Starting phenix.real_space_refine on Fri Feb 14 23:25:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kap_22779/02_2025/7kap_22779.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kap_22779/02_2025/7kap_22779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kap_22779/02_2025/7kap_22779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kap_22779/02_2025/7kap_22779.map" model { file = "/net/cci-nas-00/data/ceres_data/7kap_22779/02_2025/7kap_22779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kap_22779/02_2025/7kap_22779.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.063 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 38 5.16 5 C 6980 2.51 5 N 1807 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 33 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10715 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3307 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 19, 'TRANS': 415} Chain breaks: 3 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 62 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: {'PHE:plan': 1, 'ASP: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: {'GLN:plan1': 2, 'GLU:plan': 12, 'PHE:plan': 1, 'ASP:plan': 8} 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: {'GLN:plan1': 1, 'GLU:plan': 3, '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: 6.05, per 1000 atoms: 0.56 Number of scatterers: 10715 At special positions: 0 Unit cell: (109.25, 124.2, 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 38 16.00 O 1890 8.00 N 1807 7.00 C 6980 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: 2.74 Conformation dependent library (CDL) restraints added in 1.5 seconds 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2642 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 6 sheets defined 70.5% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 Processing helix chain 'A' and resid 82 through 98 Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.789A pdb=" N ILE A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 174 removed outlier: 3.893A pdb=" N GLY A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 199 removed outlier: 3.609A pdb=" N ALA A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 removed outlier: 3.571A pdb=" N ALA A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 removed outlier: 4.162A pdb=" N VAL A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 260 Processing helix chain 'A' and resid 290 through 314 removed outlier: 4.094A pdb=" N ILE A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 341 through 347 Processing helix chain 'A' and resid 351 through 358 removed outlier: 3.528A pdb=" N ALA A 355 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 384 Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 409 through 415 Processing helix chain 'A' and resid 417 through 440 Processing helix chain 'A' and resid 444 through 466 removed outlier: 3.501A pdb=" N TYR A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 43 through 80 removed outlier: 3.593A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 4.313A 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: 3.810A 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: 4.323A pdb=" N LEU D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 78 removed outlier: 3.580A 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: 3.583A pdb=" N LEU D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 255 through 268 removed outlier: 3.728A pdb=" N ASN D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 285 removed outlier: 3.524A pdb=" N ILE D 280 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 294 removed outlier: 3.895A pdb=" N LYS D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE D 294 " --> pdb=" O PHE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 318 through 343 removed outlier: 3.537A pdb=" N ARG D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N HIS D 330 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N SER D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 362 removed outlier: 3.847A pdb=" N ALA D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 386 removed outlier: 4.127A pdb=" N THR D 384 " --> pdb=" O GLU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 397 Processing helix chain 'D' and resid 399 through 408 removed outlier: 3.766A pdb=" N GLY D 404 " --> pdb=" O ASP D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 422 removed outlier: 4.205A pdb=" N GLU D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) removed outlier: 3.648A 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 Processing helix chain 'D' and resid 537 through 541 Processing helix chain 'D' and resid 554 through 558 removed outlier: 3.591A pdb=" N HIS D 558 " --> pdb=" O LEU D 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 86 removed outlier: 3.534A pdb=" N PHE E 76 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 124 removed outlier: 3.721A 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: 3.990A pdb=" N LYS E 132 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 182 removed outlier: 3.817A pdb=" N PHE E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 removed outlier: 4.337A pdb=" N GLU E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N CYS E 190 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.512A pdb=" N GLY E 202 " --> pdb=" O ASN E 199 " (cutoff:3.500A) removed outlier: 3.793A 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 Processing helix chain 'F' and resid 52 through 71 removed outlier: 3.846A pdb=" N ASN F 68 " --> pdb=" O SER F 64 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 3.865A 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: 3.638A 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: 3.704A pdb=" N PHE F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL F 144 " --> pdb=" O PRO F 140 " (cutoff:3.500A) removed outlier: 4.454A 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: 3.877A pdb=" N ALA F 178 " --> pdb=" O MET F 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 170 removed outlier: 3.531A pdb=" N UNK G 165 " --> pdb=" O UNK G 161 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N UNK G 166 " --> pdb=" O UNK G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 205 removed outlier: 3.525A pdb=" N UNK G 205 " --> pdb=" O UNK G 201 " (cutoff:3.500A) 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 326 through 327 Processing sheet with id=AA4, first strand: chain 'D' and resid 430 through 436 removed outlier: 3.600A pdb=" N ASP D 434 " --> pdb=" O SER D 452 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532 removed outlier: 3.669A pdb=" N ILE D 604 " --> pdb=" O VAL D 590 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 6 692 hydrogen bonds defined for protein. 2028 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.95 Time building geometry restraints manager: 3.13 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: 3396 1.34 - 1.46: 2366 1.46 - 1.58: 5100 1.58 - 1.69: 0 1.69 - 1.81: 59 Bond restraints: 10921 Sorted by residual: bond pdb=" C ILE D 425 " pdb=" N PRO D 426 " ideal model delta sigma weight residual 1.334 1.324 0.010 1.11e-02 8.12e+03 7.55e-01 bond pdb=" CB PRO A 84 " pdb=" CG PRO A 84 " ideal model delta sigma weight residual 1.492 1.454 0.038 5.00e-02 4.00e+02 5.76e-01 bond pdb=" CA LEU F 102 " pdb=" C LEU F 102 " ideal model delta sigma weight residual 1.521 1.529 -0.009 1.14e-02 7.69e+03 5.69e-01 bond pdb=" C LYS D 493 " pdb=" N GLN D 494 " ideal model delta sigma weight residual 1.340 1.298 0.042 5.87e-02 2.90e+02 5.19e-01 bond pdb=" C TRP D 14 " pdb=" N PRO D 15 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.36e-02 5.41e+03 5.15e-01 ... (remaining 10916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 14711 2.36 - 4.71: 84 4.71 - 7.07: 21 7.07 - 9.43: 1 9.43 - 11.79: 1 Bond angle restraints: 14818 Sorted by residual: angle pdb=" C ILE A 417 " pdb=" N ILE A 418 " pdb=" CA ILE A 418 " ideal model delta sigma weight residual 120.33 122.23 -1.90 8.00e-01 1.56e+00 5.65e+00 angle pdb=" N VAL E 160 " pdb=" CA VAL E 160 " pdb=" C VAL E 160 " ideal model delta sigma weight residual 111.90 110.01 1.89 8.10e-01 1.52e+00 5.43e+00 angle pdb=" C ILE A 418 " pdb=" CA ILE A 418 " pdb=" CB ILE A 418 " ideal model delta sigma weight residual 114.00 111.00 3.00 1.31e+00 5.83e-01 5.25e+00 angle pdb=" N PRO D 426 " pdb=" CA PRO D 426 " pdb=" C PRO D 426 " ideal model delta sigma weight residual 110.55 114.11 -3.56 1.63e+00 3.76e-01 4.76e+00 angle pdb=" CA LEU A 162 " pdb=" CB LEU A 162 " pdb=" CG LEU A 162 " ideal model delta sigma weight residual 116.30 123.64 -7.34 3.50e+00 8.16e-02 4.40e+00 ... (remaining 14813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6248 17.95 - 35.90: 262 35.90 - 53.86: 46 53.86 - 71.81: 10 71.81 - 89.76: 8 Dihedral angle restraints: 6574 sinusoidal: 2509 harmonic: 4065 Sorted by residual: dihedral pdb=" CA ASP E 201 " pdb=" CB ASP E 201 " pdb=" CG ASP E 201 " pdb=" OD1 ASP E 201 " ideal model delta sinusoidal sigma weight residual -30.00 -88.28 58.28 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CB GLU C 31 " pdb=" CG GLU C 31 " pdb=" CD GLU C 31 " pdb=" OE1 GLU C 31 " ideal model delta sinusoidal sigma weight residual 0.00 -89.76 89.76 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU D 472 " pdb=" CG GLU D 472 " pdb=" CD GLU D 472 " pdb=" OE1 GLU D 472 " ideal model delta sinusoidal sigma weight residual 0.00 -87.61 87.61 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 6571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1048 0.026 - 0.053: 467 0.053 - 0.079: 162 0.079 - 0.105: 79 0.105 - 0.132: 15 Chirality restraints: 1771 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 4.34e-01 chirality pdb=" CA SER A 83 " pdb=" N SER A 83 " pdb=" C SER A 83 " pdb=" CB SER A 83 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA VAL A 27 " pdb=" N VAL A 27 " pdb=" C VAL A 27 " pdb=" CB VAL A 27 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.57e-01 ... (remaining 1768 not shown) Planarity restraints: 1850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 462 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO D 463 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 463 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 463 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 47 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO F 48 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO F 48 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 48 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 93 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO F 94 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO F 94 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 94 " -0.018 5.00e-02 4.00e+02 ... (remaining 1847 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1268 2.74 - 3.28: 11240 3.28 - 3.82: 17674 3.82 - 4.36: 19269 4.36 - 4.90: 34039 Nonbonded interactions: 83490 Sorted by model distance: nonbonded pdb=" NH1 ARG F 92 " pdb=" OE1 GLU F 96 " model vdw 2.205 3.120 nonbonded pdb=" O THR D 444 " pdb=" OG SER D 447 " model vdw 2.248 3.040 nonbonded pdb=" NZ LYS A 284 " pdb=" OE1 GLU A 460 " model vdw 2.276 3.120 nonbonded pdb=" OE2 GLU E 151 " pdb=" NH2 ARG E 154 " model vdw 2.309 3.120 nonbonded pdb=" NH2 ARG D 458 " pdb=" O GLN D 462 " model vdw 2.317 3.120 ... (remaining 83485 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: 0.850 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: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.530 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 0.042 10921 Z= 0.176 Angle : 0.545 11.785 14818 Z= 0.287 Chirality : 0.037 0.132 1771 Planarity : 0.003 0.039 1850 Dihedral : 11.241 89.758 3932 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.22), residues: 1318 helix: 0.26 (0.17), residues: 818 sheet: -2.91 (0.44), residues: 86 loop : -2.02 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 380 HIS 0.006 0.001 HIS D 334 PHE 0.009 0.001 PHE A 92 TYR 0.014 0.001 TYR F 190 ARG 0.002 0.000 ARG A 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 PHE cc_start: 0.8786 (t80) cc_final: 0.8393 (t80) REVERT: A 169 GLU cc_start: 0.9369 (tp30) cc_final: 0.8959 (tp30) REVERT: A 249 MET cc_start: 0.8686 (mmp) cc_final: 0.8401 (mmm) REVERT: A 349 LEU cc_start: 0.8521 (mt) cc_final: 0.8277 (tt) REVERT: A 376 PHE cc_start: 0.9438 (m-10) cc_final: 0.9163 (m-10) REVERT: A 380 TRP cc_start: 0.8992 (t-100) cc_final: 0.8512 (t-100) REVERT: C 43 ASP cc_start: 0.8556 (p0) cc_final: 0.7757 (p0) REVERT: D 100 TRP cc_start: 0.9603 (m100) cc_final: 0.9029 (m100) REVERT: E 81 MET cc_start: 0.9359 (ttm) cc_final: 0.9101 (mtp) REVERT: E 141 ILE cc_start: 0.9350 (mm) cc_final: 0.8957 (tt) REVERT: F 57 MET cc_start: 0.9215 (mtp) cc_final: 0.9006 (ptp) REVERT: F 66 MET cc_start: 0.9188 (mmp) cc_final: 0.8980 (mmm) REVERT: F 101 GLN cc_start: 0.9366 (tt0) cc_final: 0.8768 (pt0) REVERT: F 108 MET cc_start: 0.9241 (mtm) cc_final: 0.8756 (mtm) REVERT: F 118 ILE cc_start: 0.9760 (mt) cc_final: 0.9515 (tp) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2314 time to fit residues: 50.4696 Evaluate side-chains 80 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 55 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 188 ASN A 192 GLN A 394 GLN A 398 GLN A 403 ASN D 4 ASN D 113 ASN D 307 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN D 494 GLN D 558 HIS E 88 HIS ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 GLN F 68 ASN F 106 HIS F 127 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.047596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.037086 restraints weight = 79809.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.038085 restraints weight = 44675.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.038623 restraints weight = 30334.898| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10921 Z= 0.258 Angle : 0.598 14.464 14818 Z= 0.292 Chirality : 0.039 0.187 1771 Planarity : 0.004 0.037 1850 Dihedral : 3.349 14.401 1476 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.24), residues: 1318 helix: 1.41 (0.18), residues: 833 sheet: -2.08 (0.44), residues: 96 loop : -1.50 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 513 HIS 0.005 0.001 HIS F 122 PHE 0.010 0.001 PHE D 481 TYR 0.016 0.001 TYR F 190 ARG 0.005 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8958 (tp30) cc_final: 0.8737 (tp30) REVERT: A 249 MET cc_start: 0.9027 (mmp) cc_final: 0.8791 (tpp) REVERT: A 349 LEU cc_start: 0.8665 (mt) cc_final: 0.8448 (tt) REVERT: A 380 TRP cc_start: 0.8854 (t-100) cc_final: 0.8488 (t-100) REVERT: B 76 LYS cc_start: 0.9397 (tmtt) cc_final: 0.9165 (tptp) REVERT: D 100 TRP cc_start: 0.9496 (m100) cc_final: 0.8914 (m100) REVERT: E 123 ASN cc_start: 0.8968 (m-40) cc_final: 0.8733 (m110) outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.2131 time to fit residues: 32.6336 Evaluate side-chains 69 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 33 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 87 optimal weight: 0.0870 chunk 77 optimal weight: 9.9990 chunk 115 optimal weight: 0.0470 chunk 62 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 overall best weight: 2.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 192 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 HIS F 101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.047526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.036997 restraints weight = 80800.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.038015 restraints weight = 45117.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.038618 restraints weight = 30553.684| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10921 Z= 0.197 Angle : 0.540 12.977 14818 Z= 0.261 Chirality : 0.038 0.138 1771 Planarity : 0.003 0.037 1850 Dihedral : 3.314 16.038 1476 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.24), residues: 1318 helix: 1.86 (0.18), residues: 832 sheet: -1.89 (0.45), residues: 88 loop : -1.14 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 35 HIS 0.003 0.001 HIS E 88 PHE 0.007 0.001 PHE A 219 TYR 0.015 0.001 TYR E 75 ARG 0.002 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8942 (tp30) cc_final: 0.8696 (tp30) REVERT: A 249 MET cc_start: 0.9021 (mmp) cc_final: 0.8765 (tpp) REVERT: A 349 LEU cc_start: 0.8740 (mt) cc_final: 0.8429 (tt) REVERT: A 380 TRP cc_start: 0.8849 (t-100) cc_final: 0.8510 (t-100) REVERT: C 31 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8525 (mm-30) REVERT: C 49 LYS cc_start: 0.9426 (ptmt) cc_final: 0.9181 (ptmm) REVERT: B 76 LYS cc_start: 0.9369 (tmtt) cc_final: 0.9167 (tptt) REVERT: D 100 TRP cc_start: 0.9519 (m100) cc_final: 0.8935 (m100) REVERT: D 608 MET cc_start: 0.8969 (ptp) cc_final: 0.8633 (ptp) REVERT: E 123 ASN cc_start: 0.9016 (m-40) cc_final: 0.8736 (m110) REVERT: E 141 ILE cc_start: 0.9312 (mm) cc_final: 0.8995 (tt) REVERT: F 87 MET cc_start: 0.9013 (tpt) cc_final: 0.8124 (tpp) REVERT: F 177 ARG cc_start: 0.8518 (mtt90) cc_final: 0.8271 (mtt-85) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2111 time to fit residues: 31.9759 Evaluate side-chains 69 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 95 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 134 optimal weight: 40.0000 chunk 38 optimal weight: 0.0570 chunk 112 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 overall best weight: 3.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.046557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.036142 restraints weight = 80135.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.037084 restraints weight = 45129.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.037729 restraints weight = 30736.179| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10921 Z= 0.270 Angle : 0.584 13.683 14818 Z= 0.287 Chirality : 0.039 0.162 1771 Planarity : 0.003 0.038 1850 Dihedral : 3.459 17.038 1476 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.24), residues: 1318 helix: 1.97 (0.18), residues: 833 sheet: -1.50 (0.47), residues: 88 loop : -0.81 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 159 HIS 0.005 0.001 HIS E 88 PHE 0.008 0.001 PHE D 323 TYR 0.014 0.001 TYR F 190 ARG 0.006 0.000 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8884 (tp30) cc_final: 0.8613 (tp30) REVERT: A 249 MET cc_start: 0.9044 (mmp) cc_final: 0.8819 (tpp) REVERT: A 380 TRP cc_start: 0.8831 (t-100) cc_final: 0.8539 (t-100) REVERT: C 31 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8488 (mm-30) REVERT: B 76 LYS cc_start: 0.9342 (tmtt) cc_final: 0.9138 (tptt) REVERT: D 100 TRP cc_start: 0.9500 (m100) cc_final: 0.8841 (m100) REVERT: D 525 ILE cc_start: 0.9408 (mt) cc_final: 0.9162 (mt) REVERT: E 141 ILE cc_start: 0.9302 (mm) cc_final: 0.9011 (tt) REVERT: F 66 MET cc_start: 0.9002 (mmp) cc_final: 0.8797 (mmm) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1965 time to fit residues: 26.7607 Evaluate side-chains 63 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 134 optimal weight: 50.0000 chunk 107 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 chunk 133 optimal weight: 30.0000 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.046422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.036140 restraints weight = 79687.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.037101 restraints weight = 44721.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.037740 restraints weight = 30297.618| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10921 Z= 0.250 Angle : 0.573 13.598 14818 Z= 0.281 Chirality : 0.040 0.154 1771 Planarity : 0.004 0.041 1850 Dihedral : 3.504 17.769 1476 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.24), residues: 1318 helix: 2.10 (0.18), residues: 833 sheet: -1.27 (0.49), residues: 88 loop : -0.63 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 159 HIS 0.005 0.001 HIS E 88 PHE 0.014 0.001 PHE A 254 TYR 0.014 0.001 TYR F 190 ARG 0.003 0.000 ARG E 186 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8849 (tp30) cc_final: 0.8610 (tp30) REVERT: A 249 MET cc_start: 0.9061 (mmp) cc_final: 0.8795 (tpp) REVERT: A 380 TRP cc_start: 0.8778 (t-100) cc_final: 0.8517 (t-100) REVERT: C 31 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8430 (mm-30) REVERT: D 29 MET cc_start: 0.9206 (mmp) cc_final: 0.9001 (mmm) REVERT: D 525 ILE cc_start: 0.9415 (mt) cc_final: 0.9199 (mt) REVERT: E 141 ILE cc_start: 0.9318 (mm) cc_final: 0.9070 (tt) REVERT: F 108 MET cc_start: 0.9141 (mtm) cc_final: 0.8407 (mtm) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1842 time to fit residues: 25.9079 Evaluate side-chains 61 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 96 optimal weight: 7.9990 chunk 129 optimal weight: 0.0050 chunk 30 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 116 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 overall best weight: 4.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.045593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.035396 restraints weight = 80765.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.036342 restraints weight = 45299.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.036923 restraints weight = 30706.874| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10921 Z= 0.334 Angle : 0.630 13.933 14818 Z= 0.313 Chirality : 0.040 0.135 1771 Planarity : 0.004 0.039 1850 Dihedral : 3.690 18.680 1476 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.24), residues: 1318 helix: 1.98 (0.18), residues: 836 sheet: -1.30 (0.49), residues: 90 loop : -0.52 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 159 HIS 0.005 0.001 HIS E 88 PHE 0.012 0.001 PHE A 159 TYR 0.016 0.002 TYR F 190 ARG 0.003 0.000 ARG E 186 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8861 (tp30) cc_final: 0.8580 (tp30) REVERT: A 249 MET cc_start: 0.9079 (mmp) cc_final: 0.8818 (tpp) REVERT: A 380 TRP cc_start: 0.8790 (t-100) cc_final: 0.8542 (t-100) REVERT: C 31 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8464 (mm-30) REVERT: D 525 ILE cc_start: 0.9413 (mt) cc_final: 0.9161 (mt) REVERT: E 141 ILE cc_start: 0.9356 (mm) cc_final: 0.9114 (tt) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1870 time to fit residues: 23.6646 Evaluate side-chains 61 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 48 optimal weight: 0.0020 chunk 115 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 192 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.046629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.036327 restraints weight = 81314.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.037308 restraints weight = 45101.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.037962 restraints weight = 30376.537| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10921 Z= 0.196 Angle : 0.551 12.587 14818 Z= 0.268 Chirality : 0.039 0.133 1771 Planarity : 0.003 0.040 1850 Dihedral : 3.537 18.146 1476 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.24), residues: 1318 helix: 2.16 (0.18), residues: 836 sheet: -1.15 (0.51), residues: 88 loop : -0.40 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 35 HIS 0.004 0.001 HIS D 330 PHE 0.012 0.001 PHE A 254 TYR 0.014 0.001 TYR F 190 ARG 0.003 0.000 ARG E 186 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.9038 (mmp) cc_final: 0.8802 (tpp) REVERT: A 380 TRP cc_start: 0.8713 (t-100) cc_final: 0.8468 (t-100) REVERT: C 31 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8456 (mm-30) REVERT: B 59 PHE cc_start: 0.9061 (m-10) cc_final: 0.8522 (t80) REVERT: D 29 MET cc_start: 0.9188 (mmp) cc_final: 0.8972 (mmm) REVERT: D 525 ILE cc_start: 0.9403 (mt) cc_final: 0.9199 (mt) REVERT: E 141 ILE cc_start: 0.9334 (mm) cc_final: 0.9100 (tt) REVERT: F 108 MET cc_start: 0.9077 (mtm) cc_final: 0.8333 (mtm) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1789 time to fit residues: 25.2455 Evaluate side-chains 64 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 107 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.045787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.035520 restraints weight = 80778.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.036455 restraints weight = 45148.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.037049 restraints weight = 30567.724| |-----------------------------------------------------------------------------| r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10921 Z= 0.295 Angle : 0.605 13.553 14818 Z= 0.300 Chirality : 0.040 0.132 1771 Planarity : 0.004 0.038 1850 Dihedral : 3.680 19.269 1476 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.24), residues: 1318 helix: 2.02 (0.18), residues: 841 sheet: -1.25 (0.50), residues: 88 loop : -0.56 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 159 HIS 0.005 0.001 HIS E 88 PHE 0.013 0.001 PHE D 435 TYR 0.017 0.001 TYR F 190 ARG 0.003 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.9079 (mmp) cc_final: 0.8827 (tpp) REVERT: A 380 TRP cc_start: 0.8748 (t-100) cc_final: 0.8504 (t-100) REVERT: C 31 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8437 (mm-30) REVERT: B 59 PHE cc_start: 0.9095 (m-10) cc_final: 0.8561 (t80) REVERT: D 525 ILE cc_start: 0.9279 (mt) cc_final: 0.9078 (mt) REVERT: E 141 ILE cc_start: 0.9339 (mm) cc_final: 0.9114 (tt) REVERT: F 108 MET cc_start: 0.9143 (mtm) cc_final: 0.8434 (mtm) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1843 time to fit residues: 24.1680 Evaluate side-chains 61 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 62 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.046798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.036514 restraints weight = 80865.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.037504 restraints weight = 44785.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.038175 restraints weight = 30097.388| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10921 Z= 0.167 Angle : 0.559 12.305 14818 Z= 0.269 Chirality : 0.039 0.139 1771 Planarity : 0.003 0.040 1850 Dihedral : 3.546 18.203 1476 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.24), residues: 1318 helix: 2.13 (0.18), residues: 843 sheet: -1.13 (0.50), residues: 88 loop : -0.43 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 14 HIS 0.003 0.001 HIS E 88 PHE 0.026 0.001 PHE F 62 TYR 0.016 0.001 TYR A 237 ARG 0.002 0.000 ARG E 186 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.9017 (mmp) cc_final: 0.8798 (tpp) REVERT: C 31 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8338 (mm-30) REVERT: B 59 PHE cc_start: 0.9078 (m-10) cc_final: 0.8506 (t80) REVERT: D 29 MET cc_start: 0.9161 (mmp) cc_final: 0.8949 (mmm) REVERT: F 29 ASP cc_start: 0.8186 (m-30) cc_final: 0.7984 (m-30) REVERT: F 108 MET cc_start: 0.9130 (mtm) cc_final: 0.8802 (mtt) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1807 time to fit residues: 23.5883 Evaluate side-chains 61 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 35 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 121 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.046054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.035913 restraints weight = 80829.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.036875 restraints weight = 45044.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.037528 restraints weight = 30354.616| |-----------------------------------------------------------------------------| r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10921 Z= 0.248 Angle : 0.584 12.790 14818 Z= 0.286 Chirality : 0.039 0.134 1771 Planarity : 0.003 0.039 1850 Dihedral : 3.588 18.931 1476 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.24), residues: 1318 helix: 2.01 (0.18), residues: 850 sheet: -1.14 (0.51), residues: 88 loop : -0.42 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 14 HIS 0.003 0.001 HIS E 88 PHE 0.025 0.001 PHE F 62 TYR 0.017 0.001 TYR A 237 ARG 0.003 0.000 ARG E 186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.9046 (mmp) cc_final: 0.8817 (tpp) REVERT: C 31 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8348 (mm-30) REVERT: B 59 PHE cc_start: 0.9084 (m-10) cc_final: 0.8538 (t80) REVERT: D 29 MET cc_start: 0.9142 (mmp) cc_final: 0.8922 (mmm) REVERT: D 525 ILE cc_start: 0.9312 (mt) cc_final: 0.9040 (mt) REVERT: F 108 MET cc_start: 0.9128 (mtm) cc_final: 0.8906 (mtm) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1997 time to fit residues: 24.4297 Evaluate side-chains 61 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 109 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 85 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 40 optimal weight: 0.0060 chunk 60 optimal weight: 0.9990 overall best weight: 1.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN E 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.046900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.036608 restraints weight = 80052.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.037595 restraints weight = 44415.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.038183 restraints weight = 29940.255| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10921 Z= 0.161 Angle : 0.543 12.061 14818 Z= 0.261 Chirality : 0.038 0.137 1771 Planarity : 0.003 0.041 1850 Dihedral : 3.469 17.972 1476 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.09 % Allowed : 0.36 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.24), residues: 1318 helix: 2.16 (0.18), residues: 849 sheet: -1.09 (0.51), residues: 88 loop : -0.36 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP D 14 HIS 0.003 0.001 HIS F 122 PHE 0.020 0.001 PHE F 62 TYR 0.015 0.001 TYR A 237 ARG 0.002 0.000 ARG E 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2644.34 seconds wall clock time: 48 minutes 43.47 seconds (2923.47 seconds total)