Starting phenix.real_space_refine on Fri Sep 11 18:17:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kam_22775/09_2026/7kam_22775.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kam_22775/09_2026/7kam_22775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kam_22775/09_2026/7kam_22775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kam_22775/09_2026/7kam_22775.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kam_22775/09_2026/7kam_22775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kam_22775/09_2026/7kam_22775.map" } resolution = 3.8 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= 0.005 sd= 0.059 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 49 5.16 5 C 7107 2.51 5 N 1873 2.21 5 O 1887 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10916 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3386 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 8, 'HIS:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 70 Chain: "C" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 440 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 54} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 245 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 30} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3678 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 31, 'TRANS': 444} Chain breaks: 5 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 5, 'ARG:plan': 5, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 71 Chain: "E" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1359 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "F" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1454 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 15, 'TRANS': 178} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 37 Chain: "G" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 354 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 3, 'TRANS': 58} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 3, 'TRP:plan': 2, 'ARG:plan': 2, 'TYR:plan': 1, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 69 Time building chain proxies: 2.25, per 1000 atoms: 0.21 Number of scatterers: 10916 At special positions: 0 Unit cell: (107.16, 125.4, 139.08, 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 49 16.00 O 1887 8.00 N 1873 7.00 C 7107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.86 Conformation dependent library (CDL) restraints added in 398.2 milliseconds 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2694 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 6 sheets defined 68.2% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 28 through 48 removed outlier: 3.681A pdb=" N LEU A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A 43 " --> pdb=" O THR A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 99 Processing helix chain 'A' and resid 107 through 136 Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 148 through 173 removed outlier: 3.711A pdb=" N LEU A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 160 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLU A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.685A pdb=" N ILE A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 198 removed outlier: 3.879A pdb=" N ILE A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N CYS A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 224 removed outlier: 3.714A pdb=" N LEU A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.974A pdb=" N GLU A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 262 removed outlier: 3.732A pdb=" N LEU A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 312 Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 350 through 357 removed outlier: 4.080A pdb=" N ASP A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 383 removed outlier: 3.663A pdb=" N THR A 361 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 382 " --> pdb=" O THR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 removed outlier: 3.925A pdb=" N LYS A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 439 removed outlier: 4.457A pdb=" N GLU A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Proline residue: A 418 - end of helix removed outlier: 4.015A pdb=" N ALA A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 439 " --> pdb=" O SER A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 465 removed outlier: 3.671A pdb=" N ILE A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 26 Processing helix chain 'C' and resid 30 through 67 Proline residue: C 61 - end of helix Processing helix chain 'B' and resid 95 through 123 Processing helix chain 'D' and resid 14 through 28 removed outlier: 3.541A pdb=" N PHE D 18 " --> pdb=" O PHE D 14 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 35 removed outlier: 3.985A pdb=" N LEU D 34 " --> pdb=" O LEU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 68 removed outlier: 4.116A pdb=" N LEU D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 98 removed outlier: 4.570A pdb=" N ILE D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ALA D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 228 removed outlier: 4.672A pdb=" N LEU D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Proline residue: D 218 - end of helix Processing helix chain 'D' and resid 237 through 247 removed outlier: 3.827A pdb=" N ARG D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 262 removed outlier: 4.025A pdb=" N VAL D 258 " --> pdb=" O GLY D 254 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN D 259 " --> pdb=" O GLY D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 3.923A pdb=" N GLU D 269 " --> pdb=" O GLU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 276 removed outlier: 3.752A pdb=" N LYS D 275 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA D 276 " --> pdb=" O GLY D 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 272 through 276' Processing helix chain 'D' and resid 279 through 291 removed outlier: 3.763A pdb=" N ASP D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 4.070A pdb=" N VAL D 302 " --> pdb=" O LYS D 298 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE D 306 " --> pdb=" O VAL D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 324 Processing helix chain 'D' and resid 331 through 358 removed outlier: 4.296A pdb=" N GLU D 335 " --> pdb=" O VAL D 331 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER D 341 " --> pdb=" O TYR D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 376 removed outlier: 3.587A pdb=" N ARG D 368 " --> pdb=" O ILE D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 387 removed outlier: 3.694A pdb=" N LEU D 385 " --> pdb=" O SER D 382 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN D 386 " --> pdb=" O PRO D 383 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU D 387 " --> pdb=" O LEU D 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 382 through 387' Processing helix chain 'D' and resid 391 through 399 removed outlier: 3.516A pdb=" N GLU D 399 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 414 Processing helix chain 'D' and resid 418 through 424 Processing helix chain 'D' and resid 431 through 443 removed outlier: 3.988A pdb=" N SER D 437 " --> pdb=" O ASP D 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 37 Proline residue: E 9 - end of helix removed outlier: 3.648A pdb=" N LEU E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 60 Processing helix chain 'E' and resid 71 through 106 removed outlier: 4.503A pdb=" N GLN E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ARG E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY E 106 " --> pdb=" O LEU E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 138 removed outlier: 4.149A pdb=" N TRP E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 167 Processing helix chain 'E' and resid 168 through 180 Processing helix chain 'F' and resid 31 through 56 removed outlier: 3.858A pdb=" N ASP F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 89 removed outlier: 4.384A pdb=" N SER F 72 " --> pdb=" O ASN F 68 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY F 89 " --> pdb=" O ALA F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 107 removed outlier: 3.501A pdb=" N GLY F 107 " --> pdb=" O GLU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 134 removed outlier: 4.268A pdb=" N ALA F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 152 Processing helix chain 'F' and resid 156 through 171 Processing helix chain 'F' and resid 172 through 187 Processing helix chain 'F' and resid 192 through 203 Processing helix chain 'G' and resid 245 through 266 removed outlier: 3.711A pdb=" N LEU G 266 " --> pdb=" O PHE G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 270 Processing helix chain 'G' and resid 274 through 305 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 7.047A pdb=" N GLU A 19 " --> pdb=" O VAL B 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 211 removed outlier: 3.781A pdb=" N GLU A 210 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER D 187 " --> pdb=" O ASN A 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 280 through 281 Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.792A pdb=" N VAL A 325 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 452 through 457 removed outlier: 3.651A pdb=" N LYS D 452 " --> pdb=" O LYS D 474 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL D 472 " --> pdb=" O PHE D 454 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 558 through 560 removed outlier: 3.617A pdb=" N VAL D 560 " --> pdb=" O LEU D 550 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU D 550 " --> pdb=" O VAL D 560 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE D 549 " --> pdb=" O HIS D 604 " (cutoff:3.500A) 712 hydrogen bonds defined for protein. 2124 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: 1.67 Time building geometry restraints manager: 1.19 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: 3459 1.34 - 1.46: 1604 1.46 - 1.57: 6009 1.57 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 11157 Sorted by residual: bond pdb=" C GLY D 426 " pdb=" N PRO D 427 " ideal model delta sigma weight residual 1.332 1.351 -0.019 8.20e-03 1.49e+04 5.53e+00 bond pdb=" N GLY G 245 " pdb=" CA GLY G 245 " ideal model delta sigma weight residual 1.443 1.460 -0.017 1.37e-02 5.33e+03 1.54e+00 bond pdb=" N PRO G 246 " pdb=" CA PRO G 246 " ideal model delta sigma weight residual 1.471 1.458 0.013 1.29e-02 6.01e+03 1.08e+00 bond pdb=" CA ILE G 297 " pdb=" CB ILE G 297 " ideal model delta sigma weight residual 1.540 1.528 0.012 1.25e-02 6.40e+03 9.37e-01 bond pdb=" CA VAL G 278 " pdb=" CB VAL G 278 " ideal model delta sigma weight residual 1.540 1.527 0.012 1.29e-02 6.01e+03 9.12e-01 ... (remaining 11152 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 15070 2.58 - 5.17: 90 5.17 - 7.75: 13 7.75 - 10.33: 0 10.33 - 12.92: 1 Bond angle restraints: 15174 Sorted by residual: angle pdb=" N PRO G 246 " pdb=" CA PRO G 246 " pdb=" CB PRO G 246 " ideal model delta sigma weight residual 103.44 110.18 -6.74 1.12e+00 7.97e-01 3.62e+01 angle pdb=" N VAL D 596 " pdb=" CA VAL D 596 " pdb=" C VAL D 596 " ideal model delta sigma weight residual 113.71 109.41 4.30 9.50e-01 1.11e+00 2.05e+01 angle pdb=" N GLY D 426 " pdb=" CA GLY D 426 " pdb=" C GLY D 426 " ideal model delta sigma weight residual 112.34 119.30 -6.96 2.04e+00 2.40e-01 1.16e+01 angle pdb=" N PRO D 427 " pdb=" CA PRO D 427 " pdb=" C PRO D 427 " ideal model delta sigma weight residual 114.98 110.18 4.80 1.46e+00 4.69e-01 1.08e+01 angle pdb=" CA PRO D 427 " pdb=" C PRO D 427 " pdb=" O PRO D 427 " ideal model delta sigma weight residual 118.38 121.74 -3.36 1.13e+00 7.83e-01 8.83e+00 ... (remaining 15169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 6197 17.89 - 35.78: 391 35.78 - 53.67: 62 53.67 - 71.56: 6 71.56 - 89.45: 4 Dihedral angle restraints: 6660 sinusoidal: 2486 harmonic: 4174 Sorted by residual: dihedral pdb=" CA GLY D 426 " pdb=" C GLY D 426 " pdb=" N PRO D 427 " pdb=" CA PRO D 427 " ideal model delta harmonic sigma weight residual 180.00 158.25 21.75 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CB GLU D 396 " pdb=" CG GLU D 396 " pdb=" CD GLU D 396 " pdb=" OE1 GLU D 396 " ideal model delta sinusoidal sigma weight residual 0.00 89.45 -89.45 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" N PRO G 246 " pdb=" C PRO G 246 " pdb=" CA PRO G 246 " pdb=" CB PRO G 246 " ideal model delta harmonic sigma weight residual 115.10 122.75 -7.65 0 2.50e+00 1.60e-01 9.37e+00 ... (remaining 6657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1429 0.045 - 0.091: 294 0.091 - 0.136: 49 0.136 - 0.182: 1 0.182 - 0.227: 1 Chirality restraints: 1774 Sorted by residual: chirality pdb=" CA PRO G 246 " pdb=" N PRO G 246 " pdb=" C PRO G 246 " pdb=" CB PRO G 246 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE D 478 " pdb=" CA ILE D 478 " pdb=" CG1 ILE D 478 " pdb=" CG2 ILE D 478 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CB ILE D 473 " pdb=" CA ILE D 473 " pdb=" CG1 ILE D 473 " pdb=" CG2 ILE D 473 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 1771 not shown) Planarity restraints: 1903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 426 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.39e+00 pdb=" N PRO D 427 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO D 427 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 427 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 141 " 0.014 2.00e-02 2.50e+03 9.16e-03 2.10e+00 pdb=" CG TRP E 141 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP E 141 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP E 141 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 141 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 141 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP E 141 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 141 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 141 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 141 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 391 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO D 392 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO D 392 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 392 " 0.020 5.00e-02 4.00e+02 ... (remaining 1900 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 187 2.70 - 3.25: 11047 3.25 - 3.80: 16763 3.80 - 4.35: 19014 4.35 - 4.90: 32652 Nonbonded interactions: 79663 Sorted by model distance: nonbonded pdb=" OH TYR A 287 " pdb=" OG SER A 385 " model vdw 2.150 3.040 nonbonded pdb=" NE2 GLN D 371 " pdb=" O TYR D 610 " model vdw 2.261 3.120 nonbonded pdb=" NE2 GLN D 63 " pdb=" OE2 GLU D 334 " model vdw 2.275 3.120 nonbonded pdb=" NE2 GLN D 386 " pdb=" O MET D 611 " model vdw 2.286 3.120 nonbonded pdb=" O ARG D 420 " pdb=" OG1 THR D 424 " model vdw 2.308 3.040 ... (remaining 79658 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 group one per residue 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: 1.100 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: 0.030 Process input model: 10.660 Find NCS groups from input model: 0.060 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 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 0.035 11157 Z= 0.128 Angle : 0.543 12.917 15174 Z= 0.295 Chirality : 0.037 0.227 1774 Planarity : 0.004 0.058 1903 Dihedral : 11.788 89.454 3966 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.04 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % 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 are not related in a simple way. whole: -1.16 (0.22), residues: 1414 helix: 0.23 (0.16), residues: 907 sheet: -2.34 (0.51), residues: 81 loop : -2.54 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 238 TYR 0.011 0.001 TYR A 237 PHE 0.013 0.001 PHE A 263 TRP 0.024 0.001 TRP E 141 HIS 0.003 0.001 HIS B 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (11157) covalent geometry : angle 0.54292 / 0.30 (15174) hydrogen bonds : bond 0.10402 / 6.83 ( 712) hydrogen bonds : angle 4.50465 / 3.20 ( 2124) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 401 MET cc_start: 0.8268 (tpp) cc_final: 0.7980 (ttt) REVERT: C 18 ASP cc_start: 0.8178 (m-30) cc_final: 0.7944 (m-30) REVERT: B 102 LEU cc_start: 0.8528 (tp) cc_final: 0.8108 (tp) REVERT: D 270 MET cc_start: 0.7891 (tmm) cc_final: 0.7436 (tmm) REVERT: E 92 ILE cc_start: 0.9544 (mt) cc_final: 0.9278 (mm) REVERT: E 110 ASP cc_start: 0.6936 (t70) cc_final: 0.6482 (t70) REVERT: E 151 GLU cc_start: 0.8515 (mm-30) cc_final: 0.7836 (mm-30) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1113 time to fit residues: 26.9114 Evaluate side-chains 106 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS A 290 ASN D 61 GLN D 63 GLN D 470 GLN E 56 HIS E 95 GLN E 114 GLN E 166 GLN F 43 GLN F 49 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.067472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.053076 restraints weight = 56758.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.054450 restraints weight = 30557.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.055347 restraints weight = 20642.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.055868 restraints weight = 16104.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.056249 restraints weight = 13832.292| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11157 Z= 0.151 Angle : 0.602 13.501 15174 Z= 0.294 Chirality : 0.038 0.147 1774 Planarity : 0.004 0.051 1903 Dihedral : 3.333 19.734 1550 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.25 % Favored : 96.68 % Rotamer: Outliers : 1.01 % Allowed : 12.56 % Favored : 86.43 % 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 are not related in a simple way. whole: 0.16 (0.23), residues: 1414 helix: 1.32 (0.17), residues: 920 sheet: -2.22 (0.50), residues: 83 loop : -2.21 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 50 TYR 0.012 0.001 TYR A 237 PHE 0.027 0.001 PHE D 15 TRP 0.018 0.001 TRP A 65 HIS 0.002 0.001 HIS D 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (11157) covalent geometry : angle 0.60224 / 0.29 (15174) hydrogen bonds : bond 0.03933 / 2.59 ( 712) hydrogen bonds : angle 3.83120 / 2.72 ( 2124) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 MET cc_start: 0.8614 (tpp) cc_final: 0.8158 (ttt) REVERT: C 18 ASP cc_start: 0.8666 (m-30) cc_final: 0.8302 (m-30) REVERT: D 90 MET cc_start: 0.8896 (mmm) cc_final: 0.8555 (mmm) REVERT: E 92 ILE cc_start: 0.9497 (mt) cc_final: 0.9207 (mm) REVERT: E 151 GLU cc_start: 0.8719 (mm-30) cc_final: 0.7630 (mm-30) REVERT: F 43 GLN cc_start: 0.8647 (mt0) cc_final: 0.8416 (pm20) REVERT: F 137 MET cc_start: 0.7696 (mpp) cc_final: 0.7048 (mpp) REVERT: F 186 ILE cc_start: 0.9085 (tp) cc_final: 0.8809 (tt) outliers start: 11 outliers final: 8 residues processed: 128 average time/residue: 0.0879 time to fit residues: 17.4431 Evaluate side-chains 118 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 429 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 121 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 92 optimal weight: 0.0170 chunk 139 optimal weight: 0.4980 chunk 110 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 overall best weight: 2.2622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 604 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.067089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.053517 restraints weight = 56916.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.054558 restraints weight = 30294.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.055092 restraints weight = 20049.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.055341 restraints weight = 17995.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.055376 restraints weight = 15992.765| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11157 Z= 0.148 Angle : 0.575 13.354 15174 Z= 0.279 Chirality : 0.037 0.133 1774 Planarity : 0.004 0.049 1903 Dihedral : 3.281 15.232 1550 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.69 % Favored : 97.24 % Rotamer: Outliers : 1.19 % Allowed : 15.22 % Favored : 83.59 % 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 are not related in a simple way. whole: 0.71 (0.23), residues: 1414 helix: 1.77 (0.17), residues: 925 sheet: -2.09 (0.50), residues: 83 loop : -2.11 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 50 TYR 0.012 0.001 TYR A 237 PHE 0.026 0.001 PHE D 563 TRP 0.011 0.001 TRP E 141 HIS 0.003 0.001 HIS C 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (11157) covalent geometry : angle 0.57509 / 0.28 (15174) hydrogen bonds : bond 0.03788 / 2.52 ( 712) hydrogen bonds : angle 3.69283 / 2.62 ( 2124) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 MET cc_start: 0.9294 (mmp) cc_final: 0.8910 (mmt) REVERT: A 401 MET cc_start: 0.8631 (tpp) cc_final: 0.8157 (ttt) REVERT: C 18 ASP cc_start: 0.8696 (m-30) cc_final: 0.8321 (m-30) REVERT: D 90 MET cc_start: 0.8849 (mmm) cc_final: 0.8506 (mmm) REVERT: E 87 LYS cc_start: 0.9595 (ttmm) cc_final: 0.9297 (ttmm) REVERT: E 92 ILE cc_start: 0.9505 (mt) cc_final: 0.9202 (mm) REVERT: E 151 GLU cc_start: 0.8758 (mm-30) cc_final: 0.7610 (mm-30) REVERT: F 137 MET cc_start: 0.8168 (mpp) cc_final: 0.7467 (mpp) REVERT: F 186 ILE cc_start: 0.9200 (tp) cc_final: 0.8901 (tt) REVERT: G 266 LEU cc_start: 0.8400 (mp) cc_final: 0.8155 (mp) outliers start: 13 outliers final: 11 residues processed: 125 average time/residue: 0.0886 time to fit residues: 16.8707 Evaluate side-chains 120 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 114 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 131 optimal weight: 0.2980 chunk 59 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 ASN D 61 GLN D 371 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.067804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.053474 restraints weight = 56912.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.054826 restraints weight = 30336.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.055757 restraints weight = 20497.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.056207 restraints weight = 15927.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.056696 restraints weight = 13769.177| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11157 Z= 0.111 Angle : 0.563 13.608 15174 Z= 0.268 Chirality : 0.037 0.144 1774 Planarity : 0.004 0.052 1903 Dihedral : 3.188 14.966 1550 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.69 % Favored : 97.24 % Rotamer: Outliers : 1.56 % Allowed : 17.32 % Favored : 81.12 % 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 are not related in a simple way. whole: 1.03 (0.24), residues: 1414 helix: 1.99 (0.17), residues: 928 sheet: -1.94 (0.50), residues: 83 loop : -1.94 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 50 TYR 0.011 0.001 TYR A 237 PHE 0.022 0.001 PHE D 15 TRP 0.009 0.001 TRP F 138 HIS 0.002 0.000 HIS C 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (11157) covalent geometry : angle 0.56282 / 0.27 (15174) hydrogen bonds : bond 0.03570 / 2.37 ( 712) hydrogen bonds : angle 3.51173 / 2.50 ( 2124) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8427 (tt) REVERT: C 18 ASP cc_start: 0.8642 (m-30) cc_final: 0.8274 (m-30) REVERT: D 90 MET cc_start: 0.8817 (mmm) cc_final: 0.8454 (mmm) REVERT: E 92 ILE cc_start: 0.9496 (mt) cc_final: 0.9200 (mm) REVERT: E 151 GLU cc_start: 0.8705 (mm-30) cc_final: 0.7582 (mm-30) REVERT: F 137 MET cc_start: 0.8178 (mpp) cc_final: 0.7509 (mpp) REVERT: F 186 ILE cc_start: 0.9188 (tp) cc_final: 0.8896 (tt) outliers start: 17 outliers final: 10 residues processed: 135 average time/residue: 0.0765 time to fit residues: 16.4002 Evaluate side-chains 123 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 137 optimal weight: 9.9990 chunk 91 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 63.8759 > 50:) chunk 98 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 chunk 133 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.066785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.052362 restraints weight = 56840.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.053706 restraints weight = 30641.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.054494 restraints weight = 20802.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.055129 restraints weight = 16417.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.055418 restraints weight = 13954.392| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11157 Z= 0.161 Angle : 0.595 14.149 15174 Z= 0.285 Chirality : 0.038 0.152 1774 Planarity : 0.004 0.053 1903 Dihedral : 3.211 15.053 1550 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.18 % Favored : 96.75 % Rotamer: Outliers : 1.92 % Allowed : 18.79 % Favored : 79.29 % 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 are not related in a simple way. whole: 1.18 (0.24), residues: 1414 helix: 2.13 (0.17), residues: 927 sheet: -1.91 (0.50), residues: 83 loop : -1.93 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 50 TYR 0.012 0.001 TYR A 237 PHE 0.021 0.001 PHE D 15 TRP 0.009 0.001 TRP E 141 HIS 0.003 0.001 HIS C 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (11157) covalent geometry : angle 0.59515 / 0.29 (15174) hydrogen bonds : bond 0.03676 / 2.46 ( 712) hydrogen bonds : angle 3.60533 / 2.55 ( 2124) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8459 (tt) REVERT: A 345 MET cc_start: 0.9233 (mmp) cc_final: 0.8901 (mmp) REVERT: C 18 ASP cc_start: 0.8636 (m-30) cc_final: 0.8305 (m-30) REVERT: D 90 MET cc_start: 0.8836 (mmm) cc_final: 0.8494 (mmm) REVERT: D 206 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8761 (tp) REVERT: D 415 MET cc_start: 0.6826 (tmm) cc_final: 0.6477 (tmm) REVERT: E 87 LYS cc_start: 0.9597 (ttmm) cc_final: 0.9302 (ttmm) REVERT: E 92 ILE cc_start: 0.9509 (mt) cc_final: 0.9210 (mm) REVERT: E 121 LYS cc_start: 0.9174 (pttp) cc_final: 0.8728 (ptpp) REVERT: E 151 GLU cc_start: 0.8725 (mm-30) cc_final: 0.7607 (mm-30) REVERT: F 137 MET cc_start: 0.8140 (mpp) cc_final: 0.7519 (mpp) REVERT: F 182 GLN cc_start: 0.9012 (tp-100) cc_final: 0.8703 (tm-30) REVERT: F 186 ILE cc_start: 0.9193 (tp) cc_final: 0.8847 (tt) outliers start: 21 outliers final: 16 residues processed: 130 average time/residue: 0.0805 time to fit residues: 16.4960 Evaluate side-chains 129 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 ASN D 386 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.066737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.052684 restraints weight = 55975.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.054045 restraints weight = 29994.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.054900 restraints weight = 20563.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.055518 restraints weight = 16390.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.055846 restraints weight = 13996.266| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11157 Z= 0.206 Angle : 0.627 14.436 15174 Z= 0.302 Chirality : 0.039 0.177 1774 Planarity : 0.004 0.054 1903 Dihedral : 3.312 15.355 1550 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.54 % Favored : 96.39 % Rotamer: Outliers : 2.47 % Allowed : 19.16 % Favored : 78.37 % 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 are not related in a simple way. whole: 1.22 (0.24), residues: 1414 helix: 2.17 (0.17), residues: 932 sheet: -1.92 (0.50), residues: 83 loop : -1.97 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 50 TYR 0.013 0.001 TYR A 237 PHE 0.030 0.002 PHE D 563 TRP 0.010 0.001 TRP E 141 HIS 0.003 0.001 HIS C 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (11157) covalent geometry : angle 0.62675 / 0.30 (15174) hydrogen bonds : bond 0.03946 / 2.64 ( 712) hydrogen bonds : angle 3.74424 / 2.65 ( 2124) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 153 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8443 (tt) REVERT: A 345 MET cc_start: 0.9321 (mmp) cc_final: 0.8966 (mmp) REVERT: C 16 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8692 (tt) REVERT: C 18 ASP cc_start: 0.8770 (m-30) cc_final: 0.8430 (m-30) REVERT: D 90 MET cc_start: 0.8892 (mmm) cc_final: 0.8692 (mmt) REVERT: D 415 MET cc_start: 0.7230 (tmm) cc_final: 0.6929 (tmm) REVERT: E 87 LYS cc_start: 0.9654 (ttmm) cc_final: 0.9361 (ttmm) REVERT: E 92 ILE cc_start: 0.9447 (mt) cc_final: 0.9139 (mm) REVERT: E 121 LYS cc_start: 0.9183 (pttp) cc_final: 0.8870 (ptpp) REVERT: E 151 GLU cc_start: 0.8713 (mm-30) cc_final: 0.7535 (mm-30) REVERT: F 137 MET cc_start: 0.8233 (mpp) cc_final: 0.7622 (mpp) REVERT: F 182 GLN cc_start: 0.9160 (tp-100) cc_final: 0.8745 (tm-30) REVERT: F 186 ILE cc_start: 0.9194 (tp) cc_final: 0.8798 (tt) outliers start: 27 outliers final: 20 residues processed: 139 average time/residue: 0.0765 time to fit residues: 16.3821 Evaluate side-chains 135 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 16 optimal weight: 7.9990 chunk 117 optimal weight: 0.0270 chunk 38 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 20.0000 chunk 4 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 ASN D 386 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.066181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.051700 restraints weight = 56142.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.053035 restraints weight = 29854.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.053949 restraints weight = 20366.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.054455 restraints weight = 15920.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.054790 restraints weight = 13724.599| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11157 Z= 0.132 Angle : 0.596 15.178 15174 Z= 0.283 Chirality : 0.037 0.149 1774 Planarity : 0.004 0.054 1903 Dihedral : 3.300 17.312 1550 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.83 % Favored : 97.10 % Rotamer: Outliers : 2.20 % Allowed : 19.98 % Favored : 77.82 % 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 are not related in a simple way. whole: 1.38 (0.24), residues: 1414 helix: 2.27 (0.17), residues: 927 sheet: -1.84 (0.50), residues: 81 loop : -1.82 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 50 TYR 0.011 0.001 TYR A 237 PHE 0.023 0.001 PHE D 563 TRP 0.015 0.001 TRP E 176 HIS 0.002 0.001 HIS C 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (11157) covalent geometry : angle 0.59572 / 0.28 (15174) hydrogen bonds : bond 0.03775 / 2.53 ( 712) hydrogen bonds : angle 3.58136 / 2.54 ( 2124) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: A 153 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8320 (tt) REVERT: A 345 MET cc_start: 0.9336 (mmp) cc_final: 0.8958 (mmp) REVERT: C 16 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8687 (tt) REVERT: C 18 ASP cc_start: 0.8811 (m-30) cc_final: 0.8443 (m-30) REVERT: C 59 HIS cc_start: 0.8402 (OUTLIER) cc_final: 0.8010 (t-90) REVERT: D 415 MET cc_start: 0.7416 (tmm) cc_final: 0.7007 (tmm) REVERT: E 87 LYS cc_start: 0.9671 (ttmm) cc_final: 0.9367 (ttmm) REVERT: E 92 ILE cc_start: 0.9358 (mt) cc_final: 0.9056 (mm) REVERT: E 151 GLU cc_start: 0.8623 (mm-30) cc_final: 0.7443 (mm-30) REVERT: F 137 MET cc_start: 0.8278 (mpp) cc_final: 0.7875 (mpp) REVERT: F 186 ILE cc_start: 0.9147 (tp) cc_final: 0.8820 (tt) outliers start: 24 outliers final: 17 residues processed: 138 average time/residue: 0.0865 time to fit residues: 18.4147 Evaluate side-chains 133 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain F residue 60 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 88 optimal weight: 0.9980 chunk 117 optimal weight: 0.0270 chunk 46 optimal weight: 0.0670 chunk 34 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 40.0000 chunk 31 optimal weight: 20.0000 chunk 95 optimal weight: 0.0030 chunk 108 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.066667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.052359 restraints weight = 56273.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.053700 restraints weight = 30116.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.054574 restraints weight = 20456.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.055194 restraints weight = 16105.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.055505 restraints weight = 13659.420| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11157 Z= 0.116 Angle : 0.603 15.433 15174 Z= 0.286 Chirality : 0.037 0.154 1774 Planarity : 0.004 0.055 1903 Dihedral : 3.286 21.397 1550 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.97 % Favored : 96.96 % Rotamer: Outliers : 2.11 % Allowed : 21.26 % Favored : 76.63 % 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 are not related in a simple way. whole: 1.48 (0.23), residues: 1414 helix: 2.28 (0.17), residues: 929 sheet: -1.73 (0.50), residues: 80 loop : -1.65 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 50 TYR 0.012 0.001 TYR E 158 PHE 0.021 0.001 PHE D 15 TRP 0.010 0.001 TRP E 176 HIS 0.002 0.000 HIS C 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (11157) covalent geometry : angle 0.60350 / 0.29 (15174) hydrogen bonds : bond 0.03632 / 2.43 ( 712) hydrogen bonds : angle 3.49931 / 2.48 ( 2124) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 153 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8414 (tt) REVERT: A 345 MET cc_start: 0.9312 (mmp) cc_final: 0.8920 (mmp) REVERT: C 16 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8662 (tt) REVERT: C 18 ASP cc_start: 0.8803 (m-30) cc_final: 0.8437 (m-30) REVERT: C 59 HIS cc_start: 0.8380 (OUTLIER) cc_final: 0.7998 (t-90) REVERT: D 415 MET cc_start: 0.7406 (tmm) cc_final: 0.6990 (tmm) REVERT: D 429 LEU cc_start: 0.8039 (mp) cc_final: 0.7740 (mp) REVERT: E 92 ILE cc_start: 0.9361 (mt) cc_final: 0.9062 (mm) REVERT: E 121 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8791 (ptpp) REVERT: E 151 GLU cc_start: 0.8563 (mm-30) cc_final: 0.7387 (mm-30) REVERT: E 162 MET cc_start: 0.9063 (tpp) cc_final: 0.8426 (mpp) REVERT: F 137 MET cc_start: 0.8138 (mpp) cc_final: 0.7679 (mpp) REVERT: F 170 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8127 (mmt) REVERT: F 186 ILE cc_start: 0.9160 (tp) cc_final: 0.8820 (tt) outliers start: 23 outliers final: 15 residues processed: 131 average time/residue: 0.0807 time to fit residues: 16.5602 Evaluate side-chains 130 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 121 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 170 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 117 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 92 optimal weight: 0.1980 chunk 128 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 141 optimal weight: 30.0000 chunk 77 optimal weight: 0.0980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.068651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.054763 restraints weight = 54836.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.056223 restraints weight = 29228.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.057078 restraints weight = 19823.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.057733 restraints weight = 15708.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.058172 restraints weight = 13318.960| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11157 Z= 0.120 Angle : 0.612 15.811 15174 Z= 0.290 Chirality : 0.037 0.180 1774 Planarity : 0.004 0.055 1903 Dihedral : 3.256 20.122 1550 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.62 % Favored : 97.31 % Rotamer: Outliers : 1.92 % Allowed : 21.81 % Favored : 76.26 % 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 are not related in a simple way. whole: 1.52 (0.24), residues: 1414 helix: 2.29 (0.17), residues: 929 sheet: -1.70 (0.50), residues: 80 loop : -1.57 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 50 TYR 0.011 0.001 TYR E 158 PHE 0.020 0.001 PHE D 15 TRP 0.011 0.001 TRP A 65 HIS 0.002 0.000 HIS F 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (11157) covalent geometry : angle 0.61166 / 0.29 (15174) hydrogen bonds : bond 0.03578 / 2.38 ( 712) hydrogen bonds : angle 3.50672 / 2.48 ( 2124) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 153 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8277 (tt) REVERT: A 345 MET cc_start: 0.9275 (mmp) cc_final: 0.8879 (mmp) REVERT: C 16 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8617 (tt) REVERT: C 18 ASP cc_start: 0.8750 (m-30) cc_final: 0.8395 (m-30) REVERT: C 59 HIS cc_start: 0.8378 (OUTLIER) cc_final: 0.8027 (t-90) REVERT: D 90 MET cc_start: 0.8835 (mmm) cc_final: 0.8580 (mmt) REVERT: D 415 MET cc_start: 0.7416 (tmm) cc_final: 0.6999 (tmm) REVERT: D 429 LEU cc_start: 0.8020 (mp) cc_final: 0.7752 (mp) REVERT: D 605 MET cc_start: 0.8874 (tpp) cc_final: 0.8293 (tpt) REVERT: E 87 LYS cc_start: 0.9652 (ttmm) cc_final: 0.9387 (ttmm) REVERT: E 92 ILE cc_start: 0.9418 (mt) cc_final: 0.9131 (mm) REVERT: E 121 LYS cc_start: 0.9169 (pttp) cc_final: 0.8772 (ptpp) REVERT: E 151 GLU cc_start: 0.8580 (mm-30) cc_final: 0.7426 (mm-30) REVERT: F 137 MET cc_start: 0.8092 (mpp) cc_final: 0.7691 (mpp) REVERT: F 170 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8155 (mmt) REVERT: F 186 ILE cc_start: 0.9167 (tp) cc_final: 0.8827 (tt) outliers start: 21 outliers final: 16 residues processed: 131 average time/residue: 0.0738 time to fit residues: 15.3696 Evaluate side-chains 133 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 170 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 93 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 chunk 63 optimal weight: 0.0170 chunk 82 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 100 optimal weight: 0.3980 chunk 21 optimal weight: 8.9990 overall best weight: 2.0824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.066284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.051799 restraints weight = 56285.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.053172 restraints weight = 30050.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.053993 restraints weight = 20401.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.054582 restraints weight = 16063.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.054844 restraints weight = 13792.354| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11157 Z= 0.143 Angle : 0.616 15.701 15174 Z= 0.295 Chirality : 0.038 0.159 1774 Planarity : 0.004 0.055 1903 Dihedral : 3.267 19.609 1550 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.76 % Favored : 97.17 % Rotamer: Outliers : 1.92 % Allowed : 22.09 % Favored : 75.99 % 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 are not related in a simple way. whole: 1.58 (0.24), residues: 1414 helix: 2.35 (0.17), residues: 929 sheet: -1.72 (0.51), residues: 80 loop : -1.55 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 50 TYR 0.010 0.001 TYR E 158 PHE 0.022 0.001 PHE E 23 TRP 0.010 0.001 TRP A 65 HIS 0.003 0.001 HIS F 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (11157) covalent geometry : angle 0.61642 / 0.29 (15174) hydrogen bonds : bond 0.03636 / 2.44 ( 712) hydrogen bonds : angle 3.55624 / 2.51 ( 2124) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2828 Ramachandran restraints generated. 1414 Oldfield, 0 Emsley, 1414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 153 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8349 (tt) REVERT: A 345 MET cc_start: 0.9315 (mmp) cc_final: 0.8920 (mmp) REVERT: C 16 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8682 (tt) REVERT: C 18 ASP cc_start: 0.8820 (m-30) cc_final: 0.8456 (m-30) REVERT: C 59 HIS cc_start: 0.8393 (OUTLIER) cc_final: 0.8045 (t-90) REVERT: D 90 MET cc_start: 0.8910 (mmm) cc_final: 0.8607 (mmp) REVERT: D 415 MET cc_start: 0.7452 (tmm) cc_final: 0.7017 (tmm) REVERT: D 429 LEU cc_start: 0.7972 (mp) cc_final: 0.7687 (mp) REVERT: E 87 LYS cc_start: 0.9681 (ttmm) cc_final: 0.9420 (ttmm) REVERT: E 92 ILE cc_start: 0.9382 (mt) cc_final: 0.9091 (mm) REVERT: E 121 LYS cc_start: 0.9174 (pttp) cc_final: 0.8798 (ptpp) REVERT: E 151 GLU cc_start: 0.8551 (mm-30) cc_final: 0.7383 (mm-30) REVERT: E 162 MET cc_start: 0.9049 (tpp) cc_final: 0.8456 (mpp) REVERT: F 137 MET cc_start: 0.8192 (mpp) cc_final: 0.7725 (mpp) REVERT: F 170 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8210 (mmt) REVERT: F 186 ILE cc_start: 0.9130 (tp) cc_final: 0.8777 (tt) outliers start: 21 outliers final: 17 residues processed: 128 average time/residue: 0.0803 time to fit residues: 16.1933 Evaluate side-chains 133 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 59 HIS Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 596 VAL Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 170 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 134 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.066152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.051674 restraints weight = 56385.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.053047 restraints weight = 30021.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.053872 restraints weight = 20387.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.054476 restraints weight = 16047.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.054731 restraints weight = 13683.536| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11157 Z= 0.145 Angle : 0.621 15.766 15174 Z= 0.297 Chirality : 0.038 0.159 1774 Planarity : 0.004 0.055 1903 Dihedral : 3.292 19.214 1550 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.62 % Favored : 97.31 % Rotamer: Outliers : 2.29 % Allowed : 21.72 % Favored : 75.99 % 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 are not related in a simple way. whole: 1.62 (0.24), residues: 1414 helix: 2.38 (0.17), residues: 929 sheet: -1.71 (0.51), residues: 80 loop : -1.54 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 50 TYR 0.010 0.001 TYR A 237 PHE 0.022 0.001 PHE D 563 TRP 0.010 0.001 TRP E 141 HIS 0.003 0.001 HIS C 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (11157) covalent geometry : angle 0.62094 / 0.30 (15174) hydrogen bonds : bond 0.03655 / 2.45 ( 712) hydrogen bonds : angle 3.56271 / 2.52 ( 2124) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1714.53 seconds wall clock time: 30 minutes 22.53 seconds (1822.53 seconds total)