Starting phenix.real_space_refine on Tue Apr 29 20:26:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9blb_44652/04_2025/9blb_44652.cif Found real_map, /net/cci-nas-00/data/ceres_data/9blb_44652/04_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_44652/04_2025/9blb_44652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9blb_44652/04_2025/9blb_44652.map" model { file = "/net/cci-nas-00/data/ceres_data/9blb_44652/04_2025/9blb_44652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9blb_44652/04_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 5.78, per 1000 atoms: 0.64 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: 2.36 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: 1.12 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: 2.61 Time building geometry restraints manager: 2.79 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.810 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.510 ------------------------------------------------------------------------------- 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 : 0.985 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: 0.3046 time to fit residues: 54.6286 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 : 1.032 ------------------------------------------------------------------------------- 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 = 0.170427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.138492 restraints weight = 9888.864| |-----------------------------------------------------------------------------| 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: 3.77 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 6.897 12507 Z= 0.262 Chirality : 0.041 0.154 1384 Planarity : 0.004 0.074 1598 Dihedral : 3.584 36.554 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 0.04266 ( 425) hydrogen bonds : angle 4.58329 ( 1230) SS BOND : bond 0.00261 ( 7) SS BOND : angle 0.77087 ( 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 : 0.979 Fit side-chains REVERT: A 318 TYR cc_start: 0.7925 (t80) cc_final: 0.7461 (t80) REVERT: A 370 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7418 (tp30) REVERT: A 390 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7749 (mp10) REVERT: B 59 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.8130 (m-80) outliers start: 30 outliers final: 14 residues processed: 146 average time/residue: 0.2576 time to fit residues: 49.6887 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 : 1.051 ------------------------------------------------------------------------------- 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: 3.9990 chunk 100 optimal weight: 3.9990 chunk 45 optimal weight: 0.1980 chunk 95 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 84 optimal weight: 0.0050 chunk 70 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 56 optimal weight: 0.0000 chunk 32 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.169558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.133803 restraints weight = 10064.891| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.51 r_work: 0.3257 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9222 Z= 0.106 Angle : 0.451 7.645 12507 Z= 0.239 Chirality : 0.039 0.148 1384 Planarity : 0.003 0.062 1598 Dihedral : 3.407 12.252 1241 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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 0.001 HIS B 54 PHE 0.010 0.001 PHE N 108 TYR 0.010 0.001 TYR R 149 ARG 0.004 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 425) hydrogen bonds : angle 4.30393 ( 1230) SS BOND : bond 0.00395 ( 7) SS BOND : angle 0.71430 ( 14) covalent geometry : bond 0.00236 ( 9214) covalent geometry : angle 0.45083 (12493) Misc. bond : bond 0.00016 ( 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 162 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.948 Fit side-chains REVERT: R 187 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7551 (ttt) REVERT: R 240 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7733 (mt-10) REVERT: A 318 TYR cc_start: 0.7889 (t80) cc_final: 0.7405 (t80) REVERT: B 59 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.8178 (m-80) REVERT: B 171 ILE cc_start: 0.7442 (OUTLIER) cc_final: 0.6923 (mm) REVERT: B 325 MET cc_start: 0.7709 (tpp) cc_final: 0.7468 (mmt) outliers start: 30 outliers final: 15 residues processed: 147 average time/residue: 0.2665 time to fit residues: 51.0990 Evaluate side-chains 139 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 69 optimal weight: 0.0050 chunk 93 optimal weight: 0.0870 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN G 59 ASN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.162645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.126461 restraints weight = 10047.061| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.37 r_work: 0.3183 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9222 Z= 0.183 Angle : 0.541 7.571 12507 Z= 0.284 Chirality : 0.043 0.143 1384 Planarity : 0.004 0.058 1598 Dihedral : 3.910 15.246 1241 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.05 % Allowed : 17.46 % Favored : 78.48 % 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: 1.03 (0.25), residues: 1124 helix: 2.11 (0.25), residues: 430 sheet: -0.01 (0.31), residues: 249 loop : -0.25 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 47 HIS 0.005 0.001 HIS B 54 PHE 0.021 0.002 PHE N 108 TYR 0.013 0.002 TYR N 60 ARG 0.003 0.001 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04325 ( 425) hydrogen bonds : angle 4.36526 ( 1230) SS BOND : bond 0.00451 ( 7) SS BOND : angle 1.45289 ( 14) covalent geometry : bond 0.00437 ( 9214) covalent geometry : angle 0.53950 (12493) Misc. bond : bond 0.00002 ( 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 163 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 1.157 Fit side-chains REVERT: R 133 MET cc_start: 0.6909 (tpt) cc_final: 0.6557 (tpp) REVERT: R 187 MET cc_start: 0.8181 (mmm) cc_final: 0.7079 (ttt) REVERT: R 240 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7496 (mt-10) REVERT: R 339 LEU cc_start: 0.7166 (tp) cc_final: 0.6963 (tp) REVERT: R 343 LYS cc_start: 0.7926 (tttt) cc_final: 0.7717 (tttm) REVERT: A 292 ASN cc_start: 0.8970 (t0) cc_final: 0.8683 (m-40) REVERT: A 318 TYR cc_start: 0.8097 (t80) cc_final: 0.7698 (t80) REVERT: B 16 ASN cc_start: 0.7048 (t0) cc_final: 0.6374 (t0) REVERT: B 59 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.8273 (m-80) REVERT: B 186 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7633 (m-30) outliers start: 39 outliers final: 25 residues processed: 148 average time/residue: 0.3421 time to fit residues: 67.8241 Evaluate side-chains 143 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 4 THR 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 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 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 161 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 186 ASP 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 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: 3.9990 chunk 24 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 84 optimal weight: 0.2980 chunk 89 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 overall best weight: 1.6382 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.161562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.123635 restraints weight = 10108.639| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.57 r_work: 0.3119 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9222 Z= 0.185 Angle : 0.539 7.149 12507 Z= 0.284 Chirality : 0.042 0.145 1384 Planarity : 0.004 0.055 1598 Dihedral : 4.072 17.151 1241 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.16 % Allowed : 17.98 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.25), residues: 1124 helix: 1.94 (0.25), residues: 425 sheet: -0.09 (0.32), residues: 245 loop : -0.38 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 82 HIS 0.005 0.001 HIS B 54 PHE 0.018 0.002 PHE N 108 TYR 0.010 0.001 TYR N 60 ARG 0.005 0.000 ARG R 362 Details of bonding type rmsd hydrogen bonds : bond 0.04284 ( 425) hydrogen bonds : angle 4.39034 ( 1230) SS BOND : bond 0.00587 ( 7) SS BOND : angle 1.57887 ( 14) covalent geometry : bond 0.00445 ( 9214) covalent geometry : angle 0.53628 (12493) Misc. bond : bond 0.00003 ( 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 156 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 0.971 Fit side-chains REVERT: R 187 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7107 (ttt) REVERT: R 240 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7663 (mt-10) REVERT: R 321 ARG cc_start: 0.7272 (ttp-170) cc_final: 0.6949 (ttp80) REVERT: R 339 LEU cc_start: 0.7220 (tp) cc_final: 0.6998 (tp) REVERT: R 343 LYS cc_start: 0.7947 (tttt) cc_final: 0.7728 (tttm) REVERT: A 318 TYR cc_start: 0.8176 (t80) cc_final: 0.7823 (t80) REVERT: B 59 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.8323 (m-80) outliers start: 40 outliers final: 30 residues processed: 144 average time/residue: 0.2829 time to fit residues: 53.0969 Evaluate side-chains 141 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain P residue 19 SER Chi-restraints excluded: chain R residue 132 THR Chi-restraints excluded: chain R residue 187 MET 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 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 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 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 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 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR 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: 3.9990 chunk 37 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 0.3980 chunk 73 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.163256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.124698 restraints weight = 9971.487| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.41 r_work: 0.3155 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9222 Z= 0.131 Angle : 0.485 6.108 12507 Z= 0.257 Chirality : 0.040 0.149 1384 Planarity : 0.004 0.052 1598 Dihedral : 3.892 16.359 1241 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.53 % Allowed : 19.54 % 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: 0.87 (0.25), residues: 1124 helix: 2.04 (0.25), residues: 425 sheet: -0.12 (0.31), residues: 245 loop : -0.36 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS B 54 PHE 0.013 0.001 PHE B 151 TYR 0.010 0.001 TYR R 149 ARG 0.003 0.000 ARG R 213 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 425) hydrogen bonds : angle 4.23454 ( 1230) SS BOND : bond 0.00399 ( 7) SS BOND : angle 1.37012 ( 14) covalent geometry : bond 0.00308 ( 9214) covalent geometry : angle 0.48270 (12493) Misc. bond : bond 0.00000 ( 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: 34 poor density : 112 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: R 187 MET cc_start: 0.8278 (mmm) cc_final: 0.7054 (ttt) REVERT: R 240 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7569 (mt-10) REVERT: R 321 ARG cc_start: 0.7190 (ttp-170) cc_final: 0.6875 (ttp80) REVERT: R 343 LYS cc_start: 0.7880 (tttt) cc_final: 0.7658 (tttm) REVERT: R 362 ARG cc_start: 0.7746 (mmm160) cc_final: 0.7523 (mmm-85) REVERT: A 318 TYR cc_start: 0.8134 (t80) cc_final: 0.7755 (t80) REVERT: B 59 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.8236 (m-80) outliers start: 34 outliers final: 28 residues processed: 138 average time/residue: 0.2539 time to fit residues: 46.7681 Evaluate side-chains 136 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 4 THR 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 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 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 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.7980 chunk 56 optimal weight: 0.0270 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 6 optimal weight: 40.0000 chunk 88 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 99 optimal weight: 0.1980 chunk 15 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 overall best weight: 1.0042 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.163114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.124550 restraints weight = 10138.266| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.42 r_work: 0.3156 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9222 Z= 0.131 Angle : 0.483 6.098 12507 Z= 0.255 Chirality : 0.040 0.146 1384 Planarity : 0.004 0.049 1598 Dihedral : 3.853 16.389 1241 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.64 % Allowed : 19.33 % 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: 0.89 (0.25), residues: 1124 helix: 2.04 (0.25), residues: 429 sheet: -0.18 (0.31), residues: 250 loop : -0.31 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 PHE 0.014 0.001 PHE B 151 TYR 0.009 0.001 TYR N 60 ARG 0.005 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 425) hydrogen bonds : angle 4.17421 ( 1230) SS BOND : bond 0.00331 ( 7) SS BOND : angle 1.17935 ( 14) covalent geometry : bond 0.00310 ( 9214) covalent geometry : angle 0.48169 (12493) Misc. bond : bond 0.00002 ( 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 148 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 1.015 Fit side-chains REVERT: R 187 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7039 (ttt) REVERT: R 240 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7532 (mt-10) REVERT: R 321 ARG cc_start: 0.7189 (ttp-170) cc_final: 0.6873 (ttp80) REVERT: R 371 ILE cc_start: 0.7503 (mm) cc_final: 0.7206 (mp) REVERT: A 318 TYR cc_start: 0.8166 (t80) cc_final: 0.7788 (t80) REVERT: B 59 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.8193 (m-80) REVERT: B 338 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8661 (mm) outliers start: 35 outliers final: 30 residues processed: 138 average time/residue: 0.2571 time to fit residues: 47.1062 Evaluate side-chains 143 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain R residue 132 THR Chi-restraints excluded: chain R residue 187 MET 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 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 65 THR 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 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 57 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 97 optimal weight: 0.0770 chunk 17 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.164809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.127057 restraints weight = 10168.220| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.38 r_work: 0.3190 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2719 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= 0.104 Angle : 0.457 6.054 12507 Z= 0.242 Chirality : 0.039 0.149 1384 Planarity : 0.003 0.048 1598 Dihedral : 3.713 16.114 1241 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.12 % Allowed : 20.69 % Favored : 76.20 % 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: 1.02 (0.25), residues: 1124 helix: 2.18 (0.25), residues: 429 sheet: -0.19 (0.31), residues: 252 loop : -0.23 (0.29), residues: 443 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 0.010 0.001 PHE B 151 TYR 0.010 0.001 TYR R 149 ARG 0.004 0.000 ARG R 213 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 425) hydrogen bonds : angle 4.04974 ( 1230) SS BOND : bond 0.00281 ( 7) SS BOND : angle 0.95582 ( 14) covalent geometry : bond 0.00237 ( 9214) covalent geometry : angle 0.45626 (12493) Misc. bond : bond 0.00003 ( 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 138 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: R 187 MET cc_start: 0.8227 (mmm) cc_final: 0.7010 (ttt) REVERT: R 240 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7523 (mt-10) REVERT: R 321 ARG cc_start: 0.7095 (ttp-170) cc_final: 0.6782 (ttp80) REVERT: A 318 TYR cc_start: 0.8054 (t80) cc_final: 0.7675 (t80) REVERT: B 59 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.8163 (m-80) outliers start: 30 outliers final: 25 residues processed: 128 average time/residue: 0.2569 time to fit residues: 43.7343 Evaluate side-chains 132 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 4 THR 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 349 VAL Chi-restraints excluded: chain R residue 378 SER 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 178 THR 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 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 57 SER 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: 0.6980 chunk 88 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 77 optimal weight: 0.0970 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 69 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.165279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.128384 restraints weight = 10083.642| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.60 r_work: 0.3176 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2734 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= 0.102 Angle : 0.457 6.022 12507 Z= 0.240 Chirality : 0.039 0.147 1384 Planarity : 0.003 0.047 1598 Dihedral : 3.646 15.912 1241 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.01 % Allowed : 20.79 % Favored : 76.20 % 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: 1.08 (0.25), residues: 1124 helix: 2.25 (0.25), residues: 429 sheet: -0.13 (0.31), residues: 252 loop : -0.22 (0.29), residues: 443 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 0.016 0.001 PHE R 359 TYR 0.010 0.001 TYR R 149 ARG 0.009 0.000 ARG R 213 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 425) hydrogen bonds : angle 3.99387 ( 1230) SS BOND : bond 0.00232 ( 7) SS BOND : angle 0.92361 ( 14) covalent geometry : bond 0.00234 ( 9214) covalent geometry : angle 0.45637 (12493) Misc. bond : bond 0.00002 ( 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 138 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: R 187 MET cc_start: 0.8230 (mmm) cc_final: 0.7019 (ttt) REVERT: R 240 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7578 (mt-10) REVERT: R 321 ARG cc_start: 0.7198 (ttp-170) cc_final: 0.6886 (ttp80) REVERT: A 318 TYR cc_start: 0.8138 (t80) cc_final: 0.7737 (t80) REVERT: B 59 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.8115 (m-80) outliers start: 29 outliers final: 27 residues processed: 128 average time/residue: 0.2521 time to fit residues: 42.8908 Evaluate side-chains 136 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 4 THR 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 349 VAL Chi-restraints excluded: chain R residue 378 SER Chi-restraints excluded: chain A residue 346 LEU 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 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 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 57 SER 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: 1.9990 chunk 85 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 66 optimal weight: 0.0870 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.163938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.128659 restraints weight = 10119.464| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.68 r_work: 0.3158 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9222 Z= 0.127 Angle : 0.482 6.053 12507 Z= 0.253 Chirality : 0.040 0.144 1384 Planarity : 0.003 0.047 1598 Dihedral : 3.754 16.177 1241 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.01 % Allowed : 20.69 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.04 (0.25), residues: 1124 helix: 2.21 (0.25), residues: 429 sheet: -0.16 (0.31), residues: 251 loop : -0.25 (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 0.018 0.001 PHE R 359 TYR 0.011 0.001 TYR N 60 ARG 0.008 0.000 ARG R 213 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 425) hydrogen bonds : angle 4.06680 ( 1230) SS BOND : bond 0.00293 ( 7) SS BOND : angle 1.07526 ( 14) covalent geometry : bond 0.00298 ( 9214) covalent geometry : angle 0.48058 (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 140 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: R 187 MET cc_start: 0.8291 (mmm) cc_final: 0.7011 (ttt) REVERT: R 240 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7567 (mt-10) REVERT: R 321 ARG cc_start: 0.7230 (ttp-170) cc_final: 0.6902 (ttp80) REVERT: A 318 TYR cc_start: 0.8149 (t80) cc_final: 0.7754 (t80) REVERT: B 59 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.8212 (m-80) REVERT: N 106 ASP cc_start: 0.8175 (p0) cc_final: 0.7764 (p0) outliers start: 29 outliers final: 27 residues processed: 130 average time/residue: 0.2569 time to fit residues: 44.5388 Evaluate side-chains 136 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 4 THR 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 349 VAL Chi-restraints excluded: chain R residue 378 SER 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 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 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 57 SER 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: 8.9990 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 81 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.164999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.127337 restraints weight = 10129.815| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.38 r_work: 0.3193 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9222 Z= 0.107 Angle : 0.463 6.033 12507 Z= 0.243 Chirality : 0.039 0.145 1384 Planarity : 0.003 0.046 1598 Dihedral : 3.666 16.021 1241 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.91 % Allowed : 20.69 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.25), residues: 1124 helix: 2.30 (0.25), residues: 429 sheet: -0.13 (0.31), residues: 251 loop : -0.24 (0.29), residues: 444 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 0.019 0.001 PHE R 359 TYR 0.010 0.001 TYR R 149 ARG 0.008 0.000 ARG R 213 Details of bonding type rmsd hydrogen bonds : bond 0.03318 ( 425) hydrogen bonds : angle 3.99029 ( 1230) SS BOND : bond 0.00234 ( 7) SS BOND : angle 0.92585 ( 14) covalent geometry : bond 0.00247 ( 9214) covalent geometry : angle 0.46231 (12493) Misc. bond : bond 0.00001 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5506.67 seconds wall clock time: 95 minutes 59.10 seconds (5759.10 seconds total)