Starting phenix.real_space_refine on Wed Jun 11 06:48:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z9z_39873/06_2025/8z9z_39873.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z9z_39873/06_2025/8z9z_39873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z9z_39873/06_2025/8z9z_39873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z9z_39873/06_2025/8z9z_39873.map" model { file = "/net/cci-nas-00/data/ceres_data/8z9z_39873/06_2025/8z9z_39873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z9z_39873/06_2025/8z9z_39873.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.091 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 69 5.16 5 C 8436 2.51 5 N 1935 2.21 5 O 2202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12648 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3292 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 395} Chain breaks: 1 Chain: "B" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3292 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 395} Chain breaks: 1 Chain: "C" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3140 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 379} Chain breaks: 2 Chain: "D" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2600 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 4, 'TRANS': 314} Chain breaks: 1 Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.12, per 1000 atoms: 0.64 Number of scatterers: 12648 At special positions: 0 Unit cell: (115.56, 121.98, 130.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 69 16.00 P 6 15.00 O 2202 8.00 N 1935 7.00 C 8436 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: 3.46 Conformation dependent library (CDL) restraints added in 1.6 seconds 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2920 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 4 sheets defined 81.0% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 7 through 12 Processing helix chain 'A' and resid 12 through 23 removed outlier: 3.593A pdb=" N GLY A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 62 Processing helix chain 'A' and resid 69 through 96 removed outlier: 3.829A pdb=" N HIS A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 91 " --> pdb=" O MET A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 105 removed outlier: 3.723A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 153 removed outlier: 3.886A pdb=" N THR A 153 " --> pdb=" O TRP A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 192 through 244 removed outlier: 3.933A pdb=" N GLU A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASN A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Proline residue: A 240 - end of helix Processing helix chain 'A' and resid 304 through 336 Processing helix chain 'A' and resid 337 through 360 removed outlier: 3.839A pdb=" N VAL A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 405 removed outlier: 3.606A pdb=" N ILE A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N HIS A 388 " --> pdb=" O MET A 384 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL A 399 " --> pdb=" O GLU A 395 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N MET A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 426 Processing helix chain 'A' and resid 441 through 463 removed outlier: 3.868A pdb=" N PHE A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 12 Processing helix chain 'B' and resid 12 through 22 Processing helix chain 'B' and resid 36 through 66 Processing helix chain 'B' and resid 69 through 95 removed outlier: 3.766A pdb=" N HIS B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR B 95 " --> pdb=" O VAL B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 105 removed outlier: 3.784A pdb=" N PHE B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 116 through 153 removed outlier: 3.731A pdb=" N THR B 153 " --> pdb=" O TRP B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 237 removed outlier: 3.580A pdb=" N MET B 216 " --> pdb=" O HIS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 244 Processing helix chain 'B' and resid 304 through 336 Processing helix chain 'B' and resid 337 through 359 removed outlier: 3.848A pdb=" N VAL B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 398 removed outlier: 4.001A pdb=" N PHE B 385 " --> pdb=" O GLN B 381 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N HIS B 388 " --> pdb=" O MET B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 405 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 441 through 463 removed outlier: 3.683A pdb=" N PHE B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 12 Processing helix chain 'C' and resid 12 through 22 Processing helix chain 'C' and resid 36 through 67 removed outlier: 3.596A pdb=" N SER C 67 " --> pdb=" O MET C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 96 removed outlier: 3.857A pdb=" N HIS C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N SER C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 91 " --> pdb=" O MET C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 107 removed outlier: 3.806A pdb=" N PHE C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TRP C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 153 removed outlier: 3.694A pdb=" N THR C 150 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR C 153 " --> pdb=" O TRP C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 156 No H-bonds generated for 'chain 'C' and resid 154 through 156' Processing helix chain 'C' and resid 192 through 246 removed outlier: 3.951A pdb=" N ILE C 196 " --> pdb=" O GLY C 192 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU C 217 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 227 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Proline residue: C 240 - end of helix removed outlier: 3.644A pdb=" N GLU C 243 " --> pdb=" O ASN C 239 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 336 Processing helix chain 'C' and resid 337 through 358 removed outlier: 3.594A pdb=" N VAL C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 397 removed outlier: 3.546A pdb=" N ILE C 382 " --> pdb=" O SER C 378 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE C 385 " --> pdb=" O GLN C 381 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N HIS C 388 " --> pdb=" O MET C 384 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER C 397 " --> pdb=" O ILE C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 406 Processing helix chain 'C' and resid 407 through 411 Processing helix chain 'C' and resid 412 through 427 Processing helix chain 'C' and resid 441 through 463 Processing helix chain 'D' and resid 6 through 15 Processing helix chain 'D' and resid 20 through 42 Processing helix chain 'D' and resid 42 through 47 Processing helix chain 'D' and resid 50 through 76 removed outlier: 3.767A pdb=" N GLN D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE D 56 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N PHE D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 89 Processing helix chain 'D' and resid 94 through 117 removed outlier: 3.580A pdb=" N ASN D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE D 114 " --> pdb=" O ILE D 110 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 200 removed outlier: 3.873A pdb=" N TYR D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE D 166 " --> pdb=" O ILE D 162 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS D 168 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU D 170 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN D 175 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE D 178 " --> pdb=" O ILE D 174 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 185 " --> pdb=" O TYR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 253 removed outlier: 4.925A pdb=" N LYS D 231 " --> pdb=" O ILE D 227 " (cutoff:3.500A) Proline residue: D 232 - end of helix Processing helix chain 'D' and resid 263 through 287 removed outlier: 3.985A pdb=" N SER D 271 " --> pdb=" O CYS D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 300 removed outlier: 4.014A pdb=" N LYS D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE D 300 " --> pdb=" O LEU D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 310 through 324 removed outlier: 3.627A pdb=" N SER D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ILE D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 360 Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 163 Processing sheet with id=AA2, first strand: chain 'A' and resid 433 through 434 removed outlier: 3.766A pdb=" N PHE A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 159 through 163 Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 330 943 hydrogen bonds defined for protein. 2811 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: 3.82 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2022 1.33 - 1.45: 3677 1.45 - 1.57: 7153 1.57 - 1.69: 12 1.69 - 1.82: 112 Bond restraints: 12976 Sorted by residual: bond pdb=" CB GLU D 205 " pdb=" CG GLU D 205 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.30e+00 bond pdb=" CA PHE A 62 " pdb=" CB PHE A 62 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.21e-02 6.83e+03 1.25e+00 bond pdb=" SD MET D 13 " pdb=" CE MET D 13 " ideal model delta sigma weight residual 1.791 1.766 0.025 2.50e-02 1.60e+03 9.68e-01 bond pdb=" CB GLU D 287 " pdb=" CG GLU D 287 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.78e-01 bond pdb=" CB PHE C 90 " pdb=" CG PHE C 90 " ideal model delta sigma weight residual 1.502 1.520 -0.018 2.30e-02 1.89e+03 6.36e-01 ... (remaining 12971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 17338 1.70 - 3.40: 190 3.40 - 5.11: 29 5.11 - 6.81: 10 6.81 - 8.51: 4 Bond angle restraints: 17571 Sorted by residual: angle pdb=" CB MET D 84 " pdb=" CG MET D 84 " pdb=" SD MET D 84 " ideal model delta sigma weight residual 112.70 104.19 8.51 3.00e+00 1.11e-01 8.05e+00 angle pdb=" CA CYS A 426 " pdb=" CB CYS A 426 " pdb=" SG CYS A 426 " ideal model delta sigma weight residual 114.40 120.76 -6.36 2.30e+00 1.89e-01 7.65e+00 angle pdb=" CA GLN A 425 " pdb=" CB GLN A 425 " pdb=" CG GLN A 425 " ideal model delta sigma weight residual 114.10 108.59 5.51 2.00e+00 2.50e-01 7.60e+00 angle pdb=" CA CYS A 426 " pdb=" C CYS A 426 " pdb=" O CYS A 426 " ideal model delta sigma weight residual 120.51 124.39 -3.88 1.43e+00 4.89e-01 7.38e+00 angle pdb=" CB GLU D 287 " pdb=" CG GLU D 287 " pdb=" CD GLU D 287 " ideal model delta sigma weight residual 112.60 117.14 -4.54 1.70e+00 3.46e-01 7.13e+00 ... (remaining 17566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6334 17.97 - 35.93: 945 35.93 - 53.90: 247 53.90 - 71.86: 46 71.86 - 89.83: 15 Dihedral angle restraints: 7587 sinusoidal: 3076 harmonic: 4511 Sorted by residual: dihedral pdb=" CA ASN C 214 " pdb=" CB ASN C 214 " pdb=" CG ASN C 214 " pdb=" OD1 ASN C 214 " ideal model delta sinusoidal sigma weight residual -90.00 -162.03 72.03 2 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CG ARG D 90 " pdb=" CD ARG D 90 " pdb=" NE ARG D 90 " pdb=" CZ ARG D 90 " ideal model delta sinusoidal sigma weight residual -90.00 -134.94 44.94 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CB GLU D 64 " pdb=" CG GLU D 64 " pdb=" CD GLU D 64 " pdb=" OE1 GLU D 64 " ideal model delta sinusoidal sigma weight residual 0.00 -89.83 89.83 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 7584 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1682 0.050 - 0.100: 303 0.100 - 0.149: 25 0.149 - 0.199: 2 0.199 - 0.249: 1 Chirality restraints: 2013 Sorted by residual: chirality pdb=" CB ILE C 51 " pdb=" CA ILE C 51 " pdb=" CG1 ILE C 51 " pdb=" CG2 ILE C 51 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB ILE D 242 " pdb=" CA ILE D 242 " pdb=" CG1 ILE D 242 " pdb=" CG2 ILE D 242 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CB ILE C 237 " pdb=" CA ILE C 237 " pdb=" CG1 ILE C 237 " pdb=" CG2 ILE C 237 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.74e-01 ... (remaining 2010 not shown) Planarity restraints: 2079 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 176 " 0.041 5.00e-02 4.00e+02 6.33e-02 6.42e+00 pdb=" N PRO A 177 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 177 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 177 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 456 " -0.013 2.00e-02 2.50e+03 1.55e-02 4.23e+00 pdb=" CG PHE C 456 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE C 456 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 456 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE C 456 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 456 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 456 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 408 " 0.012 2.00e-02 2.50e+03 1.20e-02 3.61e+00 pdb=" CG TRP B 408 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP B 408 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 408 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 408 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 408 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 408 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 408 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 408 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 408 " -0.000 2.00e-02 2.50e+03 ... (remaining 2076 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1500 2.75 - 3.29: 12629 3.29 - 3.82: 22366 3.82 - 4.36: 23042 4.36 - 4.90: 42217 Nonbonded interactions: 101754 Sorted by model distance: nonbonded pdb=" O ILE D 266 " pdb=" OG SER D 270 " model vdw 2.209 3.040 nonbonded pdb=" OG1 THR B 142 " pdb=" OD1 ASN B 214 " model vdw 2.217 3.040 nonbonded pdb=" OG SER D 230 " pdb=" O12 PC1 D 401 " model vdw 2.225 3.040 nonbonded pdb=" NE2 GLN A 420 " pdb=" OE1 GLN A 424 " model vdw 2.252 3.120 nonbonded pdb=" OG1 THR A 142 " pdb=" OD1 ASN A 214 " model vdw 2.260 3.040 ... (remaining 101749 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 5 through 156 or resid 175 through 463 or resid 501)) selection = (chain 'B' and (resid 5 through 156 or resid 175 through 463 or resid 501)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 32.050 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 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 : 0.002 0.034 12976 Z= 0.111 Angle : 0.481 8.511 17571 Z= 0.255 Chirality : 0.036 0.249 2013 Planarity : 0.003 0.063 2079 Dihedral : 18.144 89.830 4667 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.29 % Allowed : 29.95 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.18 (0.22), residues: 1501 helix: 2.98 (0.15), residues: 1165 sheet: -0.02 (1.23), residues: 24 loop : -1.36 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 408 HIS 0.003 0.001 HIS D 85 PHE 0.036 0.001 PHE C 456 TYR 0.018 0.001 TYR D 243 ARG 0.002 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.08123 ( 943) hydrogen bonds : angle 3.62070 ( 2811) covalent geometry : bond 0.00232 (12976) covalent geometry : angle 0.48110 (17571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 200 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 391 GLU cc_start: 0.7976 (tt0) cc_final: 0.7701 (tt0) REVERT: C 328 TYR cc_start: 0.8320 (t80) cc_final: 0.7976 (t80) REVERT: D 13 MET cc_start: 0.7250 (mtm) cc_final: 0.6569 (mtm) REVERT: D 239 PHE cc_start: 0.7804 (t80) cc_final: 0.7600 (t80) REVERT: D 243 TYR cc_start: 0.6801 (m-10) cc_final: 0.6508 (m-10) outliers start: 4 outliers final: 1 residues processed: 201 average time/residue: 0.1924 time to fit residues: 60.3493 Evaluate side-chains 193 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 116 optimal weight: 0.1980 chunk 45 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 HIS ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN B 307 GLN B 424 GLN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.176889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.136592 restraints weight = 15338.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.137053 restraints weight = 11082.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139110 restraints weight = 9097.618| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.0670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12976 Z= 0.126 Angle : 0.456 7.955 17571 Z= 0.241 Chirality : 0.036 0.173 2013 Planarity : 0.003 0.061 2079 Dihedral : 9.736 73.753 1919 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.90 % Allowed : 26.40 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.22), residues: 1501 helix: 2.99 (0.15), residues: 1172 sheet: -0.05 (1.22), residues: 24 loop : -1.34 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 408 HIS 0.004 0.001 HIS B 322 PHE 0.021 0.001 PHE D 173 TYR 0.013 0.001 TYR C 404 ARG 0.002 0.000 ARG B 178 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 943) hydrogen bonds : angle 3.19224 ( 2811) covalent geometry : bond 0.00285 (12976) covalent geometry : angle 0.45625 (17571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 207 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 328 TYR cc_start: 0.8342 (t80) cc_final: 0.7902 (t80) REVERT: D 13 MET cc_start: 0.7237 (mtm) cc_final: 0.6715 (tmm) REVERT: D 47 PHE cc_start: 0.6686 (OUTLIER) cc_final: 0.6414 (t80) REVERT: D 54 GLN cc_start: 0.5546 (OUTLIER) cc_final: 0.5227 (mp10) REVERT: D 78 LYS cc_start: 0.8447 (ttpp) cc_final: 0.7980 (ttmt) REVERT: D 352 LEU cc_start: 0.8696 (mm) cc_final: 0.8435 (mt) outliers start: 40 outliers final: 25 residues processed: 233 average time/residue: 0.1989 time to fit residues: 71.2199 Evaluate side-chains 223 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 182 HIS Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 47 PHE Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 234 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 137 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN B 461 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.183045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.135335 restraints weight = 16855.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.139447 restraints weight = 9711.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.142088 restraints weight = 7055.967| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12976 Z= 0.120 Angle : 0.450 7.727 17571 Z= 0.237 Chirality : 0.036 0.196 2013 Planarity : 0.003 0.062 2079 Dihedral : 9.539 72.439 1917 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.70 % Allowed : 26.11 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.23 (0.22), residues: 1501 helix: 3.00 (0.15), residues: 1174 sheet: -0.34 (1.20), residues: 24 loop : -1.36 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 408 HIS 0.003 0.001 HIS B 322 PHE 0.019 0.001 PHE D 173 TYR 0.013 0.001 TYR C 374 ARG 0.001 0.000 ARG C 312 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 943) hydrogen bonds : angle 3.13895 ( 2811) covalent geometry : bond 0.00268 (12976) covalent geometry : angle 0.45022 (17571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 209 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 TYR cc_start: 0.8431 (t80) cc_final: 0.7958 (t80) REVERT: C 187 TRP cc_start: 0.6486 (p90) cc_final: 0.6234 (p90) REVERT: C 328 TYR cc_start: 0.8219 (t80) cc_final: 0.7495 (t80) REVERT: D 13 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.6518 (tmm) REVERT: D 47 PHE cc_start: 0.7049 (OUTLIER) cc_final: 0.6802 (t80) REVERT: D 78 LYS cc_start: 0.8203 (ttpp) cc_final: 0.7705 (ttmt) REVERT: D 173 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6766 (t80) outliers start: 51 outliers final: 35 residues processed: 237 average time/residue: 0.1908 time to fit residues: 71.4465 Evaluate side-chains 240 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 182 HIS Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 47 PHE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 340 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 93 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN B 461 GLN D 108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.180425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.133005 restraints weight = 16766.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.136966 restraints weight = 9824.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.139450 restraints weight = 7217.426| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12976 Z= 0.156 Angle : 0.483 8.136 17571 Z= 0.253 Chirality : 0.037 0.205 2013 Planarity : 0.003 0.063 2079 Dihedral : 9.587 71.784 1917 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.79 % Allowed : 25.74 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.08 (0.22), residues: 1501 helix: 2.85 (0.15), residues: 1180 sheet: -0.60 (1.19), residues: 24 loop : -1.32 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 408 HIS 0.004 0.001 HIS B 322 PHE 0.029 0.001 PHE D 73 TYR 0.013 0.001 TYR D 243 ARG 0.002 0.000 ARG D 321 Details of bonding type rmsd hydrogen bonds : bond 0.04268 ( 943) hydrogen bonds : angle 3.18901 ( 2811) covalent geometry : bond 0.00368 (12976) covalent geometry : angle 0.48295 (17571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 205 time to evaluate : 1.601 Fit side-chains revert: symmetry clash REVERT: A 334 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7590 (mt-10) REVERT: A 345 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7580 (mp) REVERT: A 455 TYR cc_start: 0.8475 (t80) cc_final: 0.8029 (t80) REVERT: C 328 TYR cc_start: 0.8311 (t80) cc_final: 0.7778 (t80) REVERT: D 27 TYR cc_start: 0.4442 (OUTLIER) cc_final: 0.2642 (m-80) REVERT: D 54 GLN cc_start: 0.6061 (OUTLIER) cc_final: 0.5830 (mp10) REVERT: D 78 LYS cc_start: 0.8191 (ttpp) cc_final: 0.7672 (ttmt) REVERT: D 166 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8525 (tt) REVERT: D 173 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.6985 (t80) outliers start: 66 outliers final: 42 residues processed: 245 average time/residue: 0.2554 time to fit residues: 98.4588 Evaluate side-chains 245 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 197 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 182 HIS Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 108 HIS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 234 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 148 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN B 461 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.182390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.134752 restraints weight = 16807.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.138852 restraints weight = 9743.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.141068 restraints weight = 7087.677| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12976 Z= 0.123 Angle : 0.458 7.967 17571 Z= 0.242 Chirality : 0.036 0.214 2013 Planarity : 0.003 0.062 2079 Dihedral : 9.514 70.643 1917 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.19 % Allowed : 27.34 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.19 (0.22), residues: 1501 helix: 2.99 (0.15), residues: 1171 sheet: -0.72 (1.20), residues: 24 loop : -1.41 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 408 HIS 0.009 0.001 HIS D 108 PHE 0.020 0.001 PHE D 173 TYR 0.019 0.001 TYR C 101 ARG 0.002 0.000 ARG C 312 Details of bonding type rmsd hydrogen bonds : bond 0.04056 ( 943) hydrogen bonds : angle 3.14490 ( 2811) covalent geometry : bond 0.00276 (12976) covalent geometry : angle 0.45760 (17571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 207 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 TYR cc_start: 0.8461 (t80) cc_final: 0.7964 (t80) REVERT: C 36 LEU cc_start: 0.7397 (pt) cc_final: 0.7102 (mp) REVERT: C 328 TYR cc_start: 0.8242 (t80) cc_final: 0.7498 (t80) REVERT: D 27 TYR cc_start: 0.4448 (OUTLIER) cc_final: 0.2683 (m-80) REVERT: D 54 GLN cc_start: 0.5930 (OUTLIER) cc_final: 0.5607 (mp10) REVERT: D 78 LYS cc_start: 0.8134 (ttpp) cc_final: 0.7620 (ttmt) REVERT: D 173 PHE cc_start: 0.7297 (OUTLIER) cc_final: 0.6898 (t80) outliers start: 44 outliers final: 34 residues processed: 236 average time/residue: 0.2762 time to fit residues: 101.3284 Evaluate side-chains 238 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 182 HIS Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 333 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 36 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 112 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN B 461 GLN C 420 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.182402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.134620 restraints weight = 16949.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.138690 restraints weight = 9826.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.141272 restraints weight = 7165.431| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12976 Z= 0.127 Angle : 0.458 8.155 17571 Z= 0.241 Chirality : 0.036 0.226 2013 Planarity : 0.003 0.062 2079 Dihedral : 9.423 69.781 1917 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.06 % Allowed : 26.76 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.22), residues: 1501 helix: 2.98 (0.15), residues: 1173 sheet: -0.70 (1.21), residues: 24 loop : -1.38 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 408 HIS 0.003 0.001 HIS B 322 PHE 0.027 0.001 PHE D 73 TYR 0.016 0.001 TYR C 101 ARG 0.001 0.000 ARG C 312 Details of bonding type rmsd hydrogen bonds : bond 0.04028 ( 943) hydrogen bonds : angle 3.12918 ( 2811) covalent geometry : bond 0.00292 (12976) covalent geometry : angle 0.45782 (17571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 206 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7564 (mp) REVERT: A 455 TYR cc_start: 0.8479 (t80) cc_final: 0.8029 (t80) REVERT: C 40 PHE cc_start: 0.6732 (m-80) cc_final: 0.6506 (m-80) REVERT: C 328 TYR cc_start: 0.8229 (t80) cc_final: 0.7409 (t80) REVERT: C 420 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7423 (mt0) REVERT: D 13 MET cc_start: 0.7194 (mtt) cc_final: 0.6870 (mtm) REVERT: D 27 TYR cc_start: 0.4617 (OUTLIER) cc_final: 0.2824 (m-80) REVERT: D 54 GLN cc_start: 0.5890 (OUTLIER) cc_final: 0.5579 (mp10) REVERT: D 78 LYS cc_start: 0.8169 (ttpp) cc_final: 0.7655 (ttmt) REVERT: D 173 PHE cc_start: 0.7261 (OUTLIER) cc_final: 0.7009 (t80) REVERT: D 352 LEU cc_start: 0.8501 (mm) cc_final: 0.8296 (mt) outliers start: 56 outliers final: 42 residues processed: 245 average time/residue: 0.2563 time to fit residues: 97.8094 Evaluate side-chains 246 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 420 GLN Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 333 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 15 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN B 424 GLN B 461 GLN ** C 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.183207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.135615 restraints weight = 16672.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.139713 restraints weight = 9698.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.142277 restraints weight = 7078.172| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12976 Z= 0.117 Angle : 0.462 8.519 17571 Z= 0.241 Chirality : 0.036 0.227 2013 Planarity : 0.003 0.062 2079 Dihedral : 9.323 69.085 1917 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.48 % Allowed : 27.85 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.29 (0.22), residues: 1501 helix: 3.06 (0.15), residues: 1172 sheet: -0.70 (1.20), residues: 24 loop : -1.38 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 408 HIS 0.003 0.001 HIS B 322 PHE 0.026 0.001 PHE D 73 TYR 0.013 0.001 TYR D 165 ARG 0.003 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.03922 ( 943) hydrogen bonds : angle 3.08827 ( 2811) covalent geometry : bond 0.00263 (12976) covalent geometry : angle 0.46217 (17571) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 198 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 TYR cc_start: 0.8474 (t80) cc_final: 0.8019 (t80) REVERT: B 391 GLU cc_start: 0.8044 (tt0) cc_final: 0.7771 (tt0) REVERT: C 328 TYR cc_start: 0.8195 (t80) cc_final: 0.7397 (t80) REVERT: D 27 TYR cc_start: 0.4731 (OUTLIER) cc_final: 0.2925 (m-80) REVERT: D 54 GLN cc_start: 0.5893 (OUTLIER) cc_final: 0.5602 (mp10) REVERT: D 78 LYS cc_start: 0.8173 (ttpp) cc_final: 0.7669 (ttmt) REVERT: D 173 PHE cc_start: 0.7168 (OUTLIER) cc_final: 0.6901 (t80) REVERT: D 352 LEU cc_start: 0.8498 (mm) cc_final: 0.8290 (mt) outliers start: 48 outliers final: 41 residues processed: 234 average time/residue: 0.2031 time to fit residues: 74.8328 Evaluate side-chains 237 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 193 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 173 PHE Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 333 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 84 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 2 optimal weight: 0.0060 chunk 31 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 95 optimal weight: 0.0770 chunk 102 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS B 202 GLN B 407 HIS B 424 GLN B 461 GLN C 230 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.185077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.137609 restraints weight = 16787.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.141337 restraints weight = 9662.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.144224 restraints weight = 7105.057| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12976 Z= 0.103 Angle : 0.446 8.143 17571 Z= 0.235 Chirality : 0.036 0.231 2013 Planarity : 0.003 0.061 2079 Dihedral : 9.159 67.962 1917 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.83 % Allowed : 28.35 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.38 (0.22), residues: 1501 helix: 3.13 (0.15), residues: 1172 sheet: -0.80 (1.21), residues: 24 loop : -1.36 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 408 HIS 0.003 0.000 HIS B 322 PHE 0.024 0.001 PHE D 73 TYR 0.012 0.001 TYR D 165 ARG 0.002 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 943) hydrogen bonds : angle 3.05084 ( 2811) covalent geometry : bond 0.00217 (12976) covalent geometry : angle 0.44644 (17571) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 211 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 TYR cc_start: 0.8470 (t80) cc_final: 0.8032 (t80) REVERT: B 391 GLU cc_start: 0.8022 (tt0) cc_final: 0.7732 (tt0) REVERT: C 187 TRP cc_start: 0.6452 (p90) cc_final: 0.6008 (p90) REVERT: C 328 TYR cc_start: 0.8161 (t80) cc_final: 0.7587 (t80) REVERT: D 27 TYR cc_start: 0.4604 (OUTLIER) cc_final: 0.2881 (m-80) REVERT: D 54 GLN cc_start: 0.5884 (OUTLIER) cc_final: 0.5588 (mp10) REVERT: D 78 LYS cc_start: 0.8220 (ttpp) cc_final: 0.7737 (ttmt) REVERT: D 207 LYS cc_start: 0.8198 (mptt) cc_final: 0.7966 (mmmm) REVERT: D 352 LEU cc_start: 0.8483 (mm) cc_final: 0.8229 (mt) outliers start: 39 outliers final: 30 residues processed: 237 average time/residue: 0.2118 time to fit residues: 78.3539 Evaluate side-chains 231 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 234 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 45 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS B 407 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.184493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.136765 restraints weight = 16774.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.140887 restraints weight = 9740.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.143500 restraints weight = 7085.906| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12976 Z= 0.114 Angle : 0.465 8.956 17571 Z= 0.244 Chirality : 0.036 0.243 2013 Planarity : 0.003 0.061 2079 Dihedral : 9.154 67.630 1917 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.26 % Allowed : 28.14 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.34 (0.22), residues: 1501 helix: 3.09 (0.15), residues: 1172 sheet: -0.79 (1.19), residues: 24 loop : -1.37 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 408 HIS 0.006 0.001 HIS B 407 PHE 0.026 0.001 PHE D 173 TYR 0.017 0.001 TYR D 221 ARG 0.001 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 943) hydrogen bonds : angle 3.08754 ( 2811) covalent geometry : bond 0.00257 (12976) covalent geometry : angle 0.46461 (17571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 203 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 TYR cc_start: 0.8469 (t80) cc_final: 0.8001 (t80) REVERT: B 391 GLU cc_start: 0.8013 (tt0) cc_final: 0.7728 (tt0) REVERT: C 187 TRP cc_start: 0.6477 (p90) cc_final: 0.6068 (p90) REVERT: C 328 TYR cc_start: 0.8151 (t80) cc_final: 0.7496 (t80) REVERT: D 27 TYR cc_start: 0.4616 (OUTLIER) cc_final: 0.3024 (m-80) REVERT: D 54 GLN cc_start: 0.5863 (OUTLIER) cc_final: 0.5579 (mp10) REVERT: D 78 LYS cc_start: 0.8223 (ttpp) cc_final: 0.7727 (ttmt) REVERT: D 207 LYS cc_start: 0.8212 (mptt) cc_final: 0.7956 (mmmm) REVERT: D 352 LEU cc_start: 0.8504 (mm) cc_final: 0.8221 (mt) outliers start: 45 outliers final: 36 residues processed: 234 average time/residue: 0.2217 time to fit residues: 80.6250 Evaluate side-chains 239 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 56 optimal weight: 20.0000 chunk 85 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 116 optimal weight: 0.4980 chunk 148 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 96 optimal weight: 0.0370 chunk 89 optimal weight: 3.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.184837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.137231 restraints weight = 16736.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.141352 restraints weight = 9679.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.143954 restraints weight = 7023.848| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12976 Z= 0.109 Angle : 0.462 8.875 17571 Z= 0.243 Chirality : 0.036 0.245 2013 Planarity : 0.003 0.061 2079 Dihedral : 9.133 67.278 1917 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.19 % Allowed : 28.28 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.35 (0.22), residues: 1501 helix: 3.11 (0.15), residues: 1171 sheet: -0.79 (1.20), residues: 24 loop : -1.37 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 408 HIS 0.003 0.001 HIS B 322 PHE 0.033 0.001 PHE C 456 TYR 0.015 0.001 TYR D 221 ARG 0.003 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.03753 ( 943) hydrogen bonds : angle 3.08190 ( 2811) covalent geometry : bond 0.00238 (12976) covalent geometry : angle 0.46241 (17571) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 202 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 MET cc_start: 0.7540 (mmm) cc_final: 0.7340 (mmp) REVERT: A 455 TYR cc_start: 0.8466 (t80) cc_final: 0.7998 (t80) REVERT: B 216 MET cc_start: 0.8138 (mmm) cc_final: 0.7911 (tpp) REVERT: B 391 GLU cc_start: 0.8006 (tt0) cc_final: 0.7726 (tt0) REVERT: B 424 GLN cc_start: 0.7789 (tp40) cc_final: 0.7481 (tp-100) REVERT: C 84 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8300 (t) REVERT: C 187 TRP cc_start: 0.6466 (p90) cc_final: 0.6074 (p90) REVERT: C 328 TYR cc_start: 0.8155 (t80) cc_final: 0.7602 (t80) REVERT: D 13 MET cc_start: 0.7096 (mtt) cc_final: 0.6470 (tmm) REVERT: D 27 TYR cc_start: 0.4630 (OUTLIER) cc_final: 0.3247 (m-80) REVERT: D 54 GLN cc_start: 0.5864 (OUTLIER) cc_final: 0.5579 (mp10) REVERT: D 78 LYS cc_start: 0.8228 (ttpp) cc_final: 0.7735 (ttmt) REVERT: D 207 LYS cc_start: 0.8184 (mptt) cc_final: 0.7935 (mmmm) REVERT: D 352 LEU cc_start: 0.8499 (mm) cc_final: 0.8219 (mt) outliers start: 44 outliers final: 36 residues processed: 234 average time/residue: 0.1984 time to fit residues: 72.9981 Evaluate side-chains 241 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 202 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 155 PHE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 107 TYR Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 27 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 chunk 56 optimal weight: 20.0000 chunk 98 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS C 322 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.179018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.131174 restraints weight = 16855.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.135164 restraints weight = 9973.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.137574 restraints weight = 7316.283| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12976 Z= 0.198 Angle : 0.546 8.913 17571 Z= 0.285 Chirality : 0.039 0.237 2013 Planarity : 0.003 0.063 2079 Dihedral : 9.536 68.562 1917 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.90 % Allowed : 28.72 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.22), residues: 1501 helix: 2.82 (0.15), residues: 1173 sheet: -0.80 (1.19), residues: 24 loop : -1.42 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 408 HIS 0.005 0.001 HIS B 388 PHE 0.030 0.002 PHE D 73 TYR 0.024 0.001 TYR D 243 ARG 0.003 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.04557 ( 943) hydrogen bonds : angle 3.31332 ( 2811) covalent geometry : bond 0.00477 (12976) covalent geometry : angle 0.54618 (17571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4389.93 seconds wall clock time: 79 minutes 2.24 seconds (4742.24 seconds total)