Starting phenix.real_space_refine on Wed Sep 17 13:36:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9blb_44652/09_2025/9blb_44652.cif Found real_map, /net/cci-nas-00/data/ceres_data/9blb_44652/09_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_44652/09_2025/9blb_44652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9blb_44652/09_2025/9blb_44652.map" model { file = "/net/cci-nas-00/data/ceres_data/9blb_44652/09_2025/9blb_44652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9blb_44652/09_2025/9blb_44652.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ARG:plan': 3, 'ASP:plan': 5, 'TYR:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2, 'GLU:plan': 2} 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: 2.31, per 1000 atoms: 0.26 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: 0.92 Conformation dependent library (CDL) restraints added in 353.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.30 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: 1.42 Time building geometry restraints manager: 1.14 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.960 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.150 ------------------------------------------------------------------------------- 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 : 5.29 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (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 ARG 0.008 0.000 ARG B 49 TYR 0.013 0.001 TYR R 374 PHE 0.007 0.001 PHE B 292 TRP 0.014 0.001 TRP A 281 HIS 0.002 0.000 HIS R 377 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9214) covalent geometry : angle 0.47449 (12493) SS BOND : bond 0.00135 ( 7) SS BOND : angle 0.91183 ( 14) hydrogen bonds : bond 0.21372 ( 425) hydrogen bonds : angle 6.57150 ( 1230) 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 : 0.388 Fit side-chains REVERT: R 376 MET cc_start: 0.6994 (tpp) cc_final: 0.6778 (tpt) outliers start: 3 outliers final: 2 residues processed: 136 average time/residue: 0.1283 time to fit residues: 23.0078 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 : 0.233 ------------------------------------------------------------------------------- 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 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.2980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.171072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.139573 restraints weight = 10002.626| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.35 r_work: 0.3273 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1299 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= 0.124 Angle : 0.482 6.064 12507 Z= 0.257 Chirality : 0.040 0.156 1384 Planarity : 0.004 0.073 1598 Dihedral : 3.517 36.304 1244 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.70 % Allowed : 17.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.25), residues: 1124 helix: 2.52 (0.25), residues: 425 sheet: 0.42 (0.34), residues: 227 loop : -0.18 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 49 TYR 0.010 0.001 TYR N 60 PHE 0.012 0.001 PHE B 151 TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9214) covalent geometry : angle 0.48112 (12493) SS BOND : bond 0.00312 ( 7) SS BOND : angle 0.80677 ( 14) hydrogen bonds : bond 0.04315 ( 425) hydrogen bonds : angle 4.59853 ( 1230) Misc. bond : bond 0.00004 ( 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: 26 poor density : 132 time to evaluate : 0.368 Fit side-chains REVERT: R 374 TYR cc_start: 0.8256 (m-80) cc_final: 0.7966 (m-80) REVERT: A 370 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7430 (tp30) REVERT: A 390 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7747 (mp10) REVERT: B 59 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.8053 (m-80) REVERT: N 89 GLU cc_start: 0.6565 (pp20) cc_final: 0.6364 (tp30) outliers start: 26 outliers final: 14 residues processed: 147 average time/residue: 0.1245 time to fit residues: 24.1967 Evaluate side-chains 141 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 3 ASN 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 372 ILE 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 35 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN B 340 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 = 0.168534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.130840 restraints weight = 9993.959| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.37 r_work: 0.3267 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9222 Z= 0.117 Angle : 0.458 5.948 12507 Z= 0.244 Chirality : 0.040 0.148 1384 Planarity : 0.004 0.062 1598 Dihedral : 3.441 12.360 1241 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.22 % Allowed : 16.94 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.25), residues: 1124 helix: 2.54 (0.25), residues: 425 sheet: 0.17 (0.31), residues: 250 loop : -0.18 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 49 TYR 0.013 0.001 TYR R 191 PHE 0.012 0.001 PHE N 108 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9214) covalent geometry : angle 0.45749 (12493) SS BOND : bond 0.00353 ( 7) SS BOND : angle 0.77553 ( 14) hydrogen bonds : bond 0.03850 ( 425) hydrogen bonds : angle 4.31261 ( 1230) Misc. bond : bond 0.00009 ( 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: 31 poor density : 130 time to evaluate : 0.347 Fit side-chains REVERT: R 187 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7452 (tmm) REVERT: A 318 TYR cc_start: 0.7952 (t80) cc_final: 0.7467 (t80) REVERT: A 370 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7432 (tp30) REVERT: B 59 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.8161 (m-80) REVERT: B 171 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7019 (mm) REVERT: B 325 MET cc_start: 0.7732 (tpp) cc_final: 0.7497 (mmt) REVERT: N 89 GLU cc_start: 0.6597 (pp20) cc_final: 0.6272 (tp30) outliers start: 31 outliers final: 17 residues processed: 146 average time/residue: 0.1326 time to fit residues: 25.2366 Evaluate side-chains 141 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 286 SER 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 143 THR 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 88 optimal weight: 3.9990 chunk 26 optimal weight: 0.0470 chunk 15 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 4 optimal weight: 40.0000 overall best weight: 2.2084 ------------------------------------------------------------------------------- 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 N 31 ASN N 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.160266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.128291 restraints weight = 10199.424| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.33 r_work: 0.3133 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9222 Z= 0.239 Angle : 0.616 9.338 12507 Z= 0.322 Chirality : 0.045 0.146 1384 Planarity : 0.005 0.060 1598 Dihedral : 4.217 17.239 1241 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.78 % Allowed : 17.15 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.25), residues: 1124 helix: 1.87 (0.25), residues: 426 sheet: -0.12 (0.31), residues: 255 loop : -0.35 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 283 TYR 0.014 0.002 TYR N 60 PHE 0.026 0.002 PHE N 108 TRP 0.019 0.002 TRP N 47 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00578 ( 9214) covalent geometry : angle 0.61433 (12493) SS BOND : bond 0.00762 ( 7) SS BOND : angle 1.55695 ( 14) hydrogen bonds : bond 0.04879 ( 425) hydrogen bonds : angle 4.57575 ( 1230) Misc. bond : bond 0.00005 ( 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 176 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 130 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: R 133 MET cc_start: 0.6897 (tpt) cc_final: 0.6579 (tpp) REVERT: R 187 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7475 (ttt) REVERT: R 240 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8022 (mt-10) REVERT: R 338 TYR cc_start: 0.6934 (m-80) cc_final: 0.6733 (m-80) REVERT: R 343 LYS cc_start: 0.8021 (tttt) cc_final: 0.7800 (tttm) REVERT: R 371 ILE cc_start: 0.7497 (mm) cc_final: 0.7235 (mp) REVERT: A 292 ASN cc_start: 0.9019 (t0) cc_final: 0.8675 (m-40) REVERT: A 318 TYR cc_start: 0.8200 (t80) cc_final: 0.7871 (t80) REVERT: B 59 TYR cc_start: 0.8642 (OUTLIER) cc_final: 0.8360 (m-80) REVERT: B 186 ASP cc_start: 0.7984 (OUTLIER) cc_final: 0.7771 (m-30) outliers start: 46 outliers final: 29 residues processed: 161 average time/residue: 0.1253 time to fit residues: 26.4951 Evaluate side-chains 153 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 R residue 378 SER Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 286 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 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 186 ASP 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 Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 72 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 99 optimal weight: 0.3980 chunk 93 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 208 ASN N 31 ASN N 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.164025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.127872 restraints weight = 10119.005| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.53 r_work: 0.3158 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9222 Z= 0.119 Angle : 0.478 6.107 12507 Z= 0.255 Chirality : 0.040 0.152 1384 Planarity : 0.004 0.054 1598 Dihedral : 3.853 15.931 1241 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.18 % Allowed : 19.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.25), residues: 1124 helix: 2.10 (0.25), residues: 425 sheet: -0.14 (0.31), residues: 246 loop : -0.34 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 105 TYR 0.011 0.001 TYR R 149 PHE 0.015 0.001 PHE R 359 TRP 0.017 0.002 TRP R 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9214) covalent geometry : angle 0.47585 (12493) SS BOND : bond 0.00551 ( 7) SS BOND : angle 1.52860 ( 14) hydrogen bonds : bond 0.03753 ( 425) hydrogen bonds : angle 4.24394 ( 1230) 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 135 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.335 Fit side-chains REVERT: R 187 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7272 (ttt) REVERT: R 240 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7745 (mt-10) REVERT: R 343 LYS cc_start: 0.7878 (tttt) cc_final: 0.7670 (tttm) REVERT: R 371 ILE cc_start: 0.7461 (mm) cc_final: 0.7141 (mp) REVERT: A 318 TYR cc_start: 0.8082 (t80) cc_final: 0.7712 (t80) REVERT: B 59 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.8223 (m-80) outliers start: 21 outliers final: 13 residues processed: 127 average time/residue: 0.1417 time to fit residues: 23.0912 Evaluate side-chains 120 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 339 LEU 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 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 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 6 optimal weight: 20.0000 chunk 32 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 99 optimal weight: 0.0070 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 43 optimal weight: 0.0970 chunk 96 optimal weight: 0.3980 chunk 44 optimal weight: 0.8980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 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 = 0.3746 r_free = 0.3746 target = 0.166386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.135480 restraints weight = 10094.501| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.37 r_work: 0.3214 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2469 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= 0.095 Angle : 0.446 6.025 12507 Z= 0.236 Chirality : 0.039 0.151 1384 Planarity : 0.003 0.050 1598 Dihedral : 3.615 15.399 1241 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.29 % Allowed : 20.58 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.25), residues: 1124 helix: 2.24 (0.25), residues: 429 sheet: -0.07 (0.31), residues: 247 loop : -0.22 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 362 TYR 0.010 0.001 TYR R 263 PHE 0.018 0.001 PHE R 359 TRP 0.017 0.001 TRP B 82 HIS 0.002 0.000 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 9214) covalent geometry : angle 0.44452 (12493) SS BOND : bond 0.00275 ( 7) SS BOND : angle 1.02546 ( 14) hydrogen bonds : bond 0.03268 ( 425) hydrogen bonds : angle 4.02397 ( 1230) Misc. bond : bond 0.00002 ( 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 136 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: R 48 MET cc_start: 0.6599 (tpt) cc_final: 0.6317 (tpt) REVERT: R 187 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7252 (ttt) REVERT: R 240 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7626 (mt-10) REVERT: R 371 ILE cc_start: 0.7351 (mm) cc_final: 0.7030 (mp) REVERT: A 318 TYR cc_start: 0.8082 (t80) cc_final: 0.7653 (t80) REVERT: B 59 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.8118 (m-80) REVERT: B 197 ARG cc_start: 0.7780 (mmp80) cc_final: 0.7534 (mmp80) outliers start: 22 outliers final: 12 residues processed: 127 average time/residue: 0.1383 time to fit residues: 22.7978 Evaluate side-chains 122 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 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 178 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 0.2980 chunk 70 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 99 optimal weight: 0.0980 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 60 optimal weight: 0.1980 chunk 6 optimal weight: 9.9990 chunk 79 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.167326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.136804 restraints weight = 10183.813| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.39 r_work: 0.3220 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2501 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= 0.091 Angle : 0.438 5.997 12507 Z= 0.231 Chirality : 0.039 0.148 1384 Planarity : 0.003 0.048 1598 Dihedral : 3.538 14.887 1241 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.39 % Allowed : 20.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.25), residues: 1124 helix: 2.37 (0.25), residues: 429 sheet: 0.02 (0.32), residues: 237 loop : -0.16 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 105 TYR 0.009 0.001 TYR R 263 PHE 0.018 0.001 PHE R 359 TRP 0.016 0.001 TRP B 82 HIS 0.002 0.000 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00199 ( 9214) covalent geometry : angle 0.43686 (12493) SS BOND : bond 0.00242 ( 7) SS BOND : angle 0.90580 ( 14) hydrogen bonds : bond 0.03167 ( 425) hydrogen bonds : angle 3.96646 ( 1230) 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 138 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.350 Fit side-chains REVERT: R 187 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7230 (ttt) REVERT: R 240 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7621 (mt-10) REVERT: R 343 LYS cc_start: 0.7923 (tttt) cc_final: 0.7712 (tttm) REVERT: A 318 TYR cc_start: 0.8047 (t80) cc_final: 0.7591 (t80) REVERT: B 59 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.8077 (m-80) REVERT: B 325 MET cc_start: 0.7851 (tpp) cc_final: 0.7612 (mmt) REVERT: N 31 ASN cc_start: 0.9070 (OUTLIER) cc_final: 0.8776 (p0) outliers start: 23 outliers final: 16 residues processed: 126 average time/residue: 0.1358 time to fit residues: 22.1713 Evaluate side-chains 132 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 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 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 N residue 31 ASN 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 43 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 5 optimal weight: 0.2980 chunk 95 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.165245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.130861 restraints weight = 10094.911| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.33 r_work: 0.3211 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9222 Z= 0.118 Angle : 0.467 6.022 12507 Z= 0.245 Chirality : 0.040 0.144 1384 Planarity : 0.003 0.048 1598 Dihedral : 3.634 15.059 1241 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.81 % Allowed : 20.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.25), residues: 1124 helix: 2.35 (0.25), residues: 429 sheet: -0.06 (0.31), residues: 252 loop : -0.13 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 105 TYR 0.010 0.001 TYR N 60 PHE 0.019 0.001 PHE R 359 TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9214) covalent geometry : angle 0.46637 (12493) SS BOND : bond 0.00276 ( 7) SS BOND : angle 1.03509 ( 14) hydrogen bonds : bond 0.03419 ( 425) hydrogen bonds : angle 4.02221 ( 1230) 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 136 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: R 133 MET cc_start: 0.6708 (tpt) cc_final: 0.6417 (tpp) REVERT: R 187 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7203 (ttt) REVERT: R 240 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7530 (mt-10) REVERT: A 318 TYR cc_start: 0.8100 (t80) cc_final: 0.7637 (t80) REVERT: B 59 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.8148 (m-80) REVERT: B 197 ARG cc_start: 0.7777 (mmp80) cc_final: 0.7557 (mmp80) REVERT: B 325 MET cc_start: 0.7839 (tpp) cc_final: 0.7604 (mmt) outliers start: 27 outliers final: 21 residues processed: 126 average time/residue: 0.1328 time to fit residues: 21.7203 Evaluate side-chains 130 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 339 LEU Chi-restraints excluded: chain R residue 349 VAL 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 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 321 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 91 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 40.0000 chunk 92 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.161933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.125668 restraints weight = 10094.763| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.67 r_work: 0.3129 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2868 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= 0.161 Angle : 0.525 6.862 12507 Z= 0.275 Chirality : 0.042 0.141 1384 Planarity : 0.004 0.047 1598 Dihedral : 3.954 16.609 1241 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.60 % Allowed : 20.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.25), residues: 1124 helix: 2.20 (0.25), residues: 425 sheet: -0.19 (0.31), residues: 252 loop : -0.23 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 105 TYR 0.012 0.001 TYR N 60 PHE 0.018 0.002 PHE R 359 TRP 0.014 0.002 TRP R 76 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9214) covalent geometry : angle 0.52377 (12493) SS BOND : bond 0.00412 ( 7) SS BOND : angle 1.30521 ( 14) hydrogen bonds : bond 0.03995 ( 425) hydrogen bonds : angle 4.23210 ( 1230) 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 142 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: R 187 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7187 (ttt) REVERT: R 217 VAL cc_start: 0.6934 (m) cc_final: 0.6669 (p) REVERT: R 240 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7629 (mt-10) REVERT: A 31 GLN cc_start: 0.8548 (tp-100) cc_final: 0.8326 (tp-100) REVERT: A 318 TYR cc_start: 0.8186 (t80) cc_final: 0.7771 (t80) REVERT: B 59 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.8258 (m-80) REVERT: B 197 ARG cc_start: 0.7836 (mmp80) cc_final: 0.7628 (mmp80) outliers start: 25 outliers final: 21 residues processed: 133 average time/residue: 0.1316 time to fit residues: 22.6815 Evaluate side-chains 134 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 187 MET Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 339 LEU Chi-restraints excluded: chain R residue 349 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 178 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 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 84 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 4 optimal weight: 30.0000 chunk 64 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.164490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.131582 restraints weight = 10078.971| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.40 r_work: 0.3180 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9222 Z= 0.114 Angle : 0.475 6.637 12507 Z= 0.250 Chirality : 0.040 0.145 1384 Planarity : 0.003 0.046 1598 Dihedral : 3.768 15.605 1241 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.60 % Allowed : 20.79 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.25), residues: 1124 helix: 2.25 (0.25), residues: 429 sheet: -0.20 (0.31), residues: 251 loop : -0.21 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 105 TYR 0.010 0.001 TYR R 149 PHE 0.018 0.001 PHE R 359 TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9214) covalent geometry : angle 0.47442 (12493) SS BOND : bond 0.00291 ( 7) SS BOND : angle 0.95270 ( 14) hydrogen bonds : bond 0.03477 ( 425) hydrogen bonds : angle 4.09675 ( 1230) Misc. bond : bond 0.00002 ( 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 132 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: R 187 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7214 (ttt) REVERT: R 240 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7543 (mt-10) REVERT: A 31 GLN cc_start: 0.8482 (tp-100) cc_final: 0.8262 (tp-100) REVERT: A 318 TYR cc_start: 0.8082 (t80) cc_final: 0.7697 (t80) REVERT: B 59 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.8180 (m-80) outliers start: 25 outliers final: 22 residues processed: 123 average time/residue: 0.1315 time to fit residues: 21.2227 Evaluate side-chains 130 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 339 LEU Chi-restraints excluded: chain R residue 349 VAL 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 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 321 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 13 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3709 r_free = 0.3709 target = 0.162993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.130153 restraints weight = 10064.394| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.39 r_work: 0.3167 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2878 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= 0.139 Angle : 0.499 6.830 12507 Z= 0.262 Chirality : 0.041 0.142 1384 Planarity : 0.004 0.046 1598 Dihedral : 3.836 15.965 1241 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.70 % Allowed : 20.58 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.25), residues: 1124 helix: 2.20 (0.25), residues: 425 sheet: -0.23 (0.31), residues: 251 loop : -0.31 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 105 TYR 0.010 0.001 TYR N 60 PHE 0.019 0.001 PHE R 359 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9214) covalent geometry : angle 0.49788 (12493) SS BOND : bond 0.00327 ( 7) SS BOND : angle 1.10855 ( 14) hydrogen bonds : bond 0.03682 ( 425) hydrogen bonds : angle 4.14148 ( 1230) Misc. bond : bond 0.00001 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2608.53 seconds wall clock time: 45 minutes 27.81 seconds (2727.81 seconds total)