Starting phenix.real_space_refine on Wed Mar 4 04:15:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kap_22779/03_2026/7kap_22779.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kap_22779/03_2026/7kap_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_22779/03_2026/7kap_22779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kap_22779/03_2026/7kap_22779.map" model { file = "/net/cci-nas-00/data/ceres_data/7kap_22779/03_2026/7kap_22779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kap_22779/03_2026/7kap_22779.cif" } resolution = 4.1 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= 0.009 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2} 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: {'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: 2.42, per 1000 atoms: 0.23 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: 0.95 Conformation dependent library (CDL) restraints added in 570.5 milliseconds 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: 0.26 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: 1.66 Time building geometry restraints manager: 1.28 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.460 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.510 ------------------------------------------------------------------------------- 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= 0.136 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 : 7.95 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (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 ARG 0.002 0.000 ARG A 25 TYR 0.014 0.001 TYR F 190 PHE 0.009 0.001 PHE A 92 TRP 0.008 0.001 TRP A 380 HIS 0.006 0.001 HIS D 334 Details of bonding type rmsd covalent geometry : bond 0.00272 (10921) covalent geometry : angle 0.54538 (14818) hydrogen bonds : bond 0.12947 ( 692) hydrogen bonds : angle 4.97082 ( 2028) *********************** 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 : 0.461 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: 0.0945 time to fit residues: 20.9860 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 : 0.317 ------------------------------------------------------------------------------- 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: 6.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.0170 chunk 122 optimal weight: 0.0980 chunk 91 optimal weight: 0.1980 chunk 55 optimal weight: 9.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 GLN A 398 GLN D 4 ASN D 307 GLN D 381 HIS 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 Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.049419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.038941 restraints weight = 80404.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.040005 restraints weight = 44309.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.040725 restraints weight = 29676.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.041197 restraints weight = 22568.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.041438 restraints weight = 18759.320| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10921 Z= 0.099 Angle : 0.537 13.260 14818 Z= 0.256 Chirality : 0.038 0.194 1771 Planarity : 0.003 0.036 1850 Dihedral : 3.158 13.155 1476 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.09 % Allowed : 2.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.23), residues: 1318 helix: 1.31 (0.18), residues: 834 sheet: -2.32 (0.44), residues: 90 loop : -1.58 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 76 TYR 0.013 0.001 TYR F 190 PHE 0.009 0.001 PHE A 256 TRP 0.006 0.001 TRP A 35 HIS 0.003 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00209 (10921) covalent geometry : angle 0.53748 (14818) hydrogen bonds : bond 0.03154 ( 692) hydrogen bonds : angle 3.79281 ( 2028) *********************** 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 111 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8828 (tp30) cc_final: 0.8620 (tp30) REVERT: A 249 MET cc_start: 0.8917 (mmp) cc_final: 0.8716 (tpp) REVERT: A 349 LEU cc_start: 0.8681 (mt) cc_final: 0.8432 (tt) REVERT: A 376 PHE cc_start: 0.9409 (m-10) cc_final: 0.9185 (m-10) REVERT: A 380 TRP cc_start: 0.8795 (t-100) cc_final: 0.8373 (t-100) REVERT: C 36 LEU cc_start: 0.9427 (tt) cc_final: 0.9196 (mm) REVERT: B 76 LYS cc_start: 0.9410 (tmtt) cc_final: 0.9163 (tptp) REVERT: D 100 TRP cc_start: 0.9433 (m100) cc_final: 0.8798 (m100) REVERT: E 75 TYR cc_start: 0.8728 (t80) cc_final: 0.8488 (t80) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.0947 time to fit residues: 15.9268 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 : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 125 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 0.0020 chunk 16 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 120 optimal weight: 0.1980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.049551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.039129 restraints weight = 79493.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.040149 restraints weight = 44145.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.040872 restraints weight = 29836.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.041248 restraints weight = 22596.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.041602 restraints weight = 19034.498| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10921 Z= 0.091 Angle : 0.512 11.758 14818 Z= 0.242 Chirality : 0.037 0.142 1771 Planarity : 0.003 0.037 1850 Dihedral : 3.080 12.855 1476 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.23), residues: 1318 helix: 1.73 (0.18), residues: 833 sheet: -1.88 (0.45), residues: 90 loop : -1.36 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 92 TYR 0.011 0.001 TYR F 190 PHE 0.007 0.001 PHE D 481 TRP 0.007 0.001 TRP A 35 HIS 0.002 0.000 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00191 (10921) covalent geometry : angle 0.51249 (14818) hydrogen bonds : bond 0.02815 ( 692) hydrogen bonds : angle 3.58743 ( 2028) *********************** 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 : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8820 (tp30) cc_final: 0.8612 (tp30) REVERT: A 220 HIS cc_start: 0.9159 (t70) cc_final: 0.8896 (t70) REVERT: A 249 MET cc_start: 0.8906 (mmp) cc_final: 0.8691 (tpp) REVERT: A 349 LEU cc_start: 0.8623 (mt) cc_final: 0.8410 (tt) REVERT: A 376 PHE cc_start: 0.9401 (m-10) cc_final: 0.9181 (m-10) REVERT: C 36 LEU cc_start: 0.9395 (tt) cc_final: 0.9168 (mm) REVERT: B 76 LYS cc_start: 0.9410 (tmtt) cc_final: 0.9153 (tptp) REVERT: D 100 TRP cc_start: 0.9450 (m100) cc_final: 0.8790 (m100) REVERT: E 75 TYR cc_start: 0.8690 (t80) cc_final: 0.8342 (t80) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.0891 time to fit residues: 13.7372 Evaluate side-chains 66 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 4 optimal weight: 0.0970 chunk 26 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- 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 403 ASN D 330 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.047259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.036810 restraints weight = 81298.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.037809 restraints weight = 45188.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.038475 restraints weight = 30417.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.038933 restraints weight = 23213.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.039081 restraints weight = 19359.597| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10921 Z= 0.166 Angle : 0.565 13.281 14818 Z= 0.273 Chirality : 0.039 0.209 1771 Planarity : 0.003 0.038 1850 Dihedral : 3.224 15.404 1476 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.24), residues: 1318 helix: 1.94 (0.18), residues: 837 sheet: -1.43 (0.47), residues: 88 loop : -1.04 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 92 TYR 0.013 0.001 TYR F 190 PHE 0.013 0.001 PHE A 254 TRP 0.009 0.001 TRP D 513 HIS 0.004 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00370 (10921) covalent geometry : angle 0.56455 (14818) hydrogen bonds : bond 0.02942 ( 692) hydrogen bonds : angle 3.66898 ( 2028) *********************** 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 : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLU cc_start: 0.8841 (tp30) cc_final: 0.8591 (tp30) REVERT: A 349 LEU cc_start: 0.8706 (mt) cc_final: 0.8383 (tt) REVERT: D 100 TRP cc_start: 0.9445 (m100) cc_final: 0.8893 (m100) REVERT: D 608 MET cc_start: 0.8955 (ptp) cc_final: 0.8701 (ptp) REVERT: E 75 TYR cc_start: 0.8821 (t80) cc_final: 0.8608 (t80) REVERT: E 141 ILE cc_start: 0.9291 (mm) cc_final: 0.8996 (tt) REVERT: F 90 ARG cc_start: 0.8630 (tpp-160) cc_final: 0.8280 (tpp80) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0915 time to fit residues: 12.4561 Evaluate side-chains 62 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 43 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3169 r_free = 0.3169 target = 0.047871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.037382 restraints weight = 80969.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.038376 restraints weight = 44982.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.039058 restraints weight = 30395.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.039468 restraints weight = 23222.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.039763 restraints weight = 19479.435| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10921 Z= 0.120 Angle : 0.529 12.664 14818 Z= 0.252 Chirality : 0.038 0.155 1771 Planarity : 0.003 0.039 1850 Dihedral : 3.232 15.555 1476 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.24), residues: 1318 helix: 2.08 (0.18), residues: 837 sheet: -1.19 (0.49), residues: 88 loop : -0.81 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 509 TYR 0.012 0.001 TYR A 237 PHE 0.013 0.001 PHE A 254 TRP 0.006 0.001 TRP D 513 HIS 0.003 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00266 (10921) covalent geometry : angle 0.52869 (14818) hydrogen bonds : bond 0.02767 ( 692) hydrogen bonds : angle 3.61345 ( 2028) *********************** 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 85 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 PHE cc_start: 0.9104 (t80) cc_final: 0.8897 (t80) REVERT: C 31 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8373 (mm-30) REVERT: B 76 LYS cc_start: 0.9368 (tmtt) cc_final: 0.9139 (tptp) REVERT: D 100 TRP cc_start: 0.9463 (m100) cc_final: 0.8892 (m100) REVERT: E 141 ILE cc_start: 0.9281 (mm) cc_final: 0.8985 (tt) REVERT: F 87 MET cc_start: 0.8890 (tpp) cc_final: 0.8570 (tpp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.0872 time to fit residues: 11.3669 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 : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 100 optimal weight: 9.9990 chunk 29 optimal weight: 30.0000 chunk 117 optimal weight: 0.0020 chunk 16 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 overall best weight: 4.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 192 GLN D 416 ASN F 45 ASN ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.045859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.035551 restraints weight = 81464.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.036496 restraints weight = 45833.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.037108 restraints weight = 31184.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.037466 restraints weight = 24071.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.037814 restraints weight = 20423.841| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 10921 Z= 0.236 Angle : 0.645 13.728 14818 Z= 0.318 Chirality : 0.041 0.140 1771 Planarity : 0.004 0.037 1850 Dihedral : 3.641 17.782 1476 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.24), residues: 1318 helix: 2.01 (0.18), residues: 834 sheet: -1.15 (0.50), residues: 88 loop : -0.61 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 510 TYR 0.015 0.002 TYR F 190 PHE 0.020 0.002 PHE D 343 TRP 0.017 0.002 TRP E 159 HIS 0.009 0.002 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00509 (10921) covalent geometry : angle 0.64495 (14818) hydrogen bonds : bond 0.03288 ( 692) hydrogen bonds : angle 3.96356 ( 2028) *********************** 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 79 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 PHE cc_start: 0.9177 (t80) cc_final: 0.8926 (t80) REVERT: A 249 MET cc_start: 0.8781 (mmt) cc_final: 0.8574 (tpp) REVERT: C 31 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8363 (mm-30) REVERT: D 29 MET cc_start: 0.9108 (mmt) cc_final: 0.8897 (mmm) REVERT: E 141 ILE cc_start: 0.9318 (mm) cc_final: 0.9075 (tt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0878 time to fit residues: 10.7488 Evaluate side-chains 55 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 15 optimal weight: 6.9990 chunk 90 optimal weight: 0.0770 chunk 54 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.7142 ------------------------------------------------------------------------------- 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 F 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.047633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.037413 restraints weight = 79986.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.038416 restraints weight = 43459.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.039080 restraints weight = 28874.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.039566 restraints weight = 21898.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.039907 restraints weight = 18095.209| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10921 Z= 0.098 Angle : 0.539 11.576 14818 Z= 0.256 Chirality : 0.039 0.179 1771 Planarity : 0.003 0.040 1850 Dihedral : 3.360 16.796 1476 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.09 % Allowed : 0.90 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.24), residues: 1318 helix: 2.22 (0.18), residues: 836 sheet: -1.03 (0.49), residues: 90 loop : -0.44 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 186 TYR 0.010 0.001 TYR E 75 PHE 0.015 0.001 PHE A 254 TRP 0.011 0.001 TRP D 14 HIS 0.002 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00214 (10921) covalent geometry : angle 0.53877 (14818) hydrogen bonds : bond 0.02837 ( 692) hydrogen bonds : angle 3.62485 ( 2028) *********************** 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 90 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 PHE cc_start: 0.9099 (t80) cc_final: 0.8898 (t80) REVERT: C 31 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8432 (mm-30) REVERT: D 29 MET cc_start: 0.9090 (mmt) cc_final: 0.8864 (mmm) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.0882 time to fit residues: 12.2430 Evaluate side-chains 62 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 9 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN F 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.046500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.036264 restraints weight = 80543.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.037209 restraints weight = 44572.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.037876 restraints weight = 30214.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.038277 restraints weight = 23012.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.038502 restraints weight = 19290.397| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10921 Z= 0.173 Angle : 0.575 12.491 14818 Z= 0.279 Chirality : 0.039 0.137 1771 Planarity : 0.003 0.038 1850 Dihedral : 3.417 17.816 1476 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.09 % Allowed : 0.63 % Favored : 99.28 % 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 are not related in a simple way. whole: 1.85 (0.24), residues: 1318 helix: 2.22 (0.18), residues: 835 sheet: -0.93 (0.50), residues: 88 loop : -0.39 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 186 TYR 0.013 0.001 TYR F 190 PHE 0.009 0.001 PHE A 254 TRP 0.012 0.001 TRP D 14 HIS 0.004 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00382 (10921) covalent geometry : angle 0.57471 (14818) hydrogen bonds : bond 0.02935 ( 692) hydrogen bonds : angle 3.73456 ( 2028) *********************** 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 82 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 PHE cc_start: 0.9106 (t80) cc_final: 0.8897 (t80) REVERT: C 31 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8373 (mm-30) REVERT: D 29 MET cc_start: 0.9077 (mmt) cc_final: 0.8852 (mmm) REVERT: E 141 ILE cc_start: 0.9314 (mm) cc_final: 0.9051 (tt) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.0898 time to fit residues: 11.3342 Evaluate side-chains 60 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 32 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 57 optimal weight: 0.0980 chunk 102 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 192 GLN F 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.046851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.036539 restraints weight = 79416.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.037545 restraints weight = 43037.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.038198 restraints weight = 28603.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.038619 restraints weight = 21797.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.038951 restraints weight = 18231.418| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10921 Z= 0.163 Angle : 0.570 12.370 14818 Z= 0.277 Chirality : 0.039 0.131 1771 Planarity : 0.003 0.039 1850 Dihedral : 3.460 18.213 1476 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.09 % Allowed : 0.54 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.24), residues: 1318 helix: 2.22 (0.18), residues: 835 sheet: -1.06 (0.50), residues: 90 loop : -0.35 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 90 TYR 0.013 0.001 TYR F 190 PHE 0.009 0.001 PHE A 254 TRP 0.012 0.001 TRP D 14 HIS 0.004 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00363 (10921) covalent geometry : angle 0.57019 (14818) hydrogen bonds : bond 0.02981 ( 692) hydrogen bonds : angle 3.73817 ( 2028) *********************** 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 83 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 31 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8374 (mm-30) REVERT: D 29 MET cc_start: 0.9018 (mmt) cc_final: 0.8778 (mmm) REVERT: F 182 GLU cc_start: 0.8948 (tt0) cc_final: 0.8746 (tt0) outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 0.0902 time to fit residues: 11.5027 Evaluate side-chains 59 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 100 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 8 optimal weight: 0.0980 chunk 121 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 192 GLN D 416 ASN F 70 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.047714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.037537 restraints weight = 79888.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.038565 restraints weight = 43439.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.039235 restraints weight = 28890.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.039747 restraints weight = 21965.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.040117 restraints weight = 17973.584| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10921 Z= 0.096 Angle : 0.528 11.521 14818 Z= 0.250 Chirality : 0.038 0.136 1771 Planarity : 0.003 0.040 1850 Dihedral : 3.303 17.587 1476 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.09 % Allowed : 0.18 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.24), residues: 1318 helix: 2.24 (0.18), residues: 843 sheet: -0.90 (0.50), residues: 90 loop : -0.35 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 25 TYR 0.011 0.001 TYR F 190 PHE 0.014 0.001 PHE A 254 TRP 0.020 0.001 TRP D 14 HIS 0.002 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00209 (10921) covalent geometry : angle 0.52797 (14818) hydrogen bonds : bond 0.02762 ( 692) hydrogen bonds : angle 3.57655 ( 2028) ********************** 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 86 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8215 (mmp) cc_final: 0.7895 (mpp) REVERT: A 249 MET cc_start: 0.8648 (mmt) cc_final: 0.8156 (mpp) REVERT: C 31 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8428 (mm-30) REVERT: D 29 MET cc_start: 0.9018 (mmt) cc_final: 0.8803 (mmm) REVERT: E 141 ILE cc_start: 0.9303 (mm) cc_final: 0.9066 (tt) REVERT: F 29 ASP cc_start: 0.8138 (m-30) cc_final: 0.7933 (m-30) REVERT: F 108 MET cc_start: 0.9095 (mtm) cc_final: 0.8371 (mtm) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.0892 time to fit residues: 11.8323 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 : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 86 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 7 optimal weight: 0.0770 chunk 89 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 75 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 192 GLN F 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.047443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.037312 restraints weight = 80422.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.038313 restraints weight = 44379.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.038936 restraints weight = 29730.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.039417 restraints weight = 22984.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.039662 restraints weight = 18902.233| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10921 Z= 0.109 Angle : 0.542 11.418 14818 Z= 0.256 Chirality : 0.038 0.136 1771 Planarity : 0.003 0.041 1850 Dihedral : 3.275 17.239 1476 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.09 % Allowed : 0.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.24), residues: 1318 helix: 2.25 (0.18), residues: 842 sheet: -0.80 (0.51), residues: 90 loop : -0.33 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 186 TYR 0.012 0.001 TYR F 190 PHE 0.013 0.001 PHE B 64 TRP 0.040 0.001 TRP D 14 HIS 0.002 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00241 (10921) covalent geometry : angle 0.54212 (14818) hydrogen bonds : bond 0.02777 ( 692) hydrogen bonds : angle 3.56077 ( 2028) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1616.90 seconds wall clock time: 28 minutes 48.26 seconds (1728.26 seconds total)