Starting phenix.real_space_refine on Mon May 12 10:18:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9blb_44652/05_2025/9blb_44652.cif Found real_map, /net/cci-nas-00/data/ceres_data/9blb_44652/05_2025/9blb_44652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9blb_44652/05_2025/9blb_44652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9blb_44652/05_2025/9blb_44652.map" model { file = "/net/cci-nas-00/data/ceres_data/9blb_44652/05_2025/9blb_44652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9blb_44652/05_2025/9blb_44652.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.094 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 65 5.16 5 C 5723 2.51 5 N 1576 2.21 5 O 1644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9008 Number of models: 1 Model: "" Number of chains: 7 Chain: "P" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 276 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain: "P" 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: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2855 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 15, 'TRANS': 341} Chain breaks: 1 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1873 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain breaks: 2 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Time building chain proxies: 5.55, per 1000 atoms: 0.62 Number of scatterers: 9008 At special positions: 0 Unit cell: (86, 96.32, 147.92, 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 65 16.00 O 1644 8.00 N 1576 7.00 C 5723 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.1 seconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2150 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 40.2% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 20 Processing helix chain 'R' and resid 45 through 57 Processing helix chain 'R' and resid 137 through 173 Processing helix chain 'R' and resid 178 through 205 removed outlier: 3.606A pdb=" N LEU R 183 " --> pdb=" O GLN R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.904A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.779A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE R 248 " --> pdb=" O LEU R 244 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 268 Processing helix chain 'R' and resid 270 through 284 Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 329 Proline residue: R 304 - end of helix Processing helix chain 'R' and resid 333 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 removed outlier: 3.914A pdb=" N PHE R 359 " --> pdb=" O GLN R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 382 removed outlier: 3.837A pdb=" N SER R 378 " --> pdb=" O TYR R 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 406 Processing helix chain 'A' and resid 14 through 39 removed outlier: 3.595A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.649A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.820A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.698A pdb=" N SER A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.563A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.945A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.532A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.553A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.684A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.652A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.685A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.587A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 89 through 90 removed outlier: 4.157A pdb=" N VAL R 89 " --> pdb=" O CYS R 112 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N CYS R 112 " --> pdb=" O VAL R 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'R' and resid 93 through 94 removed outlier: 3.872A pdb=" N GLN R 93 " --> pdb=" O VAL R 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.336A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.663A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.574A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.763A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.642A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 189 through 192 removed outlier: 6.410A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.628A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.527A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.552A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.578A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR N 94 " --> pdb=" O THR N 122 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1230 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.55 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2032 1.33 - 1.45: 2082 1.45 - 1.57: 5008 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 9214 Sorted by residual: bond pdb=" CA SER A 286 " pdb=" CB SER A 286 " ideal model delta sigma weight residual 1.529 1.477 0.052 1.66e-02 3.63e+03 9.94e+00 bond pdb=" N ARG A 228 " pdb=" CA ARG A 228 " ideal model delta sigma weight residual 1.453 1.493 -0.040 1.41e-02 5.03e+03 8.12e+00 bond pdb=" CA SER A 275 " pdb=" CB SER A 275 " ideal model delta sigma weight residual 1.529 1.484 0.045 1.63e-02 3.76e+03 7.72e+00 bond pdb=" N ASN A 279 " pdb=" CA ASN A 279 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.22e-02 6.72e+03 7.71e+00 bond pdb=" N VAL A 224 " pdb=" CA VAL A 224 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.52e+00 ... (remaining 9209 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 12276 1.50 - 2.99: 169 2.99 - 4.49: 40 4.49 - 5.99: 6 5.99 - 7.49: 2 Bond angle restraints: 12493 Sorted by residual: angle pdb=" N LEU A 272 " pdb=" CA LEU A 272 " pdb=" C LEU A 272 " ideal model delta sigma weight residual 112.45 104.96 7.49 1.39e+00 5.18e-01 2.90e+01 angle pdb=" CA GLY A 225 " pdb=" C GLY A 225 " pdb=" O GLY A 225 " ideal model delta sigma weight residual 121.57 117.54 4.03 8.70e-01 1.32e+00 2.15e+01 angle pdb=" CA PRO G 53 " pdb=" N PRO G 53 " pdb=" CD PRO G 53 " ideal model delta sigma weight residual 112.00 106.50 5.50 1.40e+00 5.10e-01 1.54e+01 angle pdb=" CA ASN A 279 " pdb=" C ASN A 279 " pdb=" O ASN A 279 " ideal model delta sigma weight residual 121.16 117.57 3.59 1.12e+00 7.97e-01 1.02e+01 angle pdb=" N LYS A 271 " pdb=" CA LYS A 271 " pdb=" C LYS A 271 " ideal model delta sigma weight residual 113.28 109.43 3.85 1.22e+00 6.72e-01 9.94e+00 ... (remaining 12488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 4694 17.54 - 35.07: 575 35.07 - 52.61: 154 52.61 - 70.15: 34 70.15 - 87.68: 13 Dihedral angle restraints: 5470 sinusoidal: 2145 harmonic: 3325 Sorted by residual: dihedral pdb=" CB CYS R 219 " pdb=" SG CYS R 219 " pdb=" SG CYS R 289 " pdb=" CB CYS R 289 " ideal model delta sinusoidal sigma weight residual 93.00 167.69 -74.69 1 1.00e+01 1.00e-02 7.06e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -141.75 55.75 1 1.00e+01 1.00e-02 4.20e+01 dihedral pdb=" CB CYS R 55 " pdb=" SG CYS R 55 " pdb=" SG CYS R 81 " pdb=" CB CYS R 81 " ideal model delta sinusoidal sigma weight residual 93.00 51.64 41.36 1 1.00e+01 1.00e-02 2.39e+01 ... (remaining 5467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1198 0.055 - 0.110: 161 0.110 - 0.164: 22 0.164 - 0.219: 1 0.219 - 0.274: 2 Chirality restraints: 1384 Sorted by residual: chirality pdb=" CA LEU A 272 " pdb=" N LEU A 272 " pdb=" C LEU A 272 " pdb=" CB LEU A 272 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA LYS A 280 " pdb=" N LYS A 280 " pdb=" C LYS A 280 " pdb=" CB LYS A 280 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ASP A 223 " pdb=" N ASP A 223 " pdb=" C ASP A 223 " pdb=" CB ASP A 223 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 1381 not shown) Planarity restraints: 1598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " -0.074 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO G 53 " 0.188 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 269 " -0.012 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C ALA A 269 " 0.040 2.00e-02 2.50e+03 pdb=" O ALA A 269 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU A 270 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 221 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.50e+00 pdb=" C MET A 221 " 0.032 2.00e-02 2.50e+03 pdb=" O MET A 221 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE A 222 " -0.011 2.00e-02 2.50e+03 ... (remaining 1595 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2488 2.81 - 3.33: 8146 3.33 - 3.85: 14830 3.85 - 4.38: 17104 4.38 - 4.90: 30233 Nonbonded interactions: 72801 Sorted by model distance: nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.285 3.040 nonbonded pdb=" OG1 THR N 28 " pdb=" ND2 ASN N 31 " model vdw 2.321 3.120 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.326 3.040 nonbonded pdb=" NE2 HIS B 225 " pdb=" OG1 THR B 243 " model vdw 2.331 3.120 nonbonded pdb=" O CYS B 204 " pdb=" OH TYR N 117 " model vdw 2.334 3.040 ... (remaining 72796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.390 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 22.790 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 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 0.095 9222 Z= 0.181 Angle : 0.475 7.487 12507 Z= 0.285 Chirality : 0.040 0.274 1384 Planarity : 0.004 0.109 1598 Dihedral : 16.730 87.684 3299 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.31 % Allowed : 19.23 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1124 helix: 2.10 (0.25), residues: 426 sheet: 0.65 (0.34), residues: 224 loop : -0.08 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 281 HIS 0.002 0.000 HIS R 377 PHE 0.007 0.001 PHE B 292 TYR 0.013 0.001 TYR R 374 ARG 0.008 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.21372 ( 425) hydrogen bonds : angle 6.57150 ( 1230) SS BOND : bond 0.00135 ( 7) SS BOND : angle 0.91183 ( 14) covalent geometry : bond 0.00253 ( 9214) covalent geometry : angle 0.47449 (12493) Misc. bond : bond 0.09505 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 133 time to evaluate : 1.021 Fit side-chains REVERT: R 376 MET cc_start: 0.6994 (tpp) cc_final: 0.6785 (tpt) outliers start: 3 outliers final: 2 residues processed: 136 average time/residue: 0.2583 time to fit residues: 46.5080 Evaluate side-chains 121 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 274 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 296 HIS A 220 HIS A 279 ASN B 268 ASN B 340 ASN G 59 ASN N 31 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.170426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.138490 restraints weight = 9888.913| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.39 r_work: 0.3257 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9222 Z= 0.131 Angle : 0.495 6.898 12507 Z= 0.262 Chirality : 0.041 0.154 1384 Planarity : 0.004 0.074 1598 Dihedral : 3.584 36.557 1244 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.12 % Allowed : 17.36 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.25), residues: 1124 helix: 2.44 (0.25), residues: 425 sheet: 0.36 (0.34), residues: 228 loop : -0.17 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 PHE 0.013 0.001 PHE B 151 TYR 0.015 0.001 TYR R 191 ARG 0.005 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 425) hydrogen bonds : angle 4.58316 ( 1230) SS BOND : bond 0.00262 ( 7) SS BOND : angle 0.77105 ( 14) covalent geometry : bond 0.00291 ( 9214) covalent geometry : angle 0.49416 (12493) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.925 Fit side-chains REVERT: A 318 TYR cc_start: 0.7915 (t80) cc_final: 0.7446 (t80) REVERT: A 370 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7400 (tp30) REVERT: A 390 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7738 (mp10) REVERT: B 59 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.8129 (m-80) REVERT: N 89 GLU cc_start: 0.6577 (pp20) cc_final: 0.6373 (tp30) outliers start: 30 outliers final: 14 residues processed: 146 average time/residue: 0.2503 time to fit residues: 48.4465 Evaluate side-chains 135 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 3 ASN Chi-restraints excluded: chain P residue 19 SER Chi-restraints excluded: chain R residue 132 THR Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 19 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 95 optimal weight: 0.1980 chunk 75 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 15 optimal weight: 8.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.169559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.131170 restraints weight = 10050.828| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.42 r_work: 0.3285 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9222 Z= 0.104 Angle : 0.449 7.615 12507 Z= 0.238 Chirality : 0.039 0.149 1384 Planarity : 0.003 0.062 1598 Dihedral : 3.400 12.224 1241 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.12 % Allowed : 16.94 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.25), residues: 1124 helix: 2.56 (0.25), residues: 425 sheet: 0.15 (0.31), residues: 251 loop : -0.16 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.000 HIS B 54 PHE 0.010 0.001 PHE N 108 TYR 0.010 0.001 TYR R 191 ARG 0.004 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 425) hydrogen bonds : angle 4.29142 ( 1230) SS BOND : bond 0.00367 ( 7) SS BOND : angle 0.74446 ( 14) covalent geometry : bond 0.00229 ( 9214) covalent geometry : angle 0.44885 (12493) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.924 Fit side-chains REVERT: R 187 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7546 (ttt) REVERT: R 240 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7755 (mt-10) REVERT: A 318 TYR cc_start: 0.7922 (t80) cc_final: 0.7434 (t80) REVERT: B 59 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.8168 (m-80) REVERT: B 171 ILE cc_start: 0.7453 (OUTLIER) cc_final: 0.6924 (mm) REVERT: B 325 MET cc_start: 0.7713 (tpp) cc_final: 0.7474 (mmt) REVERT: N 89 GLU cc_start: 0.6585 (pp20) cc_final: 0.6259 (tp30) outliers start: 30 outliers final: 16 residues processed: 146 average time/residue: 0.2740 time to fit residues: 52.0969 Evaluate side-chains 139 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 132 THR Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 324 VAL Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 41 optimal weight: 4.9990 chunk 103 optimal weight: 0.0570 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 69 optimal weight: 0.0670 chunk 93 optimal weight: 0.2980 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN B 268 ASN G 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.168497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.137138 restraints weight = 9960.378| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.39 r_work: 0.3239 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9222 Z= 0.103 Angle : 0.443 5.938 12507 Z= 0.234 Chirality : 0.039 0.146 1384 Planarity : 0.003 0.057 1598 Dihedral : 3.425 13.241 1241 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.81 % Allowed : 18.09 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.25), residues: 1124 helix: 2.50 (0.25), residues: 425 sheet: 0.21 (0.31), residues: 249 loop : -0.14 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 PHE 0.011 0.001 PHE N 108 TYR 0.009 0.001 TYR R 263 ARG 0.004 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 425) hydrogen bonds : angle 4.10792 ( 1230) SS BOND : bond 0.00315 ( 7) SS BOND : angle 0.99132 ( 14) covalent geometry : bond 0.00233 ( 9214) covalent geometry : angle 0.44211 (12493) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.940 Fit side-chains REVERT: R 187 MET cc_start: 0.8019 (mmm) cc_final: 0.7322 (ttt) REVERT: R 240 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7597 (mt-10) REVERT: A 318 TYR cc_start: 0.7974 (t80) cc_final: 0.7460 (t80) REVERT: B 59 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.8147 (m-80) REVERT: B 171 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.7006 (mm) REVERT: N 89 GLU cc_start: 0.6554 (pp20) cc_final: 0.6243 (tp30) outliers start: 27 outliers final: 17 residues processed: 132 average time/residue: 0.2718 time to fit residues: 47.2480 Evaluate side-chains 135 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 132 THR Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 324 VAL Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 57 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 84 optimal weight: 0.0670 chunk 89 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 26 optimal weight: 0.0670 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.168637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.138437 restraints weight = 10020.669| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.31 r_work: 0.3250 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9222 Z= 0.096 Angle : 0.433 5.922 12507 Z= 0.229 Chirality : 0.039 0.147 1384 Planarity : 0.003 0.052 1598 Dihedral : 3.400 13.815 1241 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.64 % Allowed : 17.46 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.25), residues: 1124 helix: 2.53 (0.25), residues: 425 sheet: 0.23 (0.31), residues: 247 loop : -0.14 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.000 HIS B 54 PHE 0.016 0.001 PHE R 359 TYR 0.009 0.001 TYR N 60 ARG 0.005 0.000 ARG R 362 Details of bonding type rmsd hydrogen bonds : bond 0.03302 ( 425) hydrogen bonds : angle 3.99470 ( 1230) SS BOND : bond 0.00208 ( 7) SS BOND : angle 0.81405 ( 14) covalent geometry : bond 0.00215 ( 9214) covalent geometry : angle 0.43212 (12493) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 1.060 Fit side-chains REVERT: R 187 MET cc_start: 0.8087 (mmm) cc_final: 0.7257 (ttt) REVERT: R 240 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7501 (mt-10) REVERT: B 59 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.8145 (m-80) REVERT: B 171 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.6989 (mm) REVERT: N 89 GLU cc_start: 0.6526 (pp20) cc_final: 0.6236 (tp30) outliers start: 35 outliers final: 21 residues processed: 147 average time/residue: 0.2555 time to fit residues: 49.9163 Evaluate side-chains 140 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 132 THR Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 324 VAL Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 31 optimal weight: 9.9990 chunk 108 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 84 optimal weight: 0.0870 chunk 67 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 81 optimal weight: 0.0030 chunk 73 optimal weight: 0.2980 chunk 94 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.3568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 208 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.169494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.139319 restraints weight = 9914.545| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.40 r_work: 0.3246 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9222 Z= 0.086 Angle : 0.418 5.887 12507 Z= 0.221 Chirality : 0.038 0.148 1384 Planarity : 0.003 0.049 1598 Dihedral : 3.322 13.936 1241 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.29 % Allowed : 19.54 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.25), residues: 1124 helix: 2.50 (0.25), residues: 430 sheet: 0.29 (0.31), residues: 246 loop : -0.14 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.000 HIS B 54 PHE 0.016 0.001 PHE R 359 TYR 0.009 0.001 TYR R 263 ARG 0.004 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03081 ( 425) hydrogen bonds : angle 3.89584 ( 1230) SS BOND : bond 0.00156 ( 7) SS BOND : angle 0.68561 ( 14) covalent geometry : bond 0.00186 ( 9214) covalent geometry : angle 0.41747 (12493) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.917 Fit side-chains REVERT: R 187 MET cc_start: 0.8086 (mmm) cc_final: 0.7151 (ttt) REVERT: R 240 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7578 (mt-10) REVERT: B 59 TYR cc_start: 0.8518 (OUTLIER) cc_final: 0.8102 (m-80) REVERT: B 171 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.6987 (mm) REVERT: N 89 GLU cc_start: 0.6566 (pp20) cc_final: 0.6275 (tp30) outliers start: 22 outliers final: 17 residues processed: 136 average time/residue: 0.2729 time to fit residues: 48.4934 Evaluate side-chains 139 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 132 THR Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 6 optimal weight: 40.0000 chunk 88 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.163871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.133128 restraints weight = 10129.147| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.33 r_work: 0.3180 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9222 Z= 0.166 Angle : 0.508 6.501 12507 Z= 0.266 Chirality : 0.042 0.137 1384 Planarity : 0.004 0.049 1598 Dihedral : 3.730 15.069 1241 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.12 % Allowed : 19.23 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.25), residues: 1124 helix: 2.31 (0.25), residues: 430 sheet: -0.02 (0.31), residues: 251 loop : -0.19 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.019 0.002 PHE N 108 TYR 0.013 0.001 TYR N 60 ARG 0.004 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 425) hydrogen bonds : angle 4.14644 ( 1230) SS BOND : bond 0.00352 ( 7) SS BOND : angle 1.08471 ( 14) covalent geometry : bond 0.00396 ( 9214) covalent geometry : angle 0.50678 (12493) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 1.007 Fit side-chains REVERT: R 187 MET cc_start: 0.8282 (mmm) cc_final: 0.7033 (ttt) REVERT: R 240 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7490 (mt-10) REVERT: R 339 LEU cc_start: 0.7184 (tp) cc_final: 0.6980 (tp) REVERT: A 292 ASN cc_start: 0.8939 (t0) cc_final: 0.8680 (m-40) REVERT: A 318 TYR cc_start: 0.8108 (t80) cc_final: 0.7587 (t80) REVERT: B 59 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.8224 (m-80) REVERT: N 89 GLU cc_start: 0.6531 (pp20) cc_final: 0.6281 (tp30) outliers start: 30 outliers final: 21 residues processed: 143 average time/residue: 0.2599 time to fit residues: 49.2336 Evaluate side-chains 133 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 132 THR Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 57 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 69 optimal weight: 0.0980 chunk 40 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 97 optimal weight: 0.1980 chunk 17 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 94 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.166682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.136384 restraints weight = 10146.305| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.34 r_work: 0.3216 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 9222 Z= 0.103 Angle : 0.457 5.978 12507 Z= 0.242 Chirality : 0.039 0.145 1384 Planarity : 0.003 0.047 1598 Dihedral : 3.582 15.211 1241 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.60 % Allowed : 19.85 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.25), residues: 1124 helix: 2.37 (0.25), residues: 430 sheet: 0.03 (0.31), residues: 249 loop : -0.17 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.000 HIS B 54 PHE 0.018 0.001 PHE R 359 TYR 0.009 0.001 TYR R 149 ARG 0.007 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03328 ( 425) hydrogen bonds : angle 3.99226 ( 1230) SS BOND : bond 0.00672 ( 7) SS BOND : angle 1.88803 ( 14) covalent geometry : bond 0.00235 ( 9214) covalent geometry : angle 0.45307 (12493) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.941 Fit side-chains REVERT: R 187 MET cc_start: 0.8190 (mmm) cc_final: 0.7088 (ttt) REVERT: R 240 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7498 (mt-10) REVERT: R 371 ILE cc_start: 0.7500 (mm) cc_final: 0.7140 (mp) REVERT: A 318 TYR cc_start: 0.8033 (t80) cc_final: 0.7536 (t80) REVERT: B 59 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.8110 (m-80) REVERT: N 89 GLU cc_start: 0.6531 (pp20) cc_final: 0.6287 (tp30) outliers start: 25 outliers final: 23 residues processed: 131 average time/residue: 0.2609 time to fit residues: 45.2605 Evaluate side-chains 136 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain R residue 132 THR Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 21 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 108 optimal weight: 0.0370 chunk 77 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 33 optimal weight: 0.1980 chunk 78 optimal weight: 6.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.167189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.135097 restraints weight = 10026.312| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.42 r_work: 0.3219 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9222 Z= 0.097 Angle : 0.446 5.935 12507 Z= 0.235 Chirality : 0.039 0.145 1384 Planarity : 0.003 0.046 1598 Dihedral : 3.499 15.011 1241 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.60 % Allowed : 20.17 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.25), residues: 1124 helix: 2.41 (0.25), residues: 430 sheet: 0.10 (0.31), residues: 237 loop : -0.15 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 76 HIS 0.003 0.000 HIS B 54 PHE 0.020 0.001 PHE R 359 TYR 0.009 0.001 TYR N 60 ARG 0.005 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03183 ( 425) hydrogen bonds : angle 3.89727 ( 1230) SS BOND : bond 0.00268 ( 7) SS BOND : angle 1.15151 ( 14) covalent geometry : bond 0.00221 ( 9214) covalent geometry : angle 0.44432 (12493) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.914 Fit side-chains REVERT: R 187 MET cc_start: 0.8173 (mmm) cc_final: 0.7059 (ttt) REVERT: R 240 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7546 (mt-10) REVERT: R 362 ARG cc_start: 0.7638 (mmm-85) cc_final: 0.7392 (mmm-85) REVERT: R 371 ILE cc_start: 0.7452 (mm) cc_final: 0.7118 (mp) REVERT: R 374 TYR cc_start: 0.8361 (m-80) cc_final: 0.8108 (m-80) REVERT: A 318 TYR cc_start: 0.8008 (t80) cc_final: 0.7502 (t80) REVERT: B 59 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.8115 (m-80) REVERT: N 89 GLU cc_start: 0.6574 (pp20) cc_final: 0.6280 (tp30) outliers start: 25 outliers final: 22 residues processed: 132 average time/residue: 0.2563 time to fit residues: 44.6980 Evaluate side-chains 137 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain R residue 132 THR Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 324 VAL Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 48 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.163392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.130656 restraints weight = 10072.403| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.40 r_work: 0.3164 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9222 Z= 0.156 Angle : 0.514 6.413 12507 Z= 0.270 Chirality : 0.042 0.139 1384 Planarity : 0.004 0.047 1598 Dihedral : 3.814 15.568 1241 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.91 % Allowed : 20.06 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.25), residues: 1124 helix: 2.26 (0.25), residues: 429 sheet: -0.10 (0.31), residues: 251 loop : -0.24 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 76 HIS 0.004 0.001 HIS B 54 PHE 0.019 0.002 PHE R 359 TYR 0.013 0.001 TYR N 60 ARG 0.006 0.001 ARG R 174 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 425) hydrogen bonds : angle 4.12174 ( 1230) SS BOND : bond 0.00359 ( 7) SS BOND : angle 1.28959 ( 14) covalent geometry : bond 0.00375 ( 9214) covalent geometry : angle 0.51294 (12493) Misc. bond : bond 0.00000 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: R 48 MET cc_start: 0.6291 (tpt) cc_final: 0.5699 (tpt) REVERT: R 187 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.6991 (ttt) REVERT: R 240 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7533 (mt-10) REVERT: R 343 LYS cc_start: 0.7962 (tttt) cc_final: 0.7754 (tttm) REVERT: A 318 TYR cc_start: 0.8127 (t80) cc_final: 0.7644 (t80) REVERT: B 59 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.8263 (m-80) REVERT: N 89 GLU cc_start: 0.6591 (pp20) cc_final: 0.6302 (tp30) outliers start: 28 outliers final: 23 residues processed: 134 average time/residue: 0.2631 time to fit residues: 46.4499 Evaluate side-chains 139 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain R residue 132 THR Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 324 VAL Chi-restraints excluded: chain R residue 349 VAL Chi-restraints excluded: chain R residue 378 SER Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 9 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 0.1980 chunk 63 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 81 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 208 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.165626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.128966 restraints weight = 10082.610| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.57 r_work: 0.3172 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9222 Z= 0.106 Angle : 0.462 5.994 12507 Z= 0.243 Chirality : 0.040 0.143 1384 Planarity : 0.003 0.045 1598 Dihedral : 3.635 15.510 1241 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.70 % Allowed : 20.37 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.25), residues: 1124 helix: 2.36 (0.25), residues: 429 sheet: -0.04 (0.31), residues: 251 loop : -0.22 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 PHE 0.019 0.001 PHE R 359 TYR 0.009 0.001 TYR R 149 ARG 0.009 0.000 ARG R 174 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 425) hydrogen bonds : angle 3.97406 ( 1230) SS BOND : bond 0.00279 ( 7) SS BOND : angle 1.00920 ( 14) covalent geometry : bond 0.00245 ( 9214) covalent geometry : angle 0.46110 (12493) Misc. bond : bond 0.00002 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4917.91 seconds wall clock time: 85 minutes 47.92 seconds (5147.92 seconds total)