Starting phenix.real_space_refine on Thu Sep 18 00:23:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z9z_39873/09_2025/8z9z_39873.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z9z_39873/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8z9z_39873/09_2025/8z9z_39873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z9z_39873/09_2025/8z9z_39873.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z9z_39873/09_2025/8z9z_39873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z9z_39873/09_2025/8z9z_39873.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.37, per 1000 atoms: 0.19 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: 0.93 Conformation dependent library (CDL) restraints added in 720.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.35 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: 1.73 Time building geometry restraints manager: 1.27 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 501)) selection = (chain 'B' and (resid 5 through 156 or resid 175 through 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 11.200 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.740 ------------------------------------------------------------------------------- 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 : 8.99 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.002 0.000 ARG C 41 TYR 0.018 0.001 TYR D 243 PHE 0.036 0.001 PHE C 456 TRP 0.033 0.001 TRP B 408 HIS 0.003 0.001 HIS D 85 Details of bonding type rmsd covalent geometry : bond 0.00232 (12976) covalent geometry : angle 0.48110 (17571) hydrogen bonds : bond 0.08123 ( 943) hydrogen bonds : angle 3.62070 ( 2811) *********************** 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 : 0.388 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: 0.0884 time to fit residues: 28.3175 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 : 0.413 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.3980 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 A 407 HIS ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN B 307 GLN B 424 GLN C 214 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.170699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.132070 restraints weight = 15478.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.131565 restraints weight = 13525.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.133658 restraints weight = 11471.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.133868 restraints weight = 9169.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.134006 restraints weight = 8366.260| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12976 Z= 0.235 Angle : 0.568 8.517 17571 Z= 0.296 Chirality : 0.039 0.178 2013 Planarity : 0.004 0.065 2079 Dihedral : 10.116 75.079 1919 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 5.58 % Allowed : 25.53 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.79 (0.22), residues: 1501 helix: 2.63 (0.15), residues: 1180 sheet: -0.08 (1.21), residues: 24 loop : -1.38 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 321 TYR 0.021 0.002 TYR C 404 PHE 0.020 0.002 PHE D 173 TRP 0.022 0.001 TRP B 408 HIS 0.006 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00569 (12976) covalent geometry : angle 0.56752 (17571) hydrogen bonds : bond 0.04924 ( 943) hydrogen bonds : angle 3.45030 ( 2811) *********************** 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 283 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 206 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7250 (mt-10) REVERT: B 408 TRP cc_start: 0.8634 (p-90) cc_final: 0.8299 (p-90) REVERT: D 13 MET cc_start: 0.7193 (mtm) cc_final: 0.6882 (mtt) REVERT: D 47 PHE cc_start: 0.6650 (OUTLIER) cc_final: 0.6305 (t80) REVERT: D 54 GLN cc_start: 0.5755 (OUTLIER) cc_final: 0.5480 (mp10) REVERT: D 78 LYS cc_start: 0.8505 (ttpp) cc_final: 0.8041 (ttmt) REVERT: D 352 LEU cc_start: 0.8795 (mm) cc_final: 0.8514 (mt) outliers start: 77 outliers final: 55 residues processed: 258 average time/residue: 0.0834 time to fit residues: 34.0752 Evaluate side-chains 249 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 191 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 THR 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 334 GLU Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 350 ILE 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 61 ILE Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 333 THR 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 B residue 454 THR 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 178 ARG Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 348 THR 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 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 84 MET Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 351 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 130 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 134 optimal weight: 0.2980 chunk 125 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 B 424 GLN B 439 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.175972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.137608 restraints weight = 15609.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136271 restraints weight = 13185.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.138138 restraints weight = 11867.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.139056 restraints weight = 10089.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.139070 restraints weight = 8619.436| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12976 Z= 0.118 Angle : 0.455 7.812 17571 Z= 0.241 Chirality : 0.036 0.188 2013 Planarity : 0.003 0.064 2079 Dihedral : 9.737 72.325 1917 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.05 % Allowed : 27.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.10 (0.22), residues: 1501 helix: 2.86 (0.15), residues: 1179 sheet: -0.41 (1.19), residues: 24 loop : -1.32 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 312 TYR 0.013 0.001 TYR C 374 PHE 0.020 0.001 PHE C 90 TRP 0.015 0.001 TRP B 408 HIS 0.003 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00258 (12976) covalent geometry : angle 0.45529 (17571) hydrogen bonds : bond 0.04157 ( 943) hydrogen bonds : angle 3.19985 ( 2811) *********************** 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 251 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 209 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 408 TRP cc_start: 0.8522 (p-90) cc_final: 0.8091 (p-90) REVERT: C 236 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8081 (tt0) REVERT: C 328 TYR cc_start: 0.8414 (t80) cc_final: 0.8017 (t80) REVERT: D 13 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.7013 (mtt) REVERT: D 47 PHE cc_start: 0.6723 (OUTLIER) cc_final: 0.6433 (t80) REVERT: D 54 GLN cc_start: 0.5815 (OUTLIER) cc_final: 0.5467 (mp10) REVERT: D 78 LYS cc_start: 0.8430 (ttpp) cc_final: 0.7970 (ttmt) REVERT: D 173 PHE cc_start: 0.7143 (OUTLIER) cc_final: 0.6879 (t80) outliers start: 42 outliers final: 25 residues processed: 233 average time/residue: 0.0845 time to fit residues: 31.1207 Evaluate side-chains 228 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 219 LEU 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 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 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 138 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 182 HIS Chi-restraints excluded: chain C residue 236 GLU 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 54 GLN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 84 MET 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 54 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 B 424 GLN B 425 GLN B 461 GLN C 420 GLN D 108 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.173683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.135709 restraints weight = 15558.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.135218 restraints weight = 13406.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.135843 restraints weight = 11641.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.136987 restraints weight = 11008.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.136974 restraints weight = 9044.459| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12976 Z= 0.162 Angle : 0.492 8.104 17571 Z= 0.258 Chirality : 0.037 0.198 2013 Planarity : 0.003 0.064 2079 Dihedral : 9.780 72.554 1917 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.35 % Allowed : 27.19 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.98 (0.22), residues: 1501 helix: 2.79 (0.15), residues: 1177 sheet: -0.49 (1.20), residues: 24 loop : -1.36 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 312 TYR 0.012 0.001 TYR D 165 PHE 0.029 0.001 PHE D 73 TRP 0.013 0.001 TRP B 408 HIS 0.003 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00382 (12976) covalent geometry : angle 0.49240 (17571) hydrogen bonds : bond 0.04334 ( 943) hydrogen bonds : angle 3.24409 ( 2811) *********************** 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 270 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 210 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 345 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7717 (mp) REVERT: A 455 TYR cc_start: 0.8545 (t80) cc_final: 0.8146 (t80) REVERT: B 408 TRP cc_start: 0.8566 (p-90) cc_final: 0.8243 (p-90) REVERT: C 328 TYR cc_start: 0.8454 (t80) cc_final: 0.8075 (t80) REVERT: C 420 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.7190 (mt0) REVERT: D 13 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6937 (mtt) REVERT: D 54 GLN cc_start: 0.5934 (OUTLIER) cc_final: 0.5618 (mp10) REVERT: D 78 LYS cc_start: 0.8467 (ttpp) cc_final: 0.8001 (ttmt) REVERT: D 173 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.6949 (t80) REVERT: D 352 LEU cc_start: 0.8750 (mm) cc_final: 0.8539 (mt) outliers start: 60 outliers final: 40 residues processed: 247 average time/residue: 0.0835 time to fit residues: 32.9167 Evaluate side-chains 244 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 333 THR 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 36 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 138 VAL 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 420 GLN Chi-restraints excluded: chain C residue 422 VAL 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 51 VAL Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 108 HIS 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 230 SER Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 338 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 96 optimal weight: 10.0000 chunk 145 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.173446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.135345 restraints weight = 15732.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.133799 restraints weight = 13053.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.134849 restraints weight = 11401.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.135399 restraints weight = 10192.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135558 restraints weight = 8863.070| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12976 Z= 0.162 Angle : 0.504 8.112 17571 Z= 0.264 Chirality : 0.037 0.202 2013 Planarity : 0.003 0.065 2079 Dihedral : 9.782 72.155 1917 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.57 % Allowed : 27.19 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.94 (0.22), residues: 1501 helix: 2.77 (0.15), residues: 1177 sheet: -0.61 (1.21), residues: 24 loop : -1.39 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 321 TYR 0.012 0.001 TYR D 221 PHE 0.018 0.001 PHE C 90 TRP 0.013 0.001 TRP B 408 HIS 0.008 0.001 HIS D 108 Details of bonding type rmsd covalent geometry : bond 0.00383 (12976) covalent geometry : angle 0.50368 (17571) hydrogen bonds : bond 0.04362 ( 943) hydrogen bonds : angle 3.26414 ( 2811) *********************** 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 268 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 205 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 455 TYR cc_start: 0.8571 (t80) cc_final: 0.8170 (t80) REVERT: B 408 TRP cc_start: 0.8585 (p-90) cc_final: 0.8268 (p-90) REVERT: C 328 TYR cc_start: 0.8463 (t80) cc_final: 0.8087 (t80) REVERT: D 10 PHE cc_start: 0.8243 (t80) cc_final: 0.8013 (t80) REVERT: D 13 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.7046 (mtt) REVERT: D 54 GLN cc_start: 0.5891 (OUTLIER) cc_final: 0.5547 (mp10) REVERT: D 78 LYS cc_start: 0.8420 (ttpp) cc_final: 0.7855 (ttmt) REVERT: D 173 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.6991 (t80) REVERT: D 352 LEU cc_start: 0.8780 (mm) cc_final: 0.8422 (mt) outliers start: 63 outliers final: 49 residues processed: 243 average time/residue: 0.0837 time to fit residues: 32.9010 Evaluate side-chains 250 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 198 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 50 ILE 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 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 237 ILE 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 453 VAL Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 48 THR 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 333 THR Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 338 SER 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 C residue 64 VAL Chi-restraints excluded: chain C residue 138 VAL 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 382 ILE Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 396 SER Chi-restraints excluded: chain C residue 422 VAL 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 51 VAL Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 84 MET 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 225 MET Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 234 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN D 108 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.172052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.133992 restraints weight = 15532.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.132670 restraints weight = 13582.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.133975 restraints weight = 11934.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.134372 restraints weight = 10575.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.134722 restraints weight = 9287.498| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12976 Z= 0.189 Angle : 0.531 8.373 17571 Z= 0.277 Chirality : 0.038 0.209 2013 Planarity : 0.003 0.065 2079 Dihedral : 9.948 71.874 1917 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 5.15 % Allowed : 26.90 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.80 (0.22), residues: 1501 helix: 2.65 (0.15), residues: 1181 sheet: -0.57 (1.22), residues: 24 loop : -1.42 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 312 TYR 0.019 0.001 TYR C 101 PHE 0.031 0.001 PHE D 73 TRP 0.012 0.001 TRP B 408 HIS 0.004 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00453 (12976) covalent geometry : angle 0.53122 (17571) hydrogen bonds : bond 0.04570 ( 943) hydrogen bonds : angle 3.31707 ( 2811) *********************** 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 274 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 203 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 334 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7450 (mt-10) REVERT: A 345 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7702 (mp) REVERT: A 455 TYR cc_start: 0.8599 (t80) cc_final: 0.8204 (t80) REVERT: D 10 PHE cc_start: 0.8309 (t80) cc_final: 0.8028 (t80) REVERT: D 13 MET cc_start: 0.7489 (mtm) cc_final: 0.7229 (mtt) REVERT: D 54 GLN cc_start: 0.5854 (OUTLIER) cc_final: 0.5512 (mp10) REVERT: D 78 LYS cc_start: 0.8387 (ttpp) cc_final: 0.7794 (ttmt) REVERT: D 173 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.7038 (t80) REVERT: D 352 LEU cc_start: 0.8718 (mm) cc_final: 0.8389 (mt) outliers start: 71 outliers final: 60 residues processed: 245 average time/residue: 0.0817 time to fit residues: 32.1568 Evaluate side-chains 260 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 196 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 146 THR 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 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 40 PHE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 81 LEU 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 225 VAL Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 338 SER 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 36 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 182 HIS Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 396 SER 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 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 84 MET Chi-restraints excluded: chain D residue 108 HIS 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 225 MET Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 234 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 92 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.172911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.134580 restraints weight = 15423.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.134233 restraints weight = 13614.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.135798 restraints weight = 11857.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.136126 restraints weight = 9788.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136341 restraints weight = 8727.555| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1384 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= 0.166 Angle : 0.523 8.800 17571 Z= 0.272 Chirality : 0.038 0.209 2013 Planarity : 0.003 0.065 2079 Dihedral : 9.849 71.092 1917 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 5.15 % Allowed : 27.41 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.83 (0.22), residues: 1501 helix: 2.70 (0.15), residues: 1174 sheet: -0.65 (1.23), residues: 24 loop : -1.47 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 41 TYR 0.018 0.001 TYR D 243 PHE 0.032 0.001 PHE D 73 TRP 0.013 0.001 TRP B 408 HIS 0.010 0.001 HIS D 108 Details of bonding type rmsd covalent geometry : bond 0.00394 (12976) covalent geometry : angle 0.52301 (17571) hydrogen bonds : bond 0.04451 ( 943) hydrogen bonds : angle 3.29371 ( 2811) *********************** 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 270 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 199 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 334 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7430 (mt-10) REVERT: A 345 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7756 (mp) REVERT: B 391 GLU cc_start: 0.8010 (tt0) cc_final: 0.7784 (tt0) REVERT: B 408 TRP cc_start: 0.8735 (p-90) cc_final: 0.8323 (p-90) REVERT: C 369 PHE cc_start: 0.6560 (OUTLIER) cc_final: 0.5559 (m-80) REVERT: D 10 PHE cc_start: 0.8242 (t80) cc_final: 0.7956 (t80) REVERT: D 54 GLN cc_start: 0.5758 (OUTLIER) cc_final: 0.5429 (mp10) REVERT: D 78 LYS cc_start: 0.8390 (ttpp) cc_final: 0.7799 (ttmt) REVERT: D 173 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.6994 (t80) REVERT: D 352 LEU cc_start: 0.8725 (mm) cc_final: 0.8388 (mt) outliers start: 71 outliers final: 58 residues processed: 246 average time/residue: 0.0846 time to fit residues: 33.5101 Evaluate side-chains 261 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 198 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 146 THR 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 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 40 PHE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 81 LEU 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 225 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 338 SER 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 110 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 182 HIS Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 335 CYS Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 369 PHE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 396 SER 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 84 MET 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 225 MET Chi-restraints excluded: chain D residue 234 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 104 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 123 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.174753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.136132 restraints weight = 15428.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.135028 restraints weight = 13004.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.136304 restraints weight = 11306.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.136721 restraints weight = 9552.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.136977 restraints weight = 8822.230| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12976 Z= 0.139 Angle : 0.495 8.594 17571 Z= 0.257 Chirality : 0.037 0.218 2013 Planarity : 0.003 0.064 2079 Dihedral : 9.597 70.217 1917 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.35 % Allowed : 27.92 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.98 (0.22), residues: 1501 helix: 2.81 (0.15), residues: 1174 sheet: -0.65 (1.21), residues: 24 loop : -1.42 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 41 TYR 0.015 0.001 TYR C 101 PHE 0.029 0.001 PHE D 73 TRP 0.012 0.001 TRP B 408 HIS 0.003 0.001 HIS D 108 Details of bonding type rmsd covalent geometry : bond 0.00322 (12976) covalent geometry : angle 0.49519 (17571) hydrogen bonds : bond 0.04196 ( 943) hydrogen bonds : angle 3.20372 ( 2811) *********************** 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 269 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 209 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 345 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7668 (mp) REVERT: A 455 TYR cc_start: 0.8585 (t80) cc_final: 0.8180 (t80) REVERT: B 391 GLU cc_start: 0.8045 (tt0) cc_final: 0.7809 (tt0) REVERT: B 408 TRP cc_start: 0.8715 (p-90) cc_final: 0.8280 (p-90) REVERT: C 328 TYR cc_start: 0.8456 (t80) cc_final: 0.7982 (t80) REVERT: D 54 GLN cc_start: 0.5595 (OUTLIER) cc_final: 0.5193 (mp10) REVERT: D 78 LYS cc_start: 0.8328 (ttpp) cc_final: 0.7725 (ttmt) REVERT: D 173 PHE cc_start: 0.7172 (OUTLIER) cc_final: 0.6951 (t80) REVERT: D 352 LEU cc_start: 0.8706 (mm) cc_final: 0.8372 (mt) outliers start: 60 outliers final: 49 residues processed: 252 average time/residue: 0.0851 time to fit residues: 34.5845 Evaluate side-chains 251 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 199 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 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 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 B residue 40 PHE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 81 LEU 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 225 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 338 SER 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 36 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 182 HIS Chi-restraints excluded: chain C residue 197 VAL 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 396 SER 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 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 84 MET 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 234 LEU Chi-restraints excluded: chain D residue 264 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 15 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 3 optimal weight: 9.9990 chunk 45 optimal weight: 0.4980 chunk 128 optimal weight: 10.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 424 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.173002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.135223 restraints weight = 15558.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.132885 restraints weight = 12538.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.133944 restraints weight = 11884.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.134841 restraints weight = 10155.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.135058 restraints weight = 8924.973| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12976 Z= 0.176 Angle : 0.537 8.252 17571 Z= 0.279 Chirality : 0.038 0.211 2013 Planarity : 0.003 0.065 2079 Dihedral : 9.673 70.674 1917 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.86 % Allowed : 27.92 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.83 (0.22), residues: 1501 helix: 2.70 (0.15), residues: 1174 sheet: -0.61 (1.22), residues: 24 loop : -1.45 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 41 TYR 0.021 0.001 TYR D 243 PHE 0.031 0.001 PHE D 73 TRP 0.011 0.001 TRP B 408 HIS 0.003 0.001 HIS B 226 Details of bonding type rmsd covalent geometry : bond 0.00421 (12976) covalent geometry : angle 0.53706 (17571) hydrogen bonds : bond 0.04450 ( 943) hydrogen bonds : angle 3.31561 ( 2811) *********************** 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 269 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 202 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 345 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7747 (mp) REVERT: A 455 TYR cc_start: 0.8596 (t80) cc_final: 0.8243 (t80) REVERT: B 391 GLU cc_start: 0.8021 (tt0) cc_final: 0.7806 (tt0) REVERT: D 54 GLN cc_start: 0.5600 (OUTLIER) cc_final: 0.5182 (mp10) REVERT: D 78 LYS cc_start: 0.8338 (ttpp) cc_final: 0.7731 (ttmt) REVERT: D 352 LEU cc_start: 0.8748 (mm) cc_final: 0.8464 (mt) outliers start: 67 outliers final: 59 residues processed: 248 average time/residue: 0.0904 time to fit residues: 35.6010 Evaluate side-chains 260 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 199 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 146 THR 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 335 CYS 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 B residue 26 ILE Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 81 LEU 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 225 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 335 CYS Chi-restraints excluded: chain B residue 338 SER 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 398 SER Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 182 HIS Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 238 LEU 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 396 SER 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 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 84 MET Chi-restraints excluded: chain D residue 117 VAL 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 264 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 46 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 119 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 146 optimal weight: 0.6980 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 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN B 424 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.176472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.138157 restraints weight = 15579.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.137322 restraints weight = 13467.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.138552 restraints weight = 12120.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.139330 restraints weight = 10330.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.139585 restraints weight = 8896.812| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12976 Z= 0.120 Angle : 0.491 8.518 17571 Z= 0.258 Chirality : 0.037 0.238 2013 Planarity : 0.003 0.064 2079 Dihedral : 9.469 70.619 1917 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.41 % Allowed : 29.44 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.05 (0.22), residues: 1501 helix: 2.87 (0.15), residues: 1174 sheet: -0.66 (1.21), residues: 24 loop : -1.41 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 312 TYR 0.016 0.001 TYR D 221 PHE 0.034 0.001 PHE D 173 TRP 0.012 0.001 TRP B 408 HIS 0.005 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00264 (12976) covalent geometry : angle 0.49134 (17571) hydrogen bonds : bond 0.04072 ( 943) hydrogen bonds : angle 3.18723 ( 2811) ********************** 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 252 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 205 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 345 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7648 (mp) REVERT: B 172 MET cc_start: 0.7664 (pmm) cc_final: 0.7453 (ptp) REVERT: B 391 GLU cc_start: 0.7908 (tt0) cc_final: 0.7693 (tt0) REVERT: B 408 TRP cc_start: 0.8690 (p-90) cc_final: 0.8229 (p-90) REVERT: C 328 TYR cc_start: 0.8375 (t80) cc_final: 0.7665 (t80) REVERT: D 13 MET cc_start: 0.6991 (mtt) cc_final: 0.6679 (mtm) REVERT: D 54 GLN cc_start: 0.5585 (OUTLIER) cc_final: 0.5184 (mp10) REVERT: D 78 LYS cc_start: 0.8352 (ttpp) cc_final: 0.7767 (ttmt) outliers start: 47 outliers final: 43 residues processed: 241 average time/residue: 0.0850 time to fit residues: 32.9124 Evaluate side-chains 242 residues out of total 1379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 197 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 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 324 HIS 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 B residue 40 PHE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 81 LEU 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 225 VAL 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 398 SER 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 182 HIS Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 238 LEU 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 396 SER Chi-restraints excluded: chain D residue 6 THR 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 84 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 102 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 362 ASN B 407 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.173458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.134790 restraints weight = 15535.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.133868 restraints weight = 13546.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.135044 restraints weight = 12471.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.136014 restraints weight = 10895.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.135956 restraints weight = 9374.953| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12976 Z= 0.173 Angle : 0.535 8.129 17571 Z= 0.280 Chirality : 0.038 0.228 2013 Planarity : 0.003 0.064 2079 Dihedral : 9.522 70.454 1917 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.28 % Allowed : 29.08 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.90 (0.22), residues: 1501 helix: 2.76 (0.15), residues: 1173 sheet: -0.58 (1.23), residues: 24 loop : -1.47 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 41 TYR 0.016 0.001 TYR D 221 PHE 0.023 0.001 PHE C 90 TRP 0.010 0.001 TRP B 408 HIS 0.004 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00412 (12976) covalent geometry : angle 0.53546 (17571) hydrogen bonds : bond 0.04426 ( 943) hydrogen bonds : angle 3.31359 ( 2811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1884.72 seconds wall clock time: 33 minutes 42.78 seconds (2022.78 seconds total)