Starting phenix.real_space_refine on Thu May 15 12:48:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ew0_28639/05_2025/8ew0_28639.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ew0_28639/05_2025/8ew0_28639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ew0_28639/05_2025/8ew0_28639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ew0_28639/05_2025/8ew0_28639.map" model { file = "/net/cci-nas-00/data/ceres_data/8ew0_28639/05_2025/8ew0_28639.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ew0_28639/05_2025/8ew0_28639.cif" } resolution = 2.7 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 ------------------------------------------------------------------------------- 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= -0.000 sd= 0.010 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 72 5.16 5 C 8588 2.51 5 N 2419 2.21 5 O 2557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 98 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13636 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2276 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 280} Chain breaks: 2 Chain: "B" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2268 Classifications: {'peptide': 290} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 278} Chain breaks: 2 Chain: "C" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2272 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 279} Chain breaks: 2 Chain: "D" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2272 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 279} Chain breaks: 2 Chain: "E" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2276 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 280} Chain breaks: 2 Chain: "F" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2272 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 279} Chain breaks: 2 Time building chain proxies: 7.95, per 1000 atoms: 0.58 Number of scatterers: 13636 At special positions: 0 Unit cell: (91.84, 95.94, 155.8, 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 72 16.00 O 2557 8.00 N 2419 7.00 C 8588 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: 2.95 Conformation dependent library (CDL) restraints added in 1.7 seconds 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3168 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 3 sheets defined 59.8% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 100 through 118 Processing helix chain 'A' and resid 132 through 136 removed outlier: 3.548A pdb=" N TYR A 136 " --> pdb=" O PRO A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 155 Processing helix chain 'A' and resid 172 through 186 Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.527A pdb=" N CYS A 197 " --> pdb=" O ALA A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 214 through 226 Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 375 through 391 Processing helix chain 'A' and resid 398 through 421 removed outlier: 3.603A pdb=" N LYS A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 Processing helix chain 'A' and resid 444 through 471 removed outlier: 3.804A pdb=" N ILE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 489 removed outlier: 3.550A pdb=" N ALA A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 118 Processing helix chain 'B' and resid 132 through 136 removed outlier: 3.584A pdb=" N TYR B 136 " --> pdb=" O PRO B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 155 Processing helix chain 'B' and resid 172 through 186 Processing helix chain 'B' and resid 193 through 198 removed outlier: 3.557A pdb=" N CYS B 197 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL B 198 " --> pdb=" O HIS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 226 Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 375 through 391 Processing helix chain 'B' and resid 398 through 421 Processing helix chain 'B' and resid 433 through 442 Processing helix chain 'B' and resid 444 through 471 removed outlier: 3.806A pdb=" N ILE B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 489 Processing helix chain 'C' and resid 100 through 118 Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 137 through 155 Processing helix chain 'C' and resid 172 through 186 Processing helix chain 'C' and resid 193 through 198 removed outlier: 4.218A pdb=" N VAL C 198 " --> pdb=" O HIS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 226 removed outlier: 3.546A pdb=" N PHE C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 391 Processing helix chain 'C' and resid 398 through 421 Processing helix chain 'C' and resid 433 through 442 Processing helix chain 'C' and resid 444 through 471 removed outlier: 3.867A pdb=" N ILE C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 489 removed outlier: 3.515A pdb=" N ALA C 480 " --> pdb=" O ASP C 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 118 Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 137 through 155 removed outlier: 3.674A pdb=" N LYS D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 187 removed outlier: 3.522A pdb=" N MET D 176 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 197 removed outlier: 3.511A pdb=" N CYS D 197 " --> pdb=" O ALA D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 213 through 226 Processing helix chain 'D' and resid 375 through 391 Processing helix chain 'D' and resid 398 through 421 Processing helix chain 'D' and resid 433 through 442 Processing helix chain 'D' and resid 444 through 471 removed outlier: 3.830A pdb=" N ILE D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 489 removed outlier: 3.590A pdb=" N ALA D 480 " --> pdb=" O ASP D 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 118 Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 137 through 155 Processing helix chain 'E' and resid 172 through 186 Processing helix chain 'E' and resid 193 through 198 removed outlier: 4.023A pdb=" N VAL E 198 " --> pdb=" O HIS E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 213 through 226 Processing helix chain 'E' and resid 375 through 391 Processing helix chain 'E' and resid 398 through 421 Processing helix chain 'E' and resid 433 through 442 Processing helix chain 'E' and resid 444 through 471 removed outlier: 3.836A pdb=" N ILE E 448 " --> pdb=" O SER E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 489 removed outlier: 3.771A pdb=" N ALA E 480 " --> pdb=" O ASP E 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 118 Processing helix chain 'F' and resid 132 through 136 Processing helix chain 'F' and resid 137 through 155 Processing helix chain 'F' and resid 172 through 187 Processing helix chain 'F' and resid 193 through 198 removed outlier: 4.280A pdb=" N VAL F 198 " --> pdb=" O HIS F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 226 Processing helix chain 'F' and resid 375 through 391 Processing helix chain 'F' and resid 398 through 421 removed outlier: 3.574A pdb=" N PHE F 421 " --> pdb=" O LEU F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 442 Processing helix chain 'F' and resid 444 through 471 removed outlier: 3.873A pdb=" N ILE F 448 " --> pdb=" O SER F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 489 removed outlier: 3.550A pdb=" N ALA F 480 " --> pdb=" O ASP F 476 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 163 through 166 removed outlier: 6.510A pdb=" N CYS A 89 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ALA A 166 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY A 91 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LYS A 90 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ALA A 127 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY A 92 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VAL A 129 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ARG A 94 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LYS E 90 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ALA E 127 " --> pdb=" O LYS E 90 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLY E 92 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL E 129 " --> pdb=" O GLY E 92 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ARG E 94 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS E 89 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ALA E 166 " --> pdb=" O CYS E 89 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY E 91 " --> pdb=" O ALA E 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 163 through 166 removed outlier: 6.535A pdb=" N CYS B 89 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ALA B 166 " --> pdb=" O CYS B 89 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY B 91 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LYS B 90 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ALA B 127 " --> pdb=" O LYS B 90 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLY B 92 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL B 129 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ARG B 94 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LYS D 90 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ALA D 127 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLY D 92 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL D 129 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG D 94 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N CYS D 89 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ALA D 166 " --> pdb=" O CYS D 89 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY D 91 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 163 through 166 removed outlier: 6.569A pdb=" N CYS C 89 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ALA C 166 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY C 91 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LYS C 90 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ALA C 127 " --> pdb=" O LYS C 90 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY C 92 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL C 129 " --> pdb=" O GLY C 92 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ARG C 94 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY F 92 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N CYS F 89 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ALA F 166 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY F 91 " --> pdb=" O ALA F 166 " (cutoff:3.500A) 854 hydrogen bonds defined for protein. 2469 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: 3.97 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4512 1.34 - 1.46: 2958 1.46 - 1.58: 6334 1.58 - 1.70: 0 1.70 - 1.81: 120 Bond restraints: 13924 Sorted by residual: bond pdb=" C ARG C 86 " pdb=" N THR C 87 " ideal model delta sigma weight residual 1.331 1.276 0.055 1.36e-02 5.41e+03 1.64e+01 bond pdb=" C LYS C 53 " pdb=" N PRO C 54 " ideal model delta sigma weight residual 1.329 1.353 -0.024 1.20e-02 6.94e+03 4.03e+00 bond pdb=" C LYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 1.329 1.353 -0.024 1.20e-02 6.94e+03 4.00e+00 bond pdb=" C LYS B 53 " pdb=" N PRO B 54 " ideal model delta sigma weight residual 1.329 1.352 -0.023 1.20e-02 6.94e+03 3.80e+00 bond pdb=" C LYS F 53 " pdb=" N PRO F 54 " ideal model delta sigma weight residual 1.329 1.351 -0.023 1.20e-02 6.94e+03 3.59e+00 ... (remaining 13919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 18552 2.05 - 4.10: 227 4.10 - 6.15: 16 6.15 - 8.20: 0 8.20 - 10.25: 2 Bond angle restraints: 18797 Sorted by residual: angle pdb=" N ILE F 430 " pdb=" CA ILE F 430 " pdb=" C ILE F 430 " ideal model delta sigma weight residual 113.47 108.65 4.82 1.01e+00 9.80e-01 2.27e+01 angle pdb=" C ARG C 86 " pdb=" N THR C 87 " pdb=" CA THR C 87 " ideal model delta sigma weight residual 122.70 130.94 -8.24 1.98e+00 2.55e-01 1.73e+01 angle pdb=" CB MET C 411 " pdb=" CG MET C 411 " pdb=" SD MET C 411 " ideal model delta sigma weight residual 112.70 122.95 -10.25 3.00e+00 1.11e-01 1.17e+01 angle pdb=" C SER C 213 " pdb=" N ALA C 214 " pdb=" CA ALA C 214 " ideal model delta sigma weight residual 121.54 126.48 -4.94 1.91e+00 2.74e-01 6.68e+00 angle pdb=" C LYS C 90 " pdb=" N GLY C 91 " pdb=" CA GLY C 91 " ideal model delta sigma weight residual 120.92 117.65 3.27 1.30e+00 5.92e-01 6.34e+00 ... (remaining 18792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 6973 18.07 - 36.15: 951 36.15 - 54.22: 281 54.22 - 72.29: 56 72.29 - 90.37: 20 Dihedral angle restraints: 8281 sinusoidal: 3300 harmonic: 4981 Sorted by residual: dihedral pdb=" CG ARG A 66 " pdb=" CD ARG A 66 " pdb=" NE ARG A 66 " pdb=" CZ ARG A 66 " ideal model delta sinusoidal sigma weight residual 90.00 41.03 48.97 2 1.50e+01 4.44e-03 1.21e+01 dihedral pdb=" CA ASP D 138 " pdb=" CB ASP D 138 " pdb=" CG ASP D 138 " pdb=" OD1 ASP D 138 " ideal model delta sinusoidal sigma weight residual -30.00 -89.73 59.73 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CB GLU F 103 " pdb=" CG GLU F 103 " pdb=" CD GLU F 103 " pdb=" OE1 GLU F 103 " ideal model delta sinusoidal sigma weight residual 0.00 90.37 -90.37 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 8278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1066 0.026 - 0.053: 561 0.053 - 0.079: 283 0.079 - 0.105: 102 0.105 - 0.132: 28 Chirality restraints: 2040 Sorted by residual: chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA ILE D 75 " pdb=" N ILE D 75 " pdb=" C ILE D 75 " pdb=" CB ILE D 75 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 chirality pdb=" CA ILE F 75 " pdb=" N ILE F 75 " pdb=" C ILE F 75 " pdb=" CB ILE F 75 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 2037 not shown) Planarity restraints: 2425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 428 " -0.046 5.00e-02 4.00e+02 6.92e-02 7.67e+00 pdb=" N PRO C 429 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 429 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 429 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 164 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO A 165 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 165 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 165 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 431 " -0.033 5.00e-02 4.00e+02 5.05e-02 4.08e+00 pdb=" N PRO C 432 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 432 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 432 " -0.028 5.00e-02 4.00e+02 ... (remaining 2422 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2178 2.76 - 3.29: 12520 3.29 - 3.83: 24373 3.83 - 4.36: 28413 4.36 - 4.90: 48543 Nonbonded interactions: 116027 Sorted by model distance: nonbonded pdb=" OE2 GLU E 458 " pdb=" NH1 ARG E 462 " model vdw 2.224 3.120 nonbonded pdb=" NH2 ARG C 79 " pdb=" OD1 ASP C 163 " model vdw 2.226 3.120 nonbonded pdb=" OD2 ASP E 69 " pdb=" OG SER E 71 " model vdw 2.239 3.040 nonbonded pdb=" NZ LYS E 90 " pdb=" OG1 THR E 199 " model vdw 2.239 3.120 nonbonded pdb=" O ASP B 181 " pdb=" OG SER B 185 " model vdw 2.254 3.040 ... (remaining 116022 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 53 through 422 or resid 427 through 489)) selection = chain 'B' selection = (chain 'C' and (resid 53 through 422 or resid 427 through 489)) selection = (chain 'D' and (resid 53 through 422 or resid 427 through 489)) selection = (chain 'E' and (resid 53 through 422 or resid 427 through 489)) selection = (chain 'F' and (resid 53 through 422 or resid 427 through 489)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 30.000 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.050 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:11.200 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 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 0.055 13924 Z= 0.150 Angle : 0.572 10.248 18797 Z= 0.353 Chirality : 0.041 0.132 2040 Planarity : 0.005 0.069 2425 Dihedral : 18.435 90.369 5113 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.87 % Favored : 98.01 % Rotamer: Outliers : 2.82 % Allowed : 27.20 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.98 (0.21), residues: 1711 helix: 2.65 (0.16), residues: 936 sheet: -0.31 (0.31), residues: 279 loop : -0.29 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 385 HIS 0.004 0.001 HIS D 82 PHE 0.010 0.001 PHE B 63 TYR 0.010 0.001 TYR C 190 ARG 0.010 0.000 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.12726 ( 854) hydrogen bonds : angle 4.31540 ( 2469) covalent geometry : bond 0.00291 (13924) covalent geometry : angle 0.57161 (18797) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 1.478 Fit side-chains REVERT: A 66 ARG cc_start: 0.8194 (ttt90) cc_final: 0.7939 (mtp180) REVERT: B 435 GLU cc_start: 0.7245 (pm20) cc_final: 0.6940 (pt0) REVERT: C 472 ASN cc_start: 0.7752 (t0) cc_final: 0.7529 (t0) REVERT: D 78 TYR cc_start: 0.8187 (OUTLIER) cc_final: 0.6918 (p90) outliers start: 41 outliers final: 29 residues processed: 238 average time/residue: 1.6479 time to fit residues: 419.8014 Evaluate side-chains 228 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 421 PHE Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 170 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 ASN C 132 ASN C 135 ASN C 414 GLN D 56 ASN D 84 GLN D 135 ASN E 414 GLN E 472 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.121035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.097898 restraints weight = 14050.612| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.13 r_work: 0.2794 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13924 Z= 0.253 Angle : 0.613 7.802 18797 Z= 0.335 Chirality : 0.049 0.148 2040 Planarity : 0.006 0.060 2425 Dihedral : 7.104 63.272 1975 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.99 % Favored : 97.90 % Rotamer: Outliers : 6.20 % Allowed : 22.25 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.97 (0.21), residues: 1711 helix: 2.51 (0.16), residues: 950 sheet: -0.41 (0.31), residues: 283 loop : -0.01 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 178 HIS 0.012 0.002 HIS C 195 PHE 0.012 0.002 PHE E 226 TYR 0.015 0.002 TYR C 190 ARG 0.007 0.001 ARG A 66 Details of bonding type rmsd hydrogen bonds : bond 0.06240 ( 854) hydrogen bonds : angle 3.60795 ( 2469) covalent geometry : bond 0.00621 (13924) covalent geometry : angle 0.61309 (18797) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 201 time to evaluate : 1.454 Fit side-chains REVERT: A 142 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8574 (tt0) REVERT: A 387 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.9045 (tttp) REVERT: A 397 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8778 (mt) REVERT: A 438 ASP cc_start: 0.7909 (m-30) cc_final: 0.7686 (m-30) REVERT: A 459 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8049 (ttm170) REVERT: B 78 TYR cc_start: 0.8319 (OUTLIER) cc_final: 0.7144 (p90) REVERT: C 397 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8749 (mt) REVERT: C 438 ASP cc_start: 0.7863 (m-30) cc_final: 0.7659 (m-30) REVERT: C 459 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8019 (ttm170) REVERT: C 472 ASN cc_start: 0.7952 (t0) cc_final: 0.7617 (t0) REVERT: D 78 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.7186 (p90) REVERT: D 138 ASP cc_start: 0.8607 (m-30) cc_final: 0.8370 (m-30) REVERT: D 465 MET cc_start: 0.8620 (mtt) cc_final: 0.8413 (mtt) REVERT: D 469 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7284 (mpp) REVERT: E 195 HIS cc_start: 0.7705 (OUTLIER) cc_final: 0.7320 (OUTLIER) REVERT: E 205 GLN cc_start: 0.9216 (OUTLIER) cc_final: 0.8950 (mm110) REVERT: E 435 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7675 (mp0) outliers start: 90 outliers final: 47 residues processed: 252 average time/residue: 1.6204 time to fit residues: 436.3806 Evaluate side-chains 255 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 197 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 457 MET Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 86 ARG Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 398 THR Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 435 GLU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 400 LYS Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 435 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 116 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN C 84 GLN D 84 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.125589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.103195 restraints weight = 14641.764| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.15 r_work: 0.2858 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13924 Z= 0.117 Angle : 0.469 8.028 18797 Z= 0.256 Chirality : 0.040 0.130 2040 Planarity : 0.004 0.061 2425 Dihedral : 5.929 80.333 1949 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.05 % Favored : 98.83 % Rotamer: Outliers : 4.68 % Allowed : 23.07 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.46 (0.21), residues: 1711 helix: 3.01 (0.16), residues: 950 sheet: -0.33 (0.32), residues: 282 loop : 0.05 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 385 HIS 0.005 0.001 HIS C 195 PHE 0.008 0.001 PHE B 63 TYR 0.010 0.001 TYR C 190 ARG 0.003 0.000 ARG A 86 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 854) hydrogen bonds : angle 3.30303 ( 2469) covalent geometry : bond 0.00272 (13924) covalent geometry : angle 0.46933 (18797) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 206 time to evaluate : 1.638 Fit side-chains REVERT: A 438 ASP cc_start: 0.7780 (m-30) cc_final: 0.7575 (m-30) REVERT: A 459 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.8008 (ttm170) REVERT: B 78 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.6961 (p90) REVERT: B 469 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6807 (mpp) REVERT: C 438 ASP cc_start: 0.7721 (m-30) cc_final: 0.7477 (m-30) REVERT: C 459 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.8009 (ttm170) REVERT: C 472 ASN cc_start: 0.7865 (t0) cc_final: 0.7555 (t0) REVERT: D 78 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.6954 (p90) REVERT: E 195 HIS cc_start: 0.7406 (OUTLIER) cc_final: 0.7074 (OUTLIER) REVERT: E 205 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8918 (mm110) REVERT: F 397 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8531 (mm) REVERT: F 435 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7549 (mp0) outliers start: 68 outliers final: 30 residues processed: 243 average time/residue: 1.6556 time to fit residues: 430.2705 Evaluate side-chains 237 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 421 PHE Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 398 THR Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 400 LYS Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 428 ILE Chi-restraints excluded: chain F residue 435 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 38 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 52 optimal weight: 0.0270 chunk 62 optimal weight: 10.0000 chunk 94 optimal weight: 0.2980 chunk 155 optimal weight: 6.9990 overall best weight: 5.4644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN D 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.120495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.096816 restraints weight = 14407.479| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.21 r_work: 0.2827 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 13924 Z= 0.279 Angle : 0.627 11.012 18797 Z= 0.341 Chirality : 0.050 0.152 2040 Planarity : 0.005 0.054 2425 Dihedral : 5.790 55.870 1940 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.34 % Favored : 97.55 % Rotamer: Outliers : 5.85 % Allowed : 21.76 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.05 (0.20), residues: 1711 helix: 2.55 (0.16), residues: 952 sheet: -0.34 (0.31), residues: 283 loop : 0.05 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 385 HIS 0.011 0.002 HIS C 195 PHE 0.011 0.002 PHE A 63 TYR 0.017 0.002 TYR C 190 ARG 0.007 0.001 ARG E 86 Details of bonding type rmsd hydrogen bonds : bond 0.06327 ( 854) hydrogen bonds : angle 3.49550 ( 2469) covalent geometry : bond 0.00689 (13924) covalent geometry : angle 0.62740 (18797) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 196 time to evaluate : 1.610 Fit side-chains REVERT: A 397 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8745 (mt) REVERT: A 420 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8032 (tptt) REVERT: A 438 ASP cc_start: 0.7852 (m-30) cc_final: 0.7537 (m-30) REVERT: A 459 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8026 (ttm170) REVERT: B 78 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.7085 (p90) REVERT: C 195 HIS cc_start: 0.7270 (OUTLIER) cc_final: 0.6440 (t70) REVERT: C 397 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8759 (mt) REVERT: C 438 ASP cc_start: 0.7746 (m-30) cc_final: 0.7466 (m-30) REVERT: C 459 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7952 (ttm170) REVERT: C 470 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7942 (tttt) REVERT: E 195 HIS cc_start: 0.7637 (OUTLIER) cc_final: 0.7242 (OUTLIER) REVERT: E 205 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.8916 (mm110) REVERT: F 397 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8775 (mm) REVERT: F 435 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7585 (mp0) outliers start: 85 outliers final: 40 residues processed: 243 average time/residue: 1.5685 time to fit residues: 408.8307 Evaluate side-chains 241 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 190 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 457 MET Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 421 PHE Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain C residue 470 LYS Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 398 THR Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 400 LYS Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 435 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 59 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 ASN B 84 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 414 GLN D 84 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.123695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.100621 restraints weight = 14093.764| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.14 r_work: 0.2830 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13924 Z= 0.126 Angle : 0.491 11.116 18797 Z= 0.265 Chirality : 0.041 0.130 2040 Planarity : 0.004 0.058 2425 Dihedral : 5.318 57.333 1938 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.52 % Favored : 98.36 % Rotamer: Outliers : 4.96 % Allowed : 22.87 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.46 (0.21), residues: 1711 helix: 2.98 (0.16), residues: 952 sheet: -0.31 (0.32), residues: 282 loop : 0.08 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 385 HIS 0.006 0.001 HIS C 195 PHE 0.009 0.001 PHE B 63 TYR 0.010 0.001 TYR C 190 ARG 0.005 0.000 ARG E 86 Details of bonding type rmsd hydrogen bonds : bond 0.04441 ( 854) hydrogen bonds : angle 3.26003 ( 2469) covalent geometry : bond 0.00293 (13924) covalent geometry : angle 0.49072 (18797) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 200 time to evaluate : 1.559 Fit side-chains REVERT: A 397 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8773 (mt) REVERT: A 420 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7990 (tptt) REVERT: A 438 ASP cc_start: 0.7882 (m-30) cc_final: 0.7587 (m-30) REVERT: A 459 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8179 (ttm170) REVERT: B 78 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.7096 (p90) REVERT: B 438 ASP cc_start: 0.7818 (p0) cc_final: 0.7568 (p0) REVERT: C 195 HIS cc_start: 0.7069 (OUTLIER) cc_final: 0.6283 (t70) REVERT: C 397 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8792 (mt) REVERT: C 438 ASP cc_start: 0.7827 (m-30) cc_final: 0.7572 (m-30) REVERT: C 459 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8160 (ttm170) REVERT: E 94 ARG cc_start: 0.8622 (ttm170) cc_final: 0.8383 (ttm170) REVERT: E 195 HIS cc_start: 0.7561 (OUTLIER) cc_final: 0.7248 (OUTLIER) REVERT: E 205 GLN cc_start: 0.9209 (OUTLIER) cc_final: 0.8986 (mm110) REVERT: E 428 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7444 (mt) REVERT: F 435 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7702 (mp0) outliers start: 72 outliers final: 41 residues processed: 243 average time/residue: 1.6279 time to fit residues: 423.6598 Evaluate side-chains 252 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 201 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 421 PHE Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 398 THR Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 400 LYS Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 428 ILE Chi-restraints excluded: chain F residue 435 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 113 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN D 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.120094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.097063 restraints weight = 14615.193| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.24 r_work: 0.2804 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13924 Z= 0.239 Angle : 0.593 12.218 18797 Z= 0.320 Chirality : 0.047 0.148 2040 Planarity : 0.005 0.059 2425 Dihedral : 5.624 56.102 1938 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.16 % Favored : 97.72 % Rotamer: Outliers : 5.92 % Allowed : 21.83 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.15 (0.20), residues: 1711 helix: 2.67 (0.16), residues: 952 sheet: -0.39 (0.31), residues: 282 loop : 0.07 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 385 HIS 0.009 0.001 HIS C 195 PHE 0.010 0.002 PHE A 63 TYR 0.015 0.002 TYR C 190 ARG 0.004 0.000 ARG E 86 Details of bonding type rmsd hydrogen bonds : bond 0.05895 ( 854) hydrogen bonds : angle 3.40266 ( 2469) covalent geometry : bond 0.00587 (13924) covalent geometry : angle 0.59277 (18797) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 199 time to evaluate : 2.024 Fit side-chains REVERT: A 397 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8758 (mt) REVERT: A 420 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7986 (tptt) REVERT: A 438 ASP cc_start: 0.7843 (m-30) cc_final: 0.7492 (m-30) REVERT: A 459 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7979 (ttm170) REVERT: B 78 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.7139 (p90) REVERT: B 438 ASP cc_start: 0.7824 (p0) cc_final: 0.7584 (p0) REVERT: C 195 HIS cc_start: 0.7067 (OUTLIER) cc_final: 0.6198 (t70) REVERT: C 397 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8759 (mt) REVERT: C 438 ASP cc_start: 0.7771 (m-30) cc_final: 0.7443 (m-30) REVERT: C 459 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8050 (ttm170) REVERT: E 195 HIS cc_start: 0.7662 (OUTLIER) cc_final: 0.7279 (OUTLIER) REVERT: E 205 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.8927 (mm110) REVERT: E 469 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.7119 (mpp) REVERT: F 397 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8675 (mm) REVERT: F 435 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7627 (mp0) outliers start: 86 outliers final: 49 residues processed: 247 average time/residue: 1.6409 time to fit residues: 434.1802 Evaluate side-chains 253 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 193 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 457 MET Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 421 PHE Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 168 ASP Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 398 THR Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 400 LYS Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 428 ILE Chi-restraints excluded: chain F residue 435 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 88 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 132 optimal weight: 6.9990 chunk 146 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 137 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN D 84 GLN ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.124214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.099853 restraints weight = 14804.011| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.34 r_work: 0.2839 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13924 Z= 0.105 Angle : 0.464 11.612 18797 Z= 0.248 Chirality : 0.040 0.127 2040 Planarity : 0.004 0.060 2425 Dihedral : 5.134 58.641 1938 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.34 % Favored : 98.54 % Rotamer: Outliers : 4.06 % Allowed : 23.97 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.63 (0.21), residues: 1711 helix: 3.17 (0.16), residues: 954 sheet: -0.36 (0.31), residues: 282 loop : 0.11 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 385 HIS 0.004 0.001 HIS C 195 PHE 0.009 0.001 PHE A 63 TYR 0.007 0.001 TYR C 190 ARG 0.004 0.000 ARG E 86 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 854) hydrogen bonds : angle 3.15040 ( 2469) covalent geometry : bond 0.00239 (13924) covalent geometry : angle 0.46354 (18797) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 206 time to evaluate : 1.675 Fit side-chains REVERT: A 397 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8685 (mt) REVERT: A 420 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7822 (tptt) REVERT: A 438 ASP cc_start: 0.7726 (m-30) cc_final: 0.7360 (m-30) REVERT: A 459 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7973 (ttm170) REVERT: B 78 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.6956 (p90) REVERT: B 94 ARG cc_start: 0.8471 (ttm170) cc_final: 0.8247 (ttm170) REVERT: B 438 ASP cc_start: 0.7580 (p0) cc_final: 0.7191 (p0) REVERT: C 190 TYR cc_start: 0.7667 (m-80) cc_final: 0.7448 (m-80) REVERT: C 195 HIS cc_start: 0.6895 (OUTLIER) cc_final: 0.6005 (t70) REVERT: C 397 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8721 (mt) REVERT: C 438 ASP cc_start: 0.7697 (m-30) cc_final: 0.7384 (m-30) REVERT: C 459 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7917 (ttm170) REVERT: D 469 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6845 (mpp) REVERT: E 195 HIS cc_start: 0.7330 (OUTLIER) cc_final: 0.6888 (OUTLIER) REVERT: E 428 ILE cc_start: 0.7704 (mp) cc_final: 0.7425 (mt) REVERT: E 458 GLU cc_start: 0.8675 (tt0) cc_final: 0.8334 (tm-30) REVERT: F 76 GLU cc_start: 0.8545 (pt0) cc_final: 0.7922 (tp30) REVERT: F 435 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: F 437 GLN cc_start: 0.8340 (mm-40) cc_final: 0.8057 (tp-100) outliers start: 59 outliers final: 31 residues processed: 238 average time/residue: 1.6520 time to fit residues: 421.8543 Evaluate side-chains 239 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 199 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 421 PHE Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 398 THR Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 428 ILE Chi-restraints excluded: chain F residue 435 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 76 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 173 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 144 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 414 GLN D 82 HIS D 84 GLN E 414 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.120261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.096632 restraints weight = 14557.779| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.18 r_work: 0.2841 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 13924 Z= 0.231 Angle : 0.590 13.133 18797 Z= 0.318 Chirality : 0.047 0.150 2040 Planarity : 0.005 0.063 2425 Dihedral : 5.406 57.400 1935 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.05 % Favored : 97.84 % Rotamer: Outliers : 5.51 % Allowed : 22.18 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.25 (0.20), residues: 1711 helix: 2.76 (0.16), residues: 954 sheet: -0.36 (0.31), residues: 282 loop : 0.09 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 385 HIS 0.010 0.001 HIS C 195 PHE 0.010 0.002 PHE A 63 TYR 0.014 0.002 TYR C 190 ARG 0.005 0.000 ARG D 66 Details of bonding type rmsd hydrogen bonds : bond 0.05776 ( 854) hydrogen bonds : angle 3.37912 ( 2469) covalent geometry : bond 0.00567 (13924) covalent geometry : angle 0.59004 (18797) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 196 time to evaluate : 1.513 Fit side-chains REVERT: A 134 LYS cc_start: 0.8420 (mtmp) cc_final: 0.8117 (mppt) REVERT: A 397 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8736 (mt) REVERT: A 420 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7934 (tptt) REVERT: A 438 ASP cc_start: 0.7851 (m-30) cc_final: 0.7471 (m-30) REVERT: A 459 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8067 (ttm170) REVERT: B 78 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.7119 (p90) REVERT: B 438 ASP cc_start: 0.7678 (p0) cc_final: 0.7331 (p0) REVERT: C 195 HIS cc_start: 0.7039 (OUTLIER) cc_final: 0.6103 (t70) REVERT: C 397 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8752 (mt) REVERT: C 438 ASP cc_start: 0.7786 (m-30) cc_final: 0.7467 (m-30) REVERT: C 459 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.8003 (ttm170) REVERT: C 470 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7939 (tttt) REVERT: D 465 MET cc_start: 0.8458 (mtt) cc_final: 0.8228 (mtt) REVERT: D 469 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7110 (mpp) REVERT: E 195 HIS cc_start: 0.7628 (OUTLIER) cc_final: 0.7261 (OUTLIER) REVERT: E 205 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8852 (mm110) REVERT: E 458 GLU cc_start: 0.8782 (tt0) cc_final: 0.8420 (tm-30) REVERT: F 397 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8567 (mm) REVERT: F 435 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7604 (mp0) outliers start: 80 outliers final: 47 residues processed: 238 average time/residue: 1.6235 time to fit residues: 414.0942 Evaluate side-chains 251 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 192 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 446 LYS Chi-restraints excluded: chain B residue 457 MET Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 421 PHE Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain C residue 470 LYS Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 398 THR Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 400 LYS Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 428 ILE Chi-restraints excluded: chain F residue 435 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 72 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 414 GLN D 84 GLN ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.124420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.101946 restraints weight = 14581.489| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.15 r_work: 0.2853 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13924 Z= 0.125 Angle : 0.493 12.530 18797 Z= 0.264 Chirality : 0.041 0.127 2040 Planarity : 0.004 0.066 2425 Dihedral : 5.113 58.754 1935 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.46 % Favored : 98.42 % Rotamer: Outliers : 4.20 % Allowed : 23.14 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.56 (0.21), residues: 1711 helix: 3.09 (0.16), residues: 954 sheet: -0.36 (0.31), residues: 282 loop : 0.13 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 385 HIS 0.005 0.001 HIS C 195 PHE 0.008 0.001 PHE C 63 TYR 0.014 0.001 TYR A 190 ARG 0.004 0.000 ARG D 66 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 854) hydrogen bonds : angle 3.21227 ( 2469) covalent geometry : bond 0.00296 (13924) covalent geometry : angle 0.49320 (18797) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 198 time to evaluate : 1.456 Fit side-chains REVERT: A 397 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8744 (mt) REVERT: A 420 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7947 (tptt) REVERT: A 438 ASP cc_start: 0.7871 (m-30) cc_final: 0.7559 (m-30) REVERT: A 459 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8088 (ttm170) REVERT: A 469 MET cc_start: 0.7490 (mpp) cc_final: 0.7247 (mtt) REVERT: B 78 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.7070 (p90) REVERT: B 438 ASP cc_start: 0.7655 (p0) cc_final: 0.7236 (m-30) REVERT: C 195 HIS cc_start: 0.7057 (OUTLIER) cc_final: 0.6184 (t70) REVERT: C 397 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8776 (mt) REVERT: C 438 ASP cc_start: 0.7836 (m-30) cc_final: 0.7553 (m-30) REVERT: C 459 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8098 (ttm170) REVERT: C 470 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.8026 (tttt) REVERT: D 411 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7972 (mmp) REVERT: D 465 MET cc_start: 0.8483 (mtt) cc_final: 0.8268 (mtt) REVERT: D 469 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7023 (mpp) REVERT: E 195 HIS cc_start: 0.7506 (OUTLIER) cc_final: 0.7153 (OUTLIER) REVERT: E 205 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8955 (mm110) REVERT: E 428 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7445 (mt) REVERT: E 458 GLU cc_start: 0.8766 (tt0) cc_final: 0.8419 (tm-30) REVERT: F 76 GLU cc_start: 0.8555 (pt0) cc_final: 0.8002 (tp30) REVERT: F 397 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8239 (mm) REVERT: F 437 GLN cc_start: 0.8481 (mm-40) cc_final: 0.8215 (tp-100) outliers start: 61 outliers final: 38 residues processed: 231 average time/residue: 1.6124 time to fit residues: 399.1497 Evaluate side-chains 246 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 195 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 421 PHE Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain C residue 470 LYS Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 398 THR Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 428 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 127 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 93 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN D 56 ASN D 84 GLN D 472 ASN E 414 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.126769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.104722 restraints weight = 14535.014| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.13 r_work: 0.2862 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13924 Z= 0.112 Angle : 0.478 12.398 18797 Z= 0.253 Chirality : 0.040 0.128 2040 Planarity : 0.004 0.065 2425 Dihedral : 4.968 59.706 1935 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.75 % Favored : 98.13 % Rotamer: Outliers : 3.72 % Allowed : 23.76 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.75 (0.21), residues: 1711 helix: 3.28 (0.16), residues: 954 sheet: -0.35 (0.31), residues: 282 loop : 0.13 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 385 HIS 0.005 0.001 HIS C 195 PHE 0.008 0.001 PHE C 63 TYR 0.008 0.001 TYR C 190 ARG 0.004 0.000 ARG D 66 Details of bonding type rmsd hydrogen bonds : bond 0.03973 ( 854) hydrogen bonds : angle 3.16204 ( 2469) covalent geometry : bond 0.00263 (13924) covalent geometry : angle 0.47772 (18797) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3422 Ramachandran restraints generated. 1711 Oldfield, 0 Emsley, 1711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 1.579 Fit side-chains REVERT: A 397 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8748 (mt) REVERT: A 420 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7951 (tptt) REVERT: A 438 ASP cc_start: 0.7868 (m-30) cc_final: 0.7573 (m-30) REVERT: A 459 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8059 (ttm170) REVERT: B 78 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.7049 (p90) REVERT: B 438 ASP cc_start: 0.7588 (p0) cc_final: 0.7190 (m-30) REVERT: C 195 HIS cc_start: 0.6947 (OUTLIER) cc_final: 0.6078 (t70) REVERT: C 397 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8774 (mt) REVERT: C 438 ASP cc_start: 0.7819 (m-30) cc_final: 0.7556 (m-30) REVERT: C 459 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8074 (ttm170) REVERT: D 411 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7897 (mmp) REVERT: D 465 MET cc_start: 0.8438 (mtt) cc_final: 0.8233 (mtt) REVERT: D 469 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.6872 (mpp) REVERT: E 195 HIS cc_start: 0.7324 (OUTLIER) cc_final: 0.7001 (OUTLIER) REVERT: E 205 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8935 (mm110) REVERT: E 428 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7537 (mt) REVERT: E 458 GLU cc_start: 0.8728 (tt0) cc_final: 0.8379 (tm-30) REVERT: F 76 GLU cc_start: 0.8521 (pt0) cc_final: 0.8093 (tp30) REVERT: F 458 GLU cc_start: 0.8670 (tt0) cc_final: 0.8323 (tm-30) outliers start: 54 outliers final: 35 residues processed: 225 average time/residue: 1.5745 time to fit residues: 380.1337 Evaluate side-chains 240 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 194 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 421 PHE Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 446 LYS Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 130 LYS Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 398 THR Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 224 GLU Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 428 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 40 optimal weight: 0.0770 chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 74 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 chunk 161 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN D 56 ASN D 84 GLN D 472 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.126060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.102836 restraints weight = 14778.284| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.23 r_work: 0.2878 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13924 Z= 0.094 Angle : 0.450 12.659 18797 Z= 0.239 Chirality : 0.039 0.127 2040 Planarity : 0.004 0.067 2425 Dihedral : 4.732 56.970 1935 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.23 % Favored : 98.66 % Rotamer: Outliers : 3.51 % Allowed : 23.69 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.92 (0.21), residues: 1711 helix: 3.47 (0.16), residues: 954 sheet: -0.30 (0.31), residues: 282 loop : 0.12 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 385 HIS 0.003 0.001 HIS C 195 PHE 0.007 0.001 PHE B 63 TYR 0.006 0.001 TYR C 190 ARG 0.004 0.000 ARG D 66 Details of bonding type rmsd hydrogen bonds : bond 0.03414 ( 854) hydrogen bonds : angle 3.09538 ( 2469) covalent geometry : bond 0.00214 (13924) covalent geometry : angle 0.45016 (18797) =============================================================================== Job complete usr+sys time: 10725.98 seconds wall clock time: 185 minutes 34.71 seconds (11134.71 seconds total)