ( 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 157 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 110 time to evaluate : 0.412 Fit side-chains REVERT: A 53 MET cc_start: 0.5272 (OUTLIER) cc_final: 0.4935 (mpt) REVERT: A 198 MET cc_start: 0.8262 (ttp) cc_final: 0.7789 (ttp) REVERT: A 309 ARG cc_start: 0.6086 (mtp-110) cc_final: 0.5414 (tmm-80) REVERT: A 353 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.6568 (ptp) REVERT: A 355 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7266 (mp) REVERT: B 180 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7230 (pp30) REVERT: B 260 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7836 (mp) REVERT: B 265 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6582 (tp30) REVERT: E 150 THR cc_start: 0.6364 (p) cc_final: 0.6018 (t) REVERT: G 19 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6670 (pt) REVERT: G 22 GLU cc_start: 0.5712 (mt-10) cc_final: 0.5333 (mt-10) REVERT: R 59 LEU cc_start: 0.4164 (mt) cc_final: 0.3816 (pp) REVERT: R 292 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6684 (tp) REVERT: R 322 TRP cc_start: 0.6300 (t60) cc_final: 0.6048 (t60) outliers start: 47 outliers final: 20 residues processed: 143 average time/residue: 0.5196 time to fit residues: 80.1683 Evaluate side-chains 125 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 353 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 70 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 115 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 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 252 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 82 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 238 ASN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN R 96 ASN R 331 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.195840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.159165 restraints weight = 9981.276| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 1.82 r_work: 0.3667 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.5359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9038 Z= 0.141 Angle : 0.559 6.554 12269 Z= 0.293 Chirality : 0.042 0.225 1405 Planarity : 0.004 0.036 1548 Dihedral : 4.297 18.898 1241 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.26 % Allowed : 21.60 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.26), residues: 1111 helix: 2.20 (0.26), residues: 385 sheet: 0.63 (0.31), residues: 267 loop : -0.93 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 250 TYR 0.013 0.001 TYR B 269 PHE 0.012 0.001 PHE A 189 TRP 0.014 0.001 TRP B 104 HIS 0.006 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9036) covalent geometry : angle 0.55838 (12267) SS BOND : bond 0.00474 ( 1) SS BOND : angle 1.22354 ( 2) hydrogen bonds : bond 0.03661 ( 424) hydrogen bonds : angle 4.27152 ( 1197) Misc. bond : bond 0.00052 ( 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 147 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 0.335 Fit side-chains REVERT: A 53 MET cc_start: 0.5304 (OUTLIER) cc_final: 0.4935 (mpt) REVERT: A 353 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.6180 (ttp) REVERT: A 355 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7286 (mp) REVERT: B 168 ASP cc_start: 0.7071 (OUTLIER) cc_final: 0.6433 (p0) REVERT: B 244 ASN cc_start: 0.8019 (t0) cc_final: 0.7405 (t0) REVERT: B 260 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7520 (mp) REVERT: B 265 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6477 (tp30) REVERT: E 150 THR cc_start: 0.6303 (p) cc_final: 0.5959 (t) REVERT: G 22 GLU cc_start: 0.5720 (mt-10) cc_final: 0.5348 (mt-10) REVERT: R 59 LEU cc_start: 0.4251 (mt) cc_final: 0.3945 (pp) REVERT: R 212 GLU cc_start: 0.5976 (OUTLIER) cc_final: 0.5454 (mm-30) REVERT: R 292 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6615 (tp) REVERT: R 322 TRP cc_start: 0.6324 (t60) cc_final: 0.6090 (t60) outliers start: 40 outliers final: 19 residues processed: 135 average time/residue: 0.5079 time to fit residues: 73.9510 Evaluate side-chains 125 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP 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 A residue 353 MET 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 254 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 281 VAL 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 155 VAL 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 162 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 78 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 overall best weight: 1.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4367 r_free = 0.4367 target = 0.197512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.161846 restraints weight = 9784.310| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 1.63 r_work: 0.3711 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.5487 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= 0.146 Angle : 0.575 7.646 12269 Z= 0.299 Chirality : 0.042 0.228 1405 Planarity : 0.004 0.039 1548 Dihedral : 4.352 19.003 1241 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.51 % Allowed : 22.77 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.26), residues: 1111 helix: 2.27 (0.26), residues: 381 sheet: 0.56 (0.31), residues: 272 loop : -1.02 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 250 TYR 0.015 0.001 TYR B 269 PHE 0.014 0.002 PHE A 189 TRP 0.014 0.001 TRP B 104 HIS 0.007 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9036) covalent geometry : angle 0.57466 (12267) SS BOND : bond 0.00438 ( 1) SS BOND : angle 1.58657 ( 2) hydrogen bonds : bond 0.03706 ( 424) hydrogen bonds : angle 4.27292 ( 1197) Misc. bond : bond 0.00035 ( 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 131 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 0.377 Fit side-chains REVERT: A 353 MET cc_start: 0.6671 (OUTLIER) cc_final: 0.6208 (ttp) REVERT: A 355 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7260 (mp) REVERT: B 168 ASP cc_start: 0.7054 (OUTLIER) cc_final: 0.6397 (p0) REVERT: B 260 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7759 (mp) REVERT: B 267 MET cc_start: 0.7303 (tpp) cc_final: 0.7020 (mmt) REVERT: E 150 THR cc_start: 0.6410 (p) cc_final: 0.6067 (t) REVERT: G 22 GLU cc_start: 0.5625 (mt-10) cc_final: 0.5278 (mt-10) REVERT: R 59 LEU cc_start: 0.4219 (mt) cc_final: 0.3970 (pp) REVERT: R 212 GLU cc_start: 0.5874 (OUTLIER) cc_final: 0.5431 (mm-30) REVERT: R 292 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6636 (tp) outliers start: 33 outliers final: 18 residues processed: 118 average time/residue: 0.5476 time to fit residues: 69.5359 Evaluate side-chains 118 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 353 MET 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 254 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 281 VAL 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 174 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 128 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 22 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 16 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.194808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.158027 restraints weight = 9812.068| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 1.79 r_work: 0.3647 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9038 Z= 0.202 Angle : 0.644 7.974 12269 Z= 0.336 Chirality : 0.044 0.268 1405 Planarity : 0.005 0.035 1548 Dihedral : 4.694 20.607 1241 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.83 % Allowed : 22.77 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.25), residues: 1111 helix: 2.04 (0.26), residues: 381 sheet: 0.20 (0.30), residues: 284 loop : -1.05 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 250 TYR 0.019 0.002 TYR E 235 PHE 0.024 0.002 PHE A 215 TRP 0.016 0.002 TRP B 104 HIS 0.008 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 9036) covalent geometry : angle 0.64395 (12267) SS BOND : bond 0.00566 ( 1) SS BOND : angle 1.74077 ( 2) hydrogen bonds : bond 0.04202 ( 424) hydrogen bonds : angle 4.49085 ( 1197) Misc. bond : bond 0.00057 ( 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 136 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.351 Fit side-chains REVERT: A 53 MET cc_start: 0.5453 (mpt) cc_final: 0.5009 (mpt) REVERT: B 48 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7699 (mm) REVERT: B 180 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7306 (pp30) REVERT: B 260 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7803 (mp) REVERT: E 150 THR cc_start: 0.6598 (p) cc_final: 0.6221 (t) REVERT: G 22 GLU cc_start: 0.5830 (mt-10) cc_final: 0.5562 (mt-10) REVERT: R 59 LEU cc_start: 0.4214 (mt) cc_final: 0.4000 (pp) REVERT: R 206 HIS cc_start: 0.4146 (m-70) cc_final: 0.3491 (m170) REVERT: R 212 GLU cc_start: 0.6092 (OUTLIER) cc_final: 0.5617 (mm-30) REVERT: R 292 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6737 (tp) REVERT: R 337 TRP cc_start: 0.5073 (m100) cc_final: 0.4827 (m100) outliers start: 36 outliers final: 22 residues processed: 123 average time/residue: 0.5583 time to fit residues: 73.7279 Evaluate side-chains 121 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 360 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 70 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 281 VAL 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 155 VAL 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 128 VAL Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 276 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 53 optimal weight: 0.0870 chunk 15 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.4381 r_free = 0.4381 target = 0.199113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.165039 restraints weight = 9827.189| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 1.66 r_work: 0.3730 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9038 Z= 0.114 Angle : 0.546 7.951 12269 Z= 0.284 Chirality : 0.041 0.218 1405 Planarity : 0.004 0.039 1548 Dihedral : 4.226 17.534 1241 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.87 % Allowed : 23.83 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.26), residues: 1111 helix: 2.22 (0.26), residues: 385 sheet: 0.51 (0.32), residues: 263 loop : -1.01 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 250 TYR 0.011 0.001 TYR B 64 PHE 0.012 0.001 PHE A 189 TRP 0.011 0.001 TRP B 87 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 9036) covalent geometry : angle 0.54630 (12267) SS BOND : bond 0.00341 ( 1) SS BOND : angle 1.05854 ( 2) hydrogen bonds : bond 0.03456 ( 424) hydrogen bonds : angle 4.18956 ( 1197) Misc. bond : bond 0.00021 ( 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 129 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.358 Fit side-chains REVERT: A 198 MET cc_start: 0.8315 (ttp) cc_final: 0.8074 (ttp) REVERT: B 180 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.7197 (pp30) REVERT: B 260 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7532 (mp) REVERT: E 150 THR cc_start: 0.6472 (p) cc_final: 0.6066 (t) REVERT: G 22 GLU cc_start: 0.5566 (mt-10) cc_final: 0.5215 (mt-10) REVERT: R 59 LEU cc_start: 0.4256 (mt) cc_final: 0.4020 (pp) REVERT: R 206 HIS cc_start: 0.4112 (m-70) cc_final: 0.3465 (m170) REVERT: R 212 GLU cc_start: 0.5897 (OUTLIER) cc_final: 0.5502 (mm-30) REVERT: R 292 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6565 (tp) outliers start: 27 outliers final: 19 residues processed: 120 average time/residue: 0.5718 time to fit residues: 73.5789 Evaluate side-chains 111 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 360 LEU Chi-restraints excluded: chain B residue 105 VAL 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 254 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 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 212 GLU Chi-restraints excluded: chain R residue 276 THR 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 57 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN B 147 HIS 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 = 0.4356 r_free = 0.4356 target = 0.196435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.159658 restraints weight = 9743.469| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 1.78 r_work: 0.3679 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.5731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9038 Z= 0.164 Angle : 0.604 8.682 12269 Z= 0.314 Chirality : 0.043 0.239 1405 Planarity : 0.004 0.038 1548 Dihedral : 4.448 18.895 1241 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.19 % Allowed : 23.94 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.26), residues: 1111 helix: 2.14 (0.26), residues: 381 sheet: 0.22 (0.31), residues: 281 loop : -0.92 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 250 TYR 0.015 0.002 TYR B 64 PHE 0.012 0.002 PHE A 189 TRP 0.014 0.001 TRP B 104 HIS 0.006 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9036) covalent geometry : angle 0.60401 (12267) SS BOND : bond 0.00459 ( 1) SS BOND : angle 1.53200 ( 2) hydrogen bonds : bond 0.03845 ( 424) hydrogen bonds : angle 4.34378 ( 1197) Misc. bond : bond 0.00045 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3717.45 seconds wall clock time: 64 minutes 13.43 seconds (3853.43 seconds total)