Starting phenix.real_space_refine on Thu Jul 2 18:45:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l1v_23119/07_2026/7l1v_23119.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l1v_23119/07_2026/7l1v_23119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7l1v_23119/07_2026/7l1v_23119.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l1v_23119/07_2026/7l1v_23119.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l1v_23119/07_2026/7l1v_23119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l1v_23119/07_2026/7l1v_23119.map" model { file = "/net/cci-nas-00/data/ceres_data/7l1v_23119/07_2026/7l1v_23119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l1v_23119/07_2026/7l1v_23119.cif" } resolution = 3.0 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= 0.030 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 69 5.16 5 C 6145 2.51 5 N 1649 2.21 5 O 1743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9606 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1802 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2549 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 429 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1724 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "R" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2251 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "S" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 806 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 3, 'TRANS': 107} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "R" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'XGD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.94, per 1000 atoms: 0.20 Number of scatterers: 9606 At special positions: 0 Unit cell: (107.52, 107.52, 152.88, 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 69 16.00 O 1743 8.00 N 1649 7.00 C 6145 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 210 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 95 " 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=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 306.5 milliseconds 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2344 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 16 sheets defined 33.3% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 4.247A pdb=" N ARG A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.829A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.688A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.625A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.697A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 4.128A 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 25 removed outlier: 3.693A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 6 through 24 removed outlier: 3.623A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 43 removed outlier: 3.508A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 48 removed outlier: 3.630A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'R' and resid 56 through 82 removed outlier: 3.720A pdb=" N VAL R 66 " --> pdb=" O ILE R 62 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA R 68 " --> pdb=" O VAL R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 86 removed outlier: 3.503A pdb=" N ARG R 86 " --> pdb=" O HIS R 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 83 through 86' Processing helix chain 'R' and resid 90 through 107 Processing helix chain 'R' and resid 107 through 118 Processing helix chain 'R' and resid 122 through 157 removed outlier: 3.939A pdb=" N LEU R 126 " --> pdb=" O PHE R 122 " (cutoff:3.500A) Proline residue: R 131 - end of helix Processing helix chain 'R' and resid 165 through 184 Processing helix chain 'R' and resid 185 through 190 Processing helix chain 'R' and resid 218 through 232 Processing helix chain 'R' and resid 232 through 250 Processing helix chain 'R' and resid 293 through 317 removed outlier: 4.048A pdb=" N LYS R 301 " --> pdb=" O ARG R 297 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR R 302 " --> pdb=" O ALA R 298 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA R 303 " --> pdb=" O ARG R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 329 removed outlier: 3.591A pdb=" N SER R 321 " --> pdb=" O TYR R 317 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 341 through 365 removed outlier: 3.709A pdb=" N TRP R 351 " --> pdb=" O THR R 347 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU R 352 " --> pdb=" O PHE R 348 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL R 353 " --> pdb=" O SER R 349 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 368 through 376 Processing helix chain 'S' and resid 86 through 90 removed outlier: 4.311A pdb=" N THR S 90 " --> pdb=" O PRO S 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 213 removed outlier: 6.214A pdb=" N LEU A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N PHE A 222 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 4.039A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.591A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.904A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.631A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.996A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.616A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.445A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.831A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.871A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 155 through 160 removed outlier: 3.576A pdb=" N PHE H 212 " --> pdb=" O CYS H 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 194 through 195 removed outlier: 5.575A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 191 through 196 removed outlier: 3.684A pdb=" N PHE R 207 " --> pdb=" O VAL R 196 " (cutoff:3.500A) removed outlier: 9.399A pdb=" N PHE S 102 " --> pdb=" O CYS R 210 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLU R 212 " --> pdb=" O PHE S 102 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY S 10 " --> pdb=" O THR S 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 191 through 196 removed outlier: 3.684A pdb=" N PHE R 207 " --> pdb=" O VAL R 196 " (cutoff:3.500A) removed outlier: 9.399A pdb=" N PHE S 102 " --> pdb=" O CYS R 210 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLU R 212 " --> pdb=" O PHE S 102 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ARG S 37 " --> pdb=" O TRP S 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N TRP S 46 " --> pdb=" O ARG S 37 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 3 through 7 466 hydrogen bonds defined for protein. 1323 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: 1.51 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2883 1.34 - 1.46: 2221 1.46 - 1.58: 4616 1.58 - 1.70: 1 1.70 - 1.82: 101 Bond restraints: 9822 Sorted by residual: bond pdb=" C LEU R 108 " pdb=" N PRO R 109 " ideal model delta sigma weight residual 1.336 1.388 -0.052 1.20e-02 6.94e+03 1.87e+01 bond pdb=" CG LEU A 46 " pdb=" CD1 LEU A 46 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.64e+00 bond pdb=" N XGD R 401 " pdb=" S XGD R 401 " ideal model delta sigma weight residual 1.672 1.631 0.041 2.00e-02 2.50e+03 4.10e+00 bond pdb=" CA THR R 204 " pdb=" C THR R 204 " ideal model delta sigma weight residual 1.522 1.548 -0.026 1.51e-02 4.39e+03 3.01e+00 bond pdb=" C ILE R 130 " pdb=" N PRO R 131 " ideal model delta sigma weight residual 1.335 1.356 -0.022 1.28e-02 6.10e+03 2.87e+00 ... (remaining 9817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 13190 3.10 - 6.20: 148 6.20 - 9.30: 18 9.30 - 12.39: 2 12.39 - 15.49: 2 Bond angle restraints: 13360 Sorted by residual: angle pdb=" C XGD R 401 " pdb=" N XGD R 401 " pdb=" S XGD R 401 " ideal model delta sigma weight residual 116.72 132.21 -15.49 3.00e+00 1.11e-01 2.67e+01 angle pdb=" C GLN H 183 " pdb=" N SER H 184 " pdb=" CA SER H 184 " ideal model delta sigma weight residual 120.97 131.35 -10.38 2.84e+00 1.24e-01 1.34e+01 angle pdb=" CA LEU B 146 " pdb=" CB LEU B 146 " pdb=" CG LEU B 146 " ideal model delta sigma weight residual 116.30 128.78 -12.48 3.50e+00 8.16e-02 1.27e+01 angle pdb=" C CYS R 107 " pdb=" N LEU R 108 " pdb=" CA LEU R 108 " ideal model delta sigma weight residual 120.26 124.91 -4.65 1.34e+00 5.57e-01 1.20e+01 angle pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta sigma weight residual 121.54 127.92 -6.38 1.91e+00 2.74e-01 1.12e+01 ... (remaining 13355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 5281 17.81 - 35.62: 392 35.62 - 53.43: 60 53.43 - 71.24: 9 71.24 - 89.05: 1 Dihedral angle restraints: 5743 sinusoidal: 2104 harmonic: 3639 Sorted by residual: dihedral pdb=" CA PHE R 121 " pdb=" C PHE R 121 " pdb=" N PHE R 122 " pdb=" CA PHE R 122 " ideal model delta harmonic sigma weight residual 180.00 -150.14 -29.86 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 47.16 45.84 1 1.00e+01 1.00e-02 2.91e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 157.22 22.78 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 5740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 934 0.044 - 0.088: 432 0.088 - 0.132: 122 0.132 - 0.176: 33 0.176 - 0.220: 8 Chirality restraints: 1529 Sorted by residual: chirality pdb=" CB THR H 116 " pdb=" CA THR H 116 " pdb=" OG1 THR H 116 " pdb=" CG2 THR H 116 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB VAL S 97 " pdb=" CA VAL S 97 " pdb=" CG1 VAL S 97 " pdb=" CG2 VAL S 97 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB VAL B 200 " pdb=" CA VAL B 200 " pdb=" CG1 VAL B 200 " pdb=" CG2 VAL B 200 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.98e-01 ... (remaining 1526 not shown) Planarity restraints: 1681 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N XGD R 401 " -0.178 2.00e-02 2.50e+03 1.19e-01 2.85e+02 pdb=" C XGD R 401 " 0.114 2.00e-02 2.50e+03 pdb=" C1 XGD R 401 " 0.196 2.00e-02 2.50e+03 pdb=" C14 XGD R 401 " -0.013 2.00e-02 2.50e+03 pdb=" C15 XGD R 401 " -0.051 2.00e-02 2.50e+03 pdb=" C16 XGD R 401 " -0.001 2.00e-02 2.50e+03 pdb=" C2 XGD R 401 " 0.080 2.00e-02 2.50e+03 pdb=" C3 XGD R 401 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" O XGD R 401 " 0.018 2.00e-02 2.50e+03 9.42e-02 1.11e+02 pdb=" C4 XGD R 401 " -0.115 2.00e-02 2.50e+03 pdb=" C5 XGD R 401 " 0.043 2.00e-02 2.50e+03 pdb=" C6 XGD R 401 " -0.090 2.00e-02 2.50e+03 pdb=" N1 XGD R 401 " 0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C19 XGD R 401 " 0.071 2.00e-02 2.50e+03 4.35e-02 3.79e+01 pdb=" C20 XGD R 401 " -0.043 2.00e-02 2.50e+03 pdb=" C21 XGD R 401 " -0.017 2.00e-02 2.50e+03 pdb=" C22 XGD R 401 " 0.017 2.00e-02 2.50e+03 pdb=" C23 XGD R 401 " 0.020 2.00e-02 2.50e+03 pdb=" C24 XGD R 401 " -0.026 2.00e-02 2.50e+03 pdb=" C25 XGD R 401 " 0.045 2.00e-02 2.50e+03 pdb=" C28 XGD R 401 " -0.067 2.00e-02 2.50e+03 ... (remaining 1678 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 3001 2.82 - 3.34: 7886 3.34 - 3.86: 15682 3.86 - 4.38: 18094 4.38 - 4.90: 32904 Nonbonded interactions: 77567 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.306 3.040 nonbonded pdb=" OG1 THR B 34 " pdb=" O LEU B 300 " model vdw 2.315 3.040 nonbonded pdb=" OE2 GLU A 15 " pdb=" OH TYR H 175 " model vdw 2.322 3.040 nonbonded pdb=" O SER H 52 " pdb=" NH1 ARG H 72 " model vdw 2.341 3.120 nonbonded pdb=" OG SER H 161 " pdb=" O LYS H 163 " model vdw 2.343 3.040 ... (remaining 77562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.960 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 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 : 0.007 0.071 9826 Z= 0.302 Angle : 0.914 15.494 13368 Z= 0.509 Chirality : 0.056 0.220 1529 Planarity : 0.008 0.119 1681 Dihedral : 12.646 89.055 3387 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.30 % Allowed : 6.36 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 are not related in a simple way. whole: -2.91 (0.20), residues: 1235 helix: -1.94 (0.20), residues: 383 sheet: -1.12 (0.26), residues: 341 loop : -2.37 (0.22), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 67 TYR 0.028 0.003 TYR B 59 PHE 0.021 0.003 PHE B 241 TRP 0.019 0.002 TRP B 82 HIS 0.006 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00715 / 0.30 ( 9822) covalent geometry : angle 0.91223 / 0.51 (13360) SS BOND : bond 0.00600 / 0.31 ( 4) SS BOND : angle 2.43023 / 1.25 ( 8) hydrogen bonds : bond 0.14358 / 9.86 ( 459) hydrogen bonds : angle 6.18383 / 4.42 ( 1323) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 166 time to evaluate : 0.231 Fit side-chains REVERT: H 3 GLN cc_start: 0.7596 (pt0) cc_final: 0.7297 (pt0) REVERT: H 69 THR cc_start: 0.7814 (t) cc_final: 0.7591 (m) REVERT: H 202 ARG cc_start: 0.8570 (ptt-90) cc_final: 0.8086 (ptt180) REVERT: R 151 ASP cc_start: 0.8165 (t70) cc_final: 0.7810 (t0) REVERT: R 213 ARG cc_start: 0.7833 (ttt-90) cc_final: 0.7393 (ttt180) REVERT: R 249 LYS cc_start: 0.7883 (tptm) cc_final: 0.7488 (tppt) REVERT: R 327 LYS cc_start: 0.8509 (tttt) cc_final: 0.8299 (tttm) REVERT: S 32 VAL cc_start: 0.8544 (t) cc_final: 0.8321 (p) outliers start: 3 outliers final: 2 residues processed: 169 average time/residue: 0.5885 time to fit residues: 105.1375 Evaluate side-chains 118 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain R residue 87 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 0.0470 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 385 GLN B 62 HIS B 88 ASN C 11 GLN H 13 GLN H 171 ASN H 183 GLN R 83 HIS S 38 GLN S 104 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.150307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.121846 restraints weight = 12498.056| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.05 r_work: 0.3421 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9826 Z= 0.120 Angle : 0.531 5.685 13368 Z= 0.286 Chirality : 0.042 0.137 1529 Planarity : 0.004 0.042 1681 Dihedral : 5.062 51.197 1371 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.72 % Allowed : 13.94 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 are not related in a simple way. whole: -1.30 (0.22), residues: 1235 helix: 0.34 (0.25), residues: 387 sheet: -0.73 (0.26), residues: 346 loop : -1.85 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 197 TYR 0.015 0.001 TYR S 103 PHE 0.013 0.001 PHE R 122 TRP 0.011 0.001 TRP B 99 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 9822) covalent geometry : angle 0.53077 / 0.29 (13360) SS BOND : bond 0.00859 / 0.45 ( 4) SS BOND : angle 1.20472 / 0.64 ( 8) hydrogen bonds : bond 0.04386 / 2.94 ( 459) hydrogen bonds : angle 4.62228 / 3.31 ( 1323) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.367 Fit side-chains REVERT: B 245 SER cc_start: 0.8385 (m) cc_final: 0.8140 (t) REVERT: C 36 ASP cc_start: 0.8127 (m-30) cc_final: 0.7861 (m-30) REVERT: C 37 LEU cc_start: 0.7852 (tt) cc_final: 0.7649 (mp) REVERT: H 3 GLN cc_start: 0.8157 (pt0) cc_final: 0.7947 (pt0) REVERT: H 202 ARG cc_start: 0.8714 (ptt-90) cc_final: 0.8200 (ptt180) REVERT: R 151 ASP cc_start: 0.8491 (t70) cc_final: 0.8105 (t0) REVERT: R 249 LYS cc_start: 0.8065 (tptm) cc_final: 0.7685 (tppt) REVERT: S 82 MET cc_start: 0.6836 (mtt) cc_final: 0.6565 (mpp) outliers start: 17 outliers final: 9 residues processed: 147 average time/residue: 0.5361 time to fit residues: 84.0498 Evaluate side-chains 126 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 92 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 43 optimal weight: 0.6980 chunk 105 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 119 optimal weight: 0.0470 chunk 76 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN H 13 GLN S 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.152106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.123788 restraints weight = 12612.684| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.07 r_work: 0.3428 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9826 Z= 0.101 Angle : 0.494 5.597 13368 Z= 0.264 Chirality : 0.041 0.159 1529 Planarity : 0.004 0.038 1681 Dihedral : 4.613 45.454 1371 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.12 % Allowed : 14.95 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 are not related in a simple way. whole: -0.48 (0.23), residues: 1235 helix: 1.34 (0.26), residues: 387 sheet: -0.40 (0.27), residues: 336 loop : -1.55 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 197 TYR 0.015 0.001 TYR S 103 PHE 0.010 0.001 PHE A 212 TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 9822) covalent geometry : angle 0.49354 / 0.26 (13360) SS BOND : bond 0.00676 / 0.36 ( 4) SS BOND : angle 1.10247 / 0.61 ( 8) hydrogen bonds : bond 0.03797 / 2.55 ( 459) hydrogen bonds : angle 4.29453 / 3.08 ( 1323) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.261 Fit side-chains REVERT: B 59 TYR cc_start: 0.8638 (m-80) cc_final: 0.7751 (m-80) REVERT: B 75 GLN cc_start: 0.8900 (mm-40) cc_final: 0.8549 (tp40) REVERT: C 36 ASP cc_start: 0.8079 (m-30) cc_final: 0.7740 (m-30) REVERT: C 37 LEU cc_start: 0.7704 (tt) cc_final: 0.7497 (mp) REVERT: C 42 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8113 (tt0) REVERT: R 151 ASP cc_start: 0.8481 (t70) cc_final: 0.8101 (t0) REVERT: R 249 LYS cc_start: 0.8062 (tptm) cc_final: 0.7645 (tppt) outliers start: 21 outliers final: 13 residues processed: 142 average time/residue: 0.4857 time to fit residues: 73.6195 Evaluate side-chains 128 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain S residue 92 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 ASN R 187 GLN S 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.151176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.122450 restraints weight = 12722.617| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.96 r_work: 0.3407 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9826 Z= 0.110 Angle : 0.494 5.927 13368 Z= 0.263 Chirality : 0.041 0.150 1529 Planarity : 0.004 0.042 1681 Dihedral : 4.494 43.685 1371 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.42 % Allowed : 16.77 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 are not related in a simple way. whole: -0.11 (0.24), residues: 1235 helix: 1.82 (0.27), residues: 387 sheet: -0.23 (0.28), residues: 316 loop : -1.43 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 197 TYR 0.015 0.001 TYR S 103 PHE 0.011 0.001 PHE R 227 TRP 0.010 0.001 TRP B 99 HIS 0.004 0.001 HIS R 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 9822) covalent geometry : angle 0.49339 / 0.26 (13360) SS BOND : bond 0.00581 / 0.31 ( 4) SS BOND : angle 1.18511 / 0.64 ( 8) hydrogen bonds : bond 0.03795 / 2.55 ( 459) hydrogen bonds : angle 4.20378 / 3.02 ( 1323) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.317 Fit side-chains REVERT: A 330 GLU cc_start: 0.7231 (mm-30) cc_final: 0.7006 (tp30) REVERT: B 59 TYR cc_start: 0.8633 (m-80) cc_final: 0.7836 (m-80) REVERT: B 75 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8359 (tp40) REVERT: B 217 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7716 (pmm) REVERT: B 234 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8993 (m-80) REVERT: C 36 ASP cc_start: 0.8120 (m-30) cc_final: 0.7807 (m-30) REVERT: C 37 LEU cc_start: 0.7759 (tt) cc_final: 0.7543 (mp) REVERT: C 42 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8208 (tt0) REVERT: H 202 ARG cc_start: 0.8623 (ptt-90) cc_final: 0.8370 (ptt-90) REVERT: R 151 ASP cc_start: 0.8516 (t70) cc_final: 0.8147 (t0) REVERT: R 249 LYS cc_start: 0.8068 (tptm) cc_final: 0.7648 (tppt) REVERT: R 305 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.7140 (mpp) REVERT: S 45 GLU cc_start: 0.8127 (pt0) cc_final: 0.7871 (pp20) outliers start: 24 outliers final: 16 residues processed: 131 average time/residue: 0.4818 time to fit residues: 67.5345 Evaluate side-chains 132 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 305 MET Chi-restraints excluded: chain S residue 92 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 60 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 ASN H 13 GLN R 83 HIS S 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.147102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.116596 restraints weight = 12617.677| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.12 r_work: 0.3301 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9826 Z= 0.222 Angle : 0.597 7.891 13368 Z= 0.315 Chirality : 0.045 0.147 1529 Planarity : 0.004 0.048 1681 Dihedral : 4.968 45.541 1371 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.03 % Allowed : 17.27 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 are not related in a simple way. whole: -0.19 (0.24), residues: 1235 helix: 1.68 (0.26), residues: 388 sheet: -0.42 (0.27), residues: 335 loop : -1.32 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 197 TYR 0.015 0.002 TYR A 339 PHE 0.015 0.002 PHE R 227 TRP 0.014 0.002 TRP H 47 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.22 ( 9822) covalent geometry : angle 0.59537 / 0.31 (13360) SS BOND : bond 0.00953 / 0.50 ( 4) SS BOND : angle 1.97270 / 1.06 ( 8) hydrogen bonds : bond 0.05075 / 3.39 ( 459) hydrogen bonds : angle 4.44379 / 3.18 ( 1323) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.351 Fit side-chains REVERT: B 59 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.8193 (m-80) REVERT: B 75 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8561 (tp40) REVERT: B 234 PHE cc_start: 0.9342 (OUTLIER) cc_final: 0.8889 (m-80) REVERT: C 37 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7892 (mp) REVERT: C 42 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8268 (tt0) REVERT: C 58 GLU cc_start: 0.8050 (mp0) cc_final: 0.7572 (pm20) REVERT: R 100 ASP cc_start: 0.8268 (m-30) cc_final: 0.7974 (m-30) REVERT: R 151 ASP cc_start: 0.8612 (t70) cc_final: 0.8327 (t0) REVERT: R 249 LYS cc_start: 0.8124 (tptm) cc_final: 0.7736 (tppt) REVERT: R 305 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7102 (tpp) REVERT: S 56 MET cc_start: 0.7441 (mtp) cc_final: 0.6899 (mmm) outliers start: 30 outliers final: 19 residues processed: 137 average time/residue: 0.5003 time to fit residues: 73.1999 Evaluate side-chains 140 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 222 MET Chi-restraints excluded: chain R residue 251 TRP Chi-restraints excluded: chain R residue 305 MET Chi-restraints excluded: chain S residue 92 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 5 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 ASN H 13 GLN R 83 HIS S 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.148094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.119141 restraints weight = 12554.634| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.94 r_work: 0.3377 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9826 Z= 0.129 Angle : 0.511 6.030 13368 Z= 0.272 Chirality : 0.042 0.148 1529 Planarity : 0.004 0.052 1681 Dihedral : 4.689 48.313 1371 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.93 % Allowed : 18.59 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 are not related in a simple way. whole: 0.09 (0.24), residues: 1235 helix: 1.96 (0.26), residues: 387 sheet: -0.11 (0.28), residues: 318 loop : -1.30 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 197 TYR 0.013 0.001 TYR S 103 PHE 0.012 0.001 PHE R 227 TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS R 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 9822) covalent geometry : angle 0.51045 / 0.27 (13360) SS BOND : bond 0.00654 / 0.34 ( 4) SS BOND : angle 1.29294 / 0.70 ( 8) hydrogen bonds : bond 0.04076 / 2.73 ( 459) hydrogen bonds : angle 4.25489 / 3.06 ( 1323) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.271 Fit side-chains REVERT: A 221 MET cc_start: 0.8916 (ttm) cc_final: 0.8636 (ttp) REVERT: A 330 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6945 (tp30) REVERT: B 59 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.8144 (m-80) REVERT: B 75 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8425 (tp40) REVERT: B 96 ARG cc_start: 0.8591 (tpp80) cc_final: 0.8230 (ttt-90) REVERT: B 217 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7785 (pmm) REVERT: B 234 PHE cc_start: 0.9314 (OUTLIER) cc_final: 0.8902 (m-80) REVERT: C 42 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8266 (tt0) REVERT: C 58 GLU cc_start: 0.8164 (mp0) cc_final: 0.7695 (pm20) REVERT: R 83 HIS cc_start: 0.8213 (m-70) cc_final: 0.7898 (t-90) REVERT: R 100 ASP cc_start: 0.8164 (m-30) cc_final: 0.7852 (m-30) REVERT: R 151 ASP cc_start: 0.8579 (t70) cc_final: 0.8230 (t0) REVERT: R 249 LYS cc_start: 0.8089 (tptm) cc_final: 0.7706 (tppt) REVERT: S 56 MET cc_start: 0.7467 (mtp) cc_final: 0.6958 (mmm) outliers start: 29 outliers final: 16 residues processed: 138 average time/residue: 0.4891 time to fit residues: 71.9882 Evaluate side-chains 135 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain S residue 92 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 43 optimal weight: 0.0770 chunk 76 optimal weight: 0.9980 chunk 45 optimal weight: 0.0870 chunk 108 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN S 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.150747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.122683 restraints weight = 12608.047| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.95 r_work: 0.3417 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9826 Z= 0.102 Angle : 0.493 9.451 13368 Z= 0.259 Chirality : 0.041 0.147 1529 Planarity : 0.004 0.053 1681 Dihedral : 4.468 45.661 1371 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.53 % Allowed : 19.49 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 are not related in a simple way. whole: 0.30 (0.24), residues: 1235 helix: 2.16 (0.26), residues: 387 sheet: 0.03 (0.28), residues: 316 loop : -1.19 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 197 TYR 0.011 0.001 TYR H 190 PHE 0.010 0.001 PHE R 227 TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 9822) covalent geometry : angle 0.49225 / 0.26 (13360) SS BOND : bond 0.00546 / 0.29 ( 4) SS BOND : angle 1.06166 / 0.57 ( 8) hydrogen bonds : bond 0.03646 / 2.45 ( 459) hydrogen bonds : angle 4.14640 / 2.98 ( 1323) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.303 Fit side-chains REVERT: A 221 MET cc_start: 0.8896 (ttm) cc_final: 0.8572 (ttp) REVERT: A 330 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6930 (tp30) REVERT: B 59 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.8078 (m-80) REVERT: B 75 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8357 (tp40) REVERT: B 217 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7756 (pmm) REVERT: C 42 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8283 (tt0) REVERT: C 58 GLU cc_start: 0.8200 (mp0) cc_final: 0.7751 (pm20) REVERT: R 83 HIS cc_start: 0.8186 (m-70) cc_final: 0.7949 (t-90) REVERT: R 151 ASP cc_start: 0.8563 (t70) cc_final: 0.8236 (t0) REVERT: R 249 LYS cc_start: 0.8092 (tptm) cc_final: 0.7676 (tppt) REVERT: R 305 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6943 (mpm) REVERT: S 45 GLU cc_start: 0.8118 (pt0) cc_final: 0.7819 (pp20) REVERT: S 56 MET cc_start: 0.7460 (mtp) cc_final: 0.6926 (mmm) outliers start: 25 outliers final: 15 residues processed: 136 average time/residue: 0.4654 time to fit residues: 67.7932 Evaluate side-chains 136 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 305 MET Chi-restraints excluded: chain S residue 92 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 38 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 392 ASN C 24 ASN S 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.148387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.120032 restraints weight = 12666.449| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.94 r_work: 0.3384 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9826 Z= 0.136 Angle : 0.521 8.971 13368 Z= 0.273 Chirality : 0.042 0.148 1529 Planarity : 0.004 0.060 1681 Dihedral : 4.560 44.060 1371 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.83 % Allowed : 19.29 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 are not related in a simple way. whole: 0.39 (0.24), residues: 1235 helix: 2.24 (0.26), residues: 388 sheet: 0.00 (0.28), residues: 318 loop : -1.10 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 197 TYR 0.011 0.001 TYR A 339 PHE 0.012 0.001 PHE R 227 TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 9822) covalent geometry : angle 0.52027 / 0.27 (13360) SS BOND : bond 0.00695 / 0.36 ( 4) SS BOND : angle 1.38800 / 0.74 ( 8) hydrogen bonds : bond 0.04032 / 2.71 ( 459) hydrogen bonds : angle 4.16858 / 2.99 ( 1323) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.329 Fit side-chains REVERT: A 221 MET cc_start: 0.8884 (ttm) cc_final: 0.8594 (ttp) REVERT: A 330 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6996 (tp30) REVERT: A 368 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7707 (t0) REVERT: B 59 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.8118 (m-80) REVERT: B 70 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8867 (pt) REVERT: B 75 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8368 (tp40) REVERT: B 96 ARG cc_start: 0.8571 (tpp80) cc_final: 0.8195 (ttt-90) REVERT: B 217 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7707 (pmm) REVERT: C 36 ASP cc_start: 0.8047 (m-30) cc_final: 0.7835 (m-30) REVERT: C 58 GLU cc_start: 0.8216 (mp0) cc_final: 0.7766 (pm20) REVERT: H 192 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8424 (tmm) REVERT: R 83 HIS cc_start: 0.8208 (m-70) cc_final: 0.7942 (t-90) REVERT: R 151 ASP cc_start: 0.8577 (t70) cc_final: 0.8229 (t0) REVERT: R 249 LYS cc_start: 0.8096 (tptm) cc_final: 0.7701 (tppt) REVERT: R 305 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.7021 (mpm) REVERT: S 45 GLU cc_start: 0.8155 (pt0) cc_final: 0.7785 (pp20) REVERT: S 56 MET cc_start: 0.7475 (mtp) cc_final: 0.6942 (mmm) outliers start: 28 outliers final: 20 residues processed: 125 average time/residue: 0.5045 time to fit residues: 67.3640 Evaluate side-chains 135 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 33 ILE 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 161 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 305 MET Chi-restraints excluded: chain S residue 92 VAL Chi-restraints excluded: chain S residue 103 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 91 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.151325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.120668 restraints weight = 12623.371| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.12 r_work: 0.3362 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9826 Z= 0.120 Angle : 0.511 8.704 13368 Z= 0.268 Chirality : 0.042 0.147 1529 Planarity : 0.004 0.063 1681 Dihedral : 4.529 44.861 1371 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.63 % Allowed : 19.80 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 are not related in a simple way. whole: 0.44 (0.24), residues: 1235 helix: 2.30 (0.26), residues: 389 sheet: 0.05 (0.28), residues: 312 loop : -1.11 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 197 TYR 0.011 0.001 TYR A 339 PHE 0.011 0.001 PHE R 227 TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS R 224 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 9822) covalent geometry : angle 0.51005 / 0.27 (13360) SS BOND : bond 0.00638 / 0.33 ( 4) SS BOND : angle 1.27060 / 0.68 ( 8) hydrogen bonds : bond 0.03888 / 2.61 ( 459) hydrogen bonds : angle 4.15329 / 2.98 ( 1323) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.221 Fit side-chains REVERT: A 221 MET cc_start: 0.8912 (ttm) cc_final: 0.8603 (ttp) REVERT: A 330 GLU cc_start: 0.7250 (mm-30) cc_final: 0.7018 (tp30) REVERT: B 59 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.8113 (m-80) REVERT: B 75 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8362 (tp40) REVERT: B 96 ARG cc_start: 0.8629 (tpp80) cc_final: 0.8239 (ttt-90) REVERT: B 217 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7754 (pmm) REVERT: C 58 GLU cc_start: 0.8203 (mp0) cc_final: 0.7777 (pm20) REVERT: H 192 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8450 (tmm) REVERT: R 83 HIS cc_start: 0.8209 (m-70) cc_final: 0.7959 (t-90) REVERT: R 151 ASP cc_start: 0.8594 (t70) cc_final: 0.8236 (t0) REVERT: R 249 LYS cc_start: 0.8099 (tptm) cc_final: 0.7693 (tppt) REVERT: R 305 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.7013 (mpm) REVERT: S 45 GLU cc_start: 0.8164 (pt0) cc_final: 0.7791 (pp20) REVERT: S 56 MET cc_start: 0.7493 (mtp) cc_final: 0.6951 (mmm) outliers start: 26 outliers final: 20 residues processed: 128 average time/residue: 0.4986 time to fit residues: 68.1794 Evaluate side-chains 137 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 305 MET Chi-restraints excluded: chain S residue 92 VAL Chi-restraints excluded: chain S residue 103 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN A 392 ASN S 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.144556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.115128 restraints weight = 12591.694| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.03 r_work: 0.3332 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9826 Z= 0.181 Angle : 0.558 8.876 13368 Z= 0.293 Chirality : 0.044 0.148 1529 Planarity : 0.004 0.065 1681 Dihedral : 4.725 45.294 1371 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.93 % Allowed : 19.90 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 are not related in a simple way. whole: 0.29 (0.24), residues: 1235 helix: 2.14 (0.26), residues: 390 sheet: -0.16 (0.28), residues: 320 loop : -1.08 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 197 TYR 0.013 0.001 TYR A 339 PHE 0.013 0.002 PHE R 227 TRP 0.012 0.001 TRP H 47 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.18 ( 9822) covalent geometry : angle 0.55687 / 0.29 (13360) SS BOND : bond 0.00808 / 0.42 ( 4) SS BOND : angle 1.66979 / 0.89 ( 8) hydrogen bonds : bond 0.04435 / 2.97 ( 459) hydrogen bonds : angle 4.25733 / 3.06 ( 1323) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.215 Fit side-chains REVERT: A 221 MET cc_start: 0.8926 (ttm) cc_final: 0.8571 (ttp) REVERT: A 330 GLU cc_start: 0.7271 (mm-30) cc_final: 0.7022 (tp30) REVERT: B 59 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.8133 (m-80) REVERT: B 70 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8891 (pt) REVERT: B 75 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8393 (tp40) REVERT: B 96 ARG cc_start: 0.8607 (tpp80) cc_final: 0.8219 (ttt-90) REVERT: B 217 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7751 (pmm) REVERT: C 58 GLU cc_start: 0.8232 (mp0) cc_final: 0.7788 (pm20) REVERT: R 83 HIS cc_start: 0.8206 (m-70) cc_final: 0.7921 (t-90) REVERT: R 100 ASP cc_start: 0.8198 (m-30) cc_final: 0.7808 (m-30) REVERT: R 151 ASP cc_start: 0.8626 (t70) cc_final: 0.8265 (t0) REVERT: R 249 LYS cc_start: 0.8105 (tptm) cc_final: 0.7709 (tppt) REVERT: R 305 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.7042 (mpm) REVERT: S 56 MET cc_start: 0.7472 (mtp) cc_final: 0.6968 (mmm) outliers start: 29 outliers final: 21 residues processed: 128 average time/residue: 0.4950 time to fit residues: 67.7510 Evaluate side-chains 135 residues out of total 1073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 33 ILE 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 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 238 THR Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 305 MET Chi-restraints excluded: chain S residue 92 VAL Chi-restraints excluded: chain S residue 103 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 79 optimal weight: 0.0570 chunk 14 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 101 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.149985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.121099 restraints weight = 12533.472| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.94 r_work: 0.3402 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9826 Z= 0.110 Angle : 0.500 8.368 13368 Z= 0.263 Chirality : 0.041 0.147 1529 Planarity : 0.004 0.065 1681 Dihedral : 4.524 46.173 1371 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.63 % Allowed : 20.30 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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 are not related in a simple way. whole: 0.50 (0.24), residues: 1235 helix: 2.34 (0.26), residues: 389 sheet: 0.05 (0.28), residues: 310 loop : -1.03 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 197 TYR 0.012 0.001 TYR S 103 PHE 0.011 0.001 PHE R 227 TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 9822) covalent geometry : angle 0.49965 / 0.26 (13360) SS BOND : bond 0.00577 / 0.30 ( 4) SS BOND : angle 1.08177 / 0.58 ( 8) hydrogen bonds : bond 0.03710 / 2.49 ( 459) hydrogen bonds : angle 4.13037 / 2.97 ( 1323) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2953.80 seconds wall clock time: 51 minutes 0.40 seconds (3060.40 seconds total)