Starting phenix.real_space_refine on Wed Sep 17 19:10:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kaj_22772/09_2025/7kaj_22772.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kaj_22772/09_2025/7kaj_22772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kaj_22772/09_2025/7kaj_22772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kaj_22772/09_2025/7kaj_22772.map" model { file = "/net/cci-nas-00/data/ceres_data/7kaj_22772/09_2025/7kaj_22772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kaj_22772/09_2025/7kaj_22772.cif" } resolution = 3.1 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= 0.004 sd= 0.036 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 42 5.16 5 C 6976 2.51 5 N 1804 2.21 5 O 1890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10712 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3304 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 19, 'TRANS': 416} Chain breaks: 3 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 70 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 435 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "B" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 229 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 30} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3864 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 28, 'TRANS': 463} Chain breaks: 3 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 12, 'GLN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 86 Chain: "E" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1129 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 135} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1471 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 182} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 280 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'TRANS': 55} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'UNK:plan-1': 56} Unresolved non-hydrogen planarities: 56 Time building chain proxies: 2.06, per 1000 atoms: 0.19 Number of scatterers: 10712 At special positions: 0 Unit cell: (109.48, 126.14, 136.85, 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 42 16.00 O 1890 8.00 N 1804 7.00 C 6976 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: 0.92 Conformation dependent library (CDL) restraints added in 380.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2644 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 6 sheets defined 69.8% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.527A pdb=" N GLY A 47 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 98 Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.503A pdb=" N LYS A 119 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 174 removed outlier: 3.606A pdb=" N LEU A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 214 through 224 Processing helix chain 'A' and resid 227 through 238 removed outlier: 4.125A pdb=" N VAL A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 260 removed outlier: 3.760A pdb=" N VAL A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 314 removed outlier: 3.544A pdb=" N MET A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 341 through 346 Processing helix chain 'A' and resid 351 through 358 removed outlier: 3.524A pdb=" N ASP A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 384 removed outlier: 3.609A pdb=" N THR A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR A 367 " --> pdb=" O ILE A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 409 through 416 removed outlier: 3.880A pdb=" N LYS A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 439 Processing helix chain 'A' and resid 444 through 466 Processing helix chain 'C' and resid 27 through 39 removed outlier: 3.566A pdb=" N LYS C 38 " --> pdb=" O GLN C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 80 removed outlier: 3.686A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Proline residue: C 74 - end of helix Processing helix chain 'B' and resid 53 through 82 Processing helix chain 'D' and resid 13 through 36 removed outlier: 3.531A pdb=" N PHE D 17 " --> pdb=" O THR D 13 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) Proline residue: D 28 - end of helix Processing helix chain 'D' and resid 58 through 63 removed outlier: 4.324A pdb=" N LEU D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 78 removed outlier: 3.549A pdb=" N PHE D 74 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 112 Processing helix chain 'D' and resid 212 through 217 Processing helix chain 'D' and resid 219 through 233 removed outlier: 3.753A pdb=" N LEU D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 247 Processing helix chain 'D' and resid 255 through 268 removed outlier: 3.745A pdb=" N ASN D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 285 removed outlier: 3.704A pdb=" N ILE D 280 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 294 removed outlier: 3.536A pdb=" N GLN D 292 " --> pdb=" O HIS D 288 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE D 294 " --> pdb=" O PHE D 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 288 through 294' Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 318 through 343 removed outlier: 3.682A pdb=" N ARG D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N HIS D 330 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N SER D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 362 removed outlier: 3.832A pdb=" N ALA D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 386 removed outlier: 4.168A pdb=" N THR D 384 " --> pdb=" O GLU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 397 Processing helix chain 'D' and resid 399 through 408 removed outlier: 3.504A pdb=" N ILE D 403 " --> pdb=" O GLU D 399 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY D 404 " --> pdb=" O ASP D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 423 removed outlier: 4.327A pdb=" N GLU D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR D 418 " --> pdb=" O LYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 470 Processing helix chain 'D' and resid 480 through 485 Processing helix chain 'D' and resid 490 through 494 removed outlier: 3.654A pdb=" N LYS D 493 " --> pdb=" O MET D 490 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN D 494 " --> pdb=" O MET D 491 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 490 through 494' Processing helix chain 'D' and resid 537 through 541 Processing helix chain 'D' and resid 554 through 558 removed outlier: 3.667A pdb=" N HIS D 558 " --> pdb=" O LEU D 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 86 removed outlier: 3.826A pdb=" N TYR E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE E 76 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 123 removed outlier: 3.696A pdb=" N LYS E 93 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Proline residue: E 115 - end of helix Processing helix chain 'E' and resid 128 through 156 removed outlier: 3.947A pdb=" N LYS E 132 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 182 removed outlier: 4.022A pdb=" N PHE E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 removed outlier: 4.091A pdb=" N GLU E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N CYS E 190 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.584A pdb=" N GLY E 202 " --> pdb=" O ASN E 199 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG E 203 " --> pdb=" O ASN E 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 199 through 203' Processing helix chain 'F' and resid 21 through 41 removed outlier: 3.554A pdb=" N GLU F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY F 40 " --> pdb=" O THR F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 71 removed outlier: 3.987A pdb=" N ASN F 68 " --> pdb=" O SER F 64 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN F 70 " --> pdb=" O MET F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 91 Processing helix chain 'F' and resid 97 through 120 Proline residue: F 103 - end of helix removed outlier: 3.765A pdb=" N SER F 111 " --> pdb=" O PHE F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 139 through 153 removed outlier: 3.651A pdb=" N PHE F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL F 144 " --> pdb=" O PRO F 140 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG F 145 " --> pdb=" O ASP F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 168 Processing helix chain 'F' and resid 174 through 192 removed outlier: 4.056A pdb=" N ALA F 178 " --> pdb=" O MET F 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 170 removed outlier: 3.561A pdb=" N UNK G 170 " --> pdb=" O UNK G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 205 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 211 Processing sheet with id=AA2, first strand: chain 'A' and resid 278 through 284 Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.701A pdb=" N VAL A 325 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 430 through 436 removed outlier: 3.806A pdb=" N LYS D 432 " --> pdb=" O LYS D 454 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532 removed outlier: 3.511A pdb=" N TRP D 513 " --> pdb=" O ILE D 532 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 6 682 hydrogen bonds defined for protein. 2001 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: 1.88 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3391 1.34 - 1.46: 2038 1.46 - 1.58: 5422 1.58 - 1.69: 0 1.69 - 1.81: 67 Bond restraints: 10918 Sorted by residual: bond pdb=" CA MET D 553 " pdb=" CB MET D 553 " ideal model delta sigma weight residual 1.528 1.544 -0.016 1.39e-02 5.18e+03 1.31e+00 bond pdb=" CA VAL A 325 " pdb=" CB VAL A 325 " ideal model delta sigma weight residual 1.531 1.541 -0.010 1.11e-02 8.12e+03 7.70e-01 bond pdb=" CG LEU F 129 " pdb=" CD2 LEU F 129 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.73e-01 bond pdb=" N LYS D 410 " pdb=" CA LYS D 410 " ideal model delta sigma weight residual 1.460 1.470 -0.010 1.42e-02 4.96e+03 4.83e-01 bond pdb=" C TRP D 14 " pdb=" N PRO D 15 " ideal model delta sigma weight residual 1.335 1.345 -0.009 1.36e-02 5.41e+03 4.63e-01 ... (remaining 10913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 14430 1.36 - 2.72: 293 2.72 - 4.07: 64 4.07 - 5.43: 15 5.43 - 6.79: 10 Bond angle restraints: 14812 Sorted by residual: angle pdb=" N VAL E 160 " pdb=" CA VAL E 160 " pdb=" C VAL E 160 " ideal model delta sigma weight residual 112.96 110.23 2.73 1.00e+00 1.00e+00 7.44e+00 angle pdb=" N GLU D 472 " pdb=" CA GLU D 472 " pdb=" CB GLU D 472 " ideal model delta sigma weight residual 113.65 109.84 3.81 1.47e+00 4.63e-01 6.72e+00 angle pdb=" N ILE A 418 " pdb=" CA ILE A 418 " pdb=" C ILE A 418 " ideal model delta sigma weight residual 108.88 113.24 -4.36 2.16e+00 2.14e-01 4.08e+00 angle pdb=" N TRP D 14 " pdb=" CA TRP D 14 " pdb=" C TRP D 14 " ideal model delta sigma weight residual 109.81 114.25 -4.44 2.21e+00 2.05e-01 4.04e+00 angle pdb=" N THR A 291 " pdb=" CA THR A 291 " pdb=" C THR A 291 " ideal model delta sigma weight residual 109.81 114.19 -4.38 2.21e+00 2.05e-01 3.92e+00 ... (remaining 14807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 6090 18.01 - 36.02: 400 36.02 - 54.03: 62 54.03 - 72.04: 11 72.04 - 90.04: 11 Dihedral angle restraints: 6574 sinusoidal: 2506 harmonic: 4068 Sorted by residual: dihedral pdb=" CB GLU E 153 " pdb=" CG GLU E 153 " pdb=" CD GLU E 153 " pdb=" OE1 GLU E 153 " ideal model delta sinusoidal sigma weight residual 0.00 90.04 -90.04 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CA LEU F 153 " pdb=" C LEU F 153 " pdb=" N ARG F 154 " pdb=" CA ARG F 154 " ideal model delta harmonic sigma weight residual 180.00 164.23 15.77 0 5.00e+00 4.00e-02 9.95e+00 dihedral pdb=" CB GLU F 63 " pdb=" CG GLU F 63 " pdb=" CD GLU F 63 " pdb=" OE1 GLU F 63 " ideal model delta sinusoidal sigma weight residual 0.00 -84.33 84.33 1 3.00e+01 1.11e-03 9.61e+00 ... (remaining 6571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1062 0.027 - 0.054: 439 0.054 - 0.081: 178 0.081 - 0.108: 72 0.108 - 0.135: 18 Chirality restraints: 1769 Sorted by residual: chirality pdb=" CA ILE D 470 " pdb=" N ILE D 470 " pdb=" C ILE D 470 " pdb=" CB ILE D 470 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CG LEU F 129 " pdb=" CB LEU F 129 " pdb=" CD1 LEU F 129 " pdb=" CD2 LEU F 129 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA ILE D 571 " pdb=" N ILE D 571 " pdb=" C ILE D 571 " pdb=" CB ILE D 571 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 1766 not shown) Planarity restraints: 1849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 47 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO F 48 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO F 48 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 48 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 366 " 0.022 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO D 367 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO D 367 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 367 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 298 " 0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO D 299 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 299 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 299 " 0.016 5.00e-02 4.00e+02 ... (remaining 1846 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2555 2.79 - 3.32: 10129 3.32 - 3.85: 16529 3.85 - 4.37: 17793 4.37 - 4.90: 32957 Nonbonded interactions: 79963 Sorted by model distance: nonbonded pdb=" OG1 THR A 201 " pdb=" OE1 GLU A 212 " model vdw 2.264 3.040 nonbonded pdb=" O TYR A 237 " pdb=" ND2 ASN A 243 " model vdw 2.277 3.120 nonbonded pdb=" NH1 ARG D 509 " pdb=" OD1 ASP D 596 " model vdw 2.316 3.120 nonbonded pdb=" O SER F 23 " pdb=" ND2 ASN F 27 " model vdw 2.322 3.120 nonbonded pdb=" NH1 ARG F 92 " pdb=" OE1 GLU F 96 " model vdw 2.328 3.120 ... (remaining 79958 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.780 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 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 0.033 10918 Z= 0.133 Angle : 0.537 6.792 14812 Z= 0.289 Chirality : 0.038 0.135 1769 Planarity : 0.003 0.038 1849 Dihedral : 12.812 90.044 3930 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.22), residues: 1319 helix: 0.35 (0.17), residues: 808 sheet: -2.66 (0.45), residues: 83 loop : -2.55 (0.26), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 99 TYR 0.017 0.001 TYR F 190 PHE 0.015 0.001 PHE E 163 TRP 0.008 0.001 TRP D 14 HIS 0.005 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00292 (10918) covalent geometry : angle 0.53711 (14812) hydrogen bonds : bond 0.12797 ( 682) hydrogen bonds : angle 4.99072 ( 2001) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 69 LYS cc_start: 0.9009 (tttt) cc_final: 0.8778 (tttm) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1395 time to fit residues: 17.7124 Evaluate side-chains 62 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN C 72 HIS D 307 GLN D 441 ASN E 88 HIS ** F 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.065729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.049403 restraints weight = 39917.064| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.08 r_work: 0.2788 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10918 Z= 0.185 Angle : 0.574 11.213 14812 Z= 0.285 Chirality : 0.039 0.143 1769 Planarity : 0.004 0.039 1849 Dihedral : 3.453 19.062 1476 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.63 % Allowed : 9.52 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.23), residues: 1319 helix: 1.63 (0.19), residues: 806 sheet: -2.19 (0.46), residues: 91 loop : -1.94 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 203 TYR 0.020 0.001 TYR F 190 PHE 0.013 0.001 PHE D 547 TRP 0.006 0.001 TRP D 14 HIS 0.006 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00443 (10918) covalent geometry : angle 0.57387 (14812) hydrogen bonds : bond 0.04504 ( 682) hydrogen bonds : angle 3.77096 ( 2001) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.8754 (tt0) cc_final: 0.8449 (pt0) REVERT: E 129 ASP cc_start: 0.9119 (p0) cc_final: 0.8832 (t0) REVERT: E 200 ASN cc_start: 0.8696 (t0) cc_final: 0.8387 (t0) outliers start: 7 outliers final: 2 residues processed: 69 average time/residue: 0.1189 time to fit residues: 11.7640 Evaluate side-chains 60 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 32 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 125 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.065729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.049311 restraints weight = 39773.425| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.09 r_work: 0.2799 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10918 Z= 0.140 Angle : 0.517 10.616 14812 Z= 0.255 Chirality : 0.038 0.136 1769 Planarity : 0.004 0.040 1849 Dihedral : 3.356 18.653 1476 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.26 % Allowed : 11.14 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.24), residues: 1319 helix: 2.17 (0.19), residues: 810 sheet: -1.71 (0.49), residues: 91 loop : -1.63 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 203 TYR 0.015 0.001 TYR F 190 PHE 0.013 0.001 PHE D 356 TRP 0.007 0.001 TRP F 156 HIS 0.005 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00333 (10918) covalent geometry : angle 0.51674 (14812) hydrogen bonds : bond 0.03950 ( 682) hydrogen bonds : angle 3.50932 ( 2001) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.8813 (tt0) cc_final: 0.8531 (pt0) REVERT: D 553 MET cc_start: 0.8505 (tmm) cc_final: 0.7942 (tmm) REVERT: E 129 ASP cc_start: 0.9131 (p0) cc_final: 0.8769 (t0) REVERT: E 200 ASN cc_start: 0.8805 (t0) cc_final: 0.8426 (t0) outliers start: 14 outliers final: 4 residues processed: 74 average time/residue: 0.1078 time to fit residues: 11.9098 Evaluate side-chains 64 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 474 ASN Chi-restraints excluded: chain D residue 517 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 21 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 HIS E 72 HIS F 139 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.064073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.047700 restraints weight = 40084.571| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 3.02 r_work: 0.2749 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10918 Z= 0.241 Angle : 0.596 11.068 14812 Z= 0.297 Chirality : 0.041 0.148 1769 Planarity : 0.004 0.039 1849 Dihedral : 3.602 20.083 1476 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.62 % Allowed : 13.03 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.24), residues: 1319 helix: 2.18 (0.19), residues: 819 sheet: -1.45 (0.50), residues: 91 loop : -1.50 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 203 TYR 0.021 0.001 TYR F 190 PHE 0.020 0.002 PHE D 356 TRP 0.007 0.001 TRP D 14 HIS 0.007 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00582 (10918) covalent geometry : angle 0.59556 (14812) hydrogen bonds : bond 0.04992 ( 682) hydrogen bonds : angle 3.72877 ( 2001) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.8906 (tt0) cc_final: 0.8598 (pt0) REVERT: D 553 MET cc_start: 0.8648 (tmm) cc_final: 0.8016 (tmm) REVERT: D 606 MET cc_start: 0.9346 (ptm) cc_final: 0.9145 (ptm) REVERT: E 129 ASP cc_start: 0.9200 (p0) cc_final: 0.8812 (t0) REVERT: E 200 ASN cc_start: 0.8788 (t0) cc_final: 0.8424 (t0) REVERT: F 17 ASP cc_start: 0.8757 (t0) cc_final: 0.8527 (m-30) outliers start: 18 outliers final: 8 residues processed: 72 average time/residue: 0.0945 time to fit residues: 10.6412 Evaluate side-chains 64 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 474 ASN Chi-restraints excluded: chain D residue 517 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 10 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 38 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 76 optimal weight: 0.0670 chunk 71 optimal weight: 3.9990 overall best weight: 1.0920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.066304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.050247 restraints weight = 40047.624| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.02 r_work: 0.2809 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10918 Z= 0.105 Angle : 0.503 10.091 14812 Z= 0.245 Chirality : 0.037 0.133 1769 Planarity : 0.003 0.039 1849 Dihedral : 3.329 17.482 1476 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.72 % Allowed : 14.47 % Favored : 84.82 % 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 aren not related in a simple way. whole: 1.69 (0.24), residues: 1319 helix: 2.47 (0.19), residues: 818 sheet: -1.19 (0.50), residues: 91 loop : -1.21 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 203 TYR 0.011 0.001 TYR F 190 PHE 0.008 0.001 PHE E 163 TRP 0.008 0.001 TRP F 156 HIS 0.004 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00237 (10918) covalent geometry : angle 0.50282 (14812) hydrogen bonds : bond 0.03528 ( 682) hydrogen bonds : angle 3.37144 ( 2001) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.8854 (tt0) cc_final: 0.8559 (pt0) REVERT: E 200 ASN cc_start: 0.8826 (t0) cc_final: 0.8384 (t0) REVERT: F 17 ASP cc_start: 0.8828 (t0) cc_final: 0.8510 (m-30) outliers start: 8 outliers final: 4 residues processed: 66 average time/residue: 0.0977 time to fit residues: 10.0132 Evaluate side-chains 64 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 310 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 72 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 chunk 128 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 29 optimal weight: 0.1980 chunk 117 optimal weight: 3.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.067247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.051158 restraints weight = 39379.336| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.99 r_work: 0.2842 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10918 Z= 0.091 Angle : 0.478 9.519 14812 Z= 0.230 Chirality : 0.037 0.134 1769 Planarity : 0.003 0.039 1849 Dihedral : 3.131 15.631 1476 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.08 % Allowed : 14.65 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.24), residues: 1319 helix: 2.64 (0.18), residues: 819 sheet: -0.96 (0.50), residues: 91 loop : -0.94 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 203 TYR 0.011 0.001 TYR E 130 PHE 0.007 0.001 PHE E 163 TRP 0.008 0.001 TRP E 131 HIS 0.004 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00197 (10918) covalent geometry : angle 0.47813 (14812) hydrogen bonds : bond 0.02986 ( 682) hydrogen bonds : angle 3.17690 ( 2001) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.8875 (tt0) cc_final: 0.8529 (pt0) REVERT: D 526 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8835 (pp) REVERT: D 553 MET cc_start: 0.8566 (tmm) cc_final: 0.7935 (tmm) REVERT: E 200 ASN cc_start: 0.8906 (t0) cc_final: 0.8454 (t0) REVERT: F 17 ASP cc_start: 0.8920 (t0) cc_final: 0.8447 (m-30) outliers start: 12 outliers final: 8 residues processed: 77 average time/residue: 0.0958 time to fit residues: 11.3415 Evaluate side-chains 72 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 547 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 39 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.065620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.049170 restraints weight = 39518.310| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.05 r_work: 0.2793 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10918 Z= 0.140 Angle : 0.522 9.574 14812 Z= 0.252 Chirality : 0.038 0.135 1769 Planarity : 0.003 0.038 1849 Dihedral : 3.224 17.387 1476 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.35 % Allowed : 15.00 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.24), residues: 1319 helix: 2.62 (0.18), residues: 825 sheet: -0.89 (0.50), residues: 91 loop : -0.87 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 203 TYR 0.015 0.001 TYR F 190 PHE 0.009 0.001 PHE E 163 TRP 0.006 0.001 TRP F 156 HIS 0.004 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00335 (10918) covalent geometry : angle 0.52239 (14812) hydrogen bonds : bond 0.03733 ( 682) hydrogen bonds : angle 3.26556 ( 2001) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.8890 (tt0) cc_final: 0.8555 (pt0) REVERT: D 526 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8950 (pp) REVERT: D 553 MET cc_start: 0.8557 (tmm) cc_final: 0.7930 (tmm) REVERT: E 200 ASN cc_start: 0.8975 (t0) cc_final: 0.8539 (t0) REVERT: F 17 ASP cc_start: 0.8937 (t0) cc_final: 0.8412 (m-30) outliers start: 15 outliers final: 10 residues processed: 75 average time/residue: 0.0920 time to fit residues: 10.7393 Evaluate side-chains 71 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 547 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 131 optimal weight: 0.7980 chunk 82 optimal weight: 0.4980 chunk 37 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 91 optimal weight: 0.0770 chunk 10 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.067266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.051237 restraints weight = 39681.388| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.99 r_work: 0.2839 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10918 Z= 0.089 Angle : 0.486 10.503 14812 Z= 0.231 Chirality : 0.037 0.134 1769 Planarity : 0.003 0.038 1849 Dihedral : 3.094 15.332 1476 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.90 % Allowed : 15.63 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.24), residues: 1319 helix: 2.68 (0.18), residues: 828 sheet: -0.80 (0.50), residues: 92 loop : -0.74 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 203 TYR 0.008 0.001 TYR F 190 PHE 0.007 0.001 PHE E 163 TRP 0.007 0.001 TRP E 131 HIS 0.005 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00193 (10918) covalent geometry : angle 0.48580 (14812) hydrogen bonds : bond 0.02890 ( 682) hydrogen bonds : angle 3.11767 ( 2001) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.8832 (tt0) cc_final: 0.8465 (pt0) REVERT: D 526 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8780 (pp) REVERT: D 553 MET cc_start: 0.8547 (tmm) cc_final: 0.7871 (tmm) REVERT: E 200 ASN cc_start: 0.8967 (t0) cc_final: 0.8511 (t0) outliers start: 10 outliers final: 5 residues processed: 74 average time/residue: 0.0988 time to fit residues: 11.0866 Evaluate side-chains 72 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 547 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 67 optimal weight: 5.9990 chunk 76 optimal weight: 0.0570 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 117 optimal weight: 0.0470 chunk 33 optimal weight: 2.9990 chunk 126 optimal weight: 0.0980 chunk 115 optimal weight: 0.7980 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.066942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.050461 restraints weight = 39784.251| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.09 r_work: 0.2832 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10918 Z= 0.093 Angle : 0.504 10.660 14812 Z= 0.237 Chirality : 0.037 0.134 1769 Planarity : 0.003 0.039 1849 Dihedral : 3.056 15.421 1476 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.72 % Allowed : 15.99 % Favored : 83.29 % 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 aren not related in a simple way. whole: 2.30 (0.24), residues: 1319 helix: 2.77 (0.18), residues: 828 sheet: -0.68 (0.51), residues: 92 loop : -0.68 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 90 TYR 0.011 0.001 TYR F 190 PHE 0.008 0.001 PHE E 163 TRP 0.006 0.001 TRP E 131 HIS 0.004 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00210 (10918) covalent geometry : angle 0.50394 (14812) hydrogen bonds : bond 0.02983 ( 682) hydrogen bonds : angle 3.09882 ( 2001) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.8838 (tt0) cc_final: 0.8471 (pt0) REVERT: D 526 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8798 (pp) REVERT: D 553 MET cc_start: 0.8527 (tmm) cc_final: 0.7869 (tmm) REVERT: E 200 ASN cc_start: 0.8944 (t0) cc_final: 0.8489 (t0) REVERT: F 17 ASP cc_start: 0.8639 (t0) cc_final: 0.8265 (m-30) outliers start: 8 outliers final: 7 residues processed: 71 average time/residue: 0.0945 time to fit residues: 10.4444 Evaluate side-chains 72 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 547 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 1 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 86 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.065784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.049157 restraints weight = 39991.185| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.08 r_work: 0.2799 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10918 Z= 0.133 Angle : 0.530 10.766 14812 Z= 0.254 Chirality : 0.038 0.135 1769 Planarity : 0.003 0.038 1849 Dihedral : 3.179 17.226 1476 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.90 % Allowed : 15.99 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.30 (0.24), residues: 1319 helix: 2.78 (0.18), residues: 825 sheet: -0.58 (0.50), residues: 91 loop : -0.71 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 90 TYR 0.014 0.001 TYR F 190 PHE 0.009 0.001 PHE E 163 TRP 0.008 0.001 TRP F 156 HIS 0.004 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00318 (10918) covalent geometry : angle 0.53049 (14812) hydrogen bonds : bond 0.03628 ( 682) hydrogen bonds : angle 3.21698 ( 2001) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.8848 (tt0) cc_final: 0.8478 (pt0) REVERT: D 526 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8897 (pp) REVERT: D 553 MET cc_start: 0.8590 (tmm) cc_final: 0.7945 (tmm) REVERT: E 200 ASN cc_start: 0.9030 (t0) cc_final: 0.8583 (t0) REVERT: F 17 ASP cc_start: 0.8684 (t0) cc_final: 0.8271 (m-30) outliers start: 10 outliers final: 8 residues processed: 72 average time/residue: 0.0964 time to fit residues: 10.8051 Evaluate side-chains 70 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain D residue 547 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 22 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 30 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 chunk 82 optimal weight: 0.2980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.066770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.050320 restraints weight = 39679.651| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.02 r_work: 0.2836 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10918 Z= 0.094 Angle : 0.514 10.955 14812 Z= 0.243 Chirality : 0.037 0.134 1769 Planarity : 0.003 0.038 1849 Dihedral : 3.089 15.591 1476 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.08 % Allowed : 15.99 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.37 (0.24), residues: 1319 helix: 2.81 (0.18), residues: 827 sheet: -0.56 (0.51), residues: 92 loop : -0.65 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 90 TYR 0.009 0.001 TYR F 190 PHE 0.007 0.001 PHE E 163 TRP 0.007 0.001 TRP F 156 HIS 0.004 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00210 (10918) covalent geometry : angle 0.51351 (14812) hydrogen bonds : bond 0.03005 ( 682) hydrogen bonds : angle 3.11300 ( 2001) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2659.09 seconds wall clock time: 46 minutes 26.89 seconds (2786.89 seconds total)