Starting phenix.real_space_refine on Thu Jul 31 00:30:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z9a_39858/07_2025/8z9a_39858_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z9a_39858/07_2025/8z9a_39858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z9a_39858/07_2025/8z9a_39858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z9a_39858/07_2025/8z9a_39858.map" model { file = "/net/cci-nas-00/data/ceres_data/8z9a_39858/07_2025/8z9a_39858_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z9a_39858/07_2025/8z9a_39858_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.129 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 7 5.49 5 S 72 5.16 5 C 8695 2.51 5 N 1981 2.21 5 O 2266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13021 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: 2905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2905 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 7, 'TRANS': 349} 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: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PC1': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 68 Unusual residues: {'PC1': 1, 'SOU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.70, per 1000 atoms: 0.67 Number of scatterers: 13021 At special positions: 0 Unit cell: (115.56, 129.47, 132.68, 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 72 16.00 P 7 15.00 O 2266 8.00 N 1981 7.00 C 8695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.74 Conformation dependent library (CDL) restraints added in 1.8 seconds 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2994 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 4 sheets defined 80.7% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 7 through 12 removed outlier: 3.593A pdb=" N ASP A 11 " --> pdb=" O GLY A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 23 removed outlier: 3.657A pdb=" N GLY A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 65 removed outlier: 3.740A pdb=" N MET A 63 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 64 " --> pdb=" O VAL A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 95 removed outlier: 3.754A pdb=" N HIS A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N SER A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 91 " --> pdb=" O MET A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 105 removed outlier: 3.933A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 116 through 152 Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 191 through 237 removed outlier: 3.525A pdb=" N GLU A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 245 removed outlier: 3.700A pdb=" N SER A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 336 Processing helix chain 'A' and resid 337 through 359 removed outlier: 3.787A pdb=" N VAL A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 405 removed outlier: 3.558A pdb=" N ILE A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N HIS A 388 " --> pdb=" O MET A 384 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL A 399 " --> pdb=" O GLU A 395 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N MET A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 4.487A 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: 3.549A pdb=" N PHE A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 12 removed outlier: 3.521A pdb=" N ASP B 11 " --> pdb=" O GLY B 7 " (cutoff:3.500A) 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: 3.807A pdb=" N HIS B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N SER B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR B 95 " --> pdb=" O VAL B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 105 removed outlier: 3.888A 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 152 removed outlier: 3.656A pdb=" N SER B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS B 126 " --> pdb=" O ARG B 122 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN B 133 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 143 " --> pdb=" O SER B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 156 removed outlier: 4.256A pdb=" N GLY B 156 " --> pdb=" O THR B 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 153 through 156' Processing helix chain 'B' and resid 191 through 237 removed outlier: 3.522A pdb=" N TYR B 195 " --> pdb=" O HIS B 191 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET B 216 " --> pdb=" O HIS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 245 removed outlier: 3.590A pdb=" N SER B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 336 Processing helix chain 'B' and resid 337 through 359 removed outlier: 3.834A pdb=" N VAL B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 398 removed outlier: 3.961A pdb=" N PHE B 385 " --> pdb=" O GLN B 381 " (cutoff:3.500A) removed outlier: 3.888A 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: 3.672A 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 66 Processing helix chain 'C' and resid 69 through 95 removed outlier: 3.698A pdb=" N HIS C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 91 " --> pdb=" O MET C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 107 removed outlier: 3.906A pdb=" N PHE C 100 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TRP C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 149 removed outlier: 4.176A pdb=" N LYS C 126 " --> pdb=" O ARG C 122 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C 127 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 135 " --> pdb=" O MET C 131 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE C 143 " --> pdb=" O SER C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 237 removed outlier: 3.702A pdb=" N ILE C 196 " --> pdb=" O GLY C 192 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU C 217 " --> pdb=" O SER C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 246 Processing helix chain 'C' and resid 304 through 336 Processing helix chain 'C' and resid 336 through 358 removed outlier: 3.838A pdb=" N LEU C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 397 removed outlier: 3.903A pdb=" N ILE C 382 " --> pdb=" O SER C 378 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE C 385 " --> pdb=" O GLN C 381 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N HIS C 388 " --> pdb=" O MET C 384 " (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 426 Processing helix chain 'C' and resid 441 through 463 Processing helix chain 'D' and resid 5 through 14 removed outlier: 3.954A pdb=" N MET D 9 " --> pdb=" O ASP D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 46 Processing helix chain 'D' and resid 50 through 77 removed outlier: 3.566A pdb=" N PHE D 56 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS D 77 " --> pdb=" O PHE D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 89 Processing helix chain 'D' and resid 94 through 124 Proline residue: D 119 - end of helix Processing helix chain 'D' and resid 149 through 200 removed outlier: 3.925A pdb=" N SER D 163 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 164 " --> pdb=" O TYR D 160 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE D 178 " --> pdb=" O ILE D 174 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 256 removed outlier: 5.032A 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 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 263 through 271 removed outlier: 3.952A pdb=" N ALA D 269 " --> pdb=" O SER D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 287 removed outlier: 3.746A pdb=" N ASN D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 300 removed outlier: 3.876A pdb=" N LYS D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 3.614A 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 322 Processing helix chain 'D' and resid 337 through 360 removed outlier: 3.930A pdb=" N LEU D 345 " --> pdb=" O LEU D 341 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS D 346 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET D 347 " --> pdb=" O LYS D 343 " (cutoff:3.500A) 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: 3.919A 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 330 960 hydrogen bonds defined for protein. 2862 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: 4.05 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1889 1.31 - 1.44: 3948 1.44 - 1.57: 7391 1.57 - 1.69: 15 1.69 - 1.82: 116 Bond restraints: 13359 Sorted by residual: bond pdb=" CA SER D 271 " pdb=" CB SER D 271 " ideal model delta sigma weight residual 1.536 1.443 0.093 1.53e-02 4.27e+03 3.72e+01 bond pdb=" CA SER D 270 " pdb=" CB SER D 270 " ideal model delta sigma weight residual 1.531 1.438 0.093 1.72e-02 3.38e+03 2.90e+01 bond pdb=" C21 PC1 B 502 " pdb=" O21 PC1 B 502 " ideal model delta sigma weight residual 1.331 1.406 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C21 PC1 C 501 " pdb=" O21 PC1 C 501 " ideal model delta sigma weight residual 1.331 1.405 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C21 PC1 A 502 " pdb=" O21 PC1 A 502 " ideal model delta sigma weight residual 1.331 1.405 -0.074 2.00e-02 2.50e+03 1.35e+01 ... (remaining 13354 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 17702 2.92 - 5.84: 340 5.84 - 8.77: 30 8.77 - 11.69: 4 11.69 - 14.61: 8 Bond angle restraints: 18084 Sorted by residual: angle pdb=" CA PRO D 119 " pdb=" N PRO D 119 " pdb=" CD PRO D 119 " ideal model delta sigma weight residual 112.00 103.08 8.92 1.40e+00 5.10e-01 4.06e+01 angle pdb=" N ILE D 124 " pdb=" CA ILE D 124 " pdb=" C ILE D 124 " ideal model delta sigma weight residual 112.29 106.85 5.44 9.40e-01 1.13e+00 3.35e+01 angle pdb=" N SER D 271 " pdb=" CA SER D 271 " pdb=" C SER D 271 " ideal model delta sigma weight residual 113.72 106.48 7.24 1.30e+00 5.92e-01 3.10e+01 angle pdb=" O12 PC1 C 501 " pdb=" P PC1 C 501 " pdb=" O14 PC1 C 501 " ideal model delta sigma weight residual 123.67 109.06 14.61 3.00e+00 1.11e-01 2.37e+01 angle pdb=" O12 PC1 B 502 " pdb=" P PC1 B 502 " pdb=" O14 PC1 B 502 " ideal model delta sigma weight residual 123.67 109.29 14.38 3.00e+00 1.11e-01 2.30e+01 ... (remaining 18079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 6812 17.71 - 35.42: 731 35.42 - 53.14: 212 53.14 - 70.85: 60 70.85 - 88.56: 11 Dihedral angle restraints: 7826 sinusoidal: 3199 harmonic: 4627 Sorted by residual: dihedral pdb=" CA ASP D 133 " pdb=" C ASP D 133 " pdb=" N PRO D 134 " pdb=" CA PRO D 134 " ideal model delta harmonic sigma weight residual -180.00 -134.40 -45.60 0 5.00e+00 4.00e-02 8.32e+01 dihedral pdb=" CA VAL D 307 " pdb=" C VAL D 307 " pdb=" N SER D 308 " pdb=" CA SER D 308 " ideal model delta harmonic sigma weight residual -180.00 -156.93 -23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA SER D 310 " pdb=" C SER D 310 " pdb=" N PHE D 311 " pdb=" CA PHE D 311 " ideal model delta harmonic sigma weight residual 180.00 160.14 19.86 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 7823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1357 0.032 - 0.064: 505 0.064 - 0.096: 151 0.096 - 0.127: 42 0.127 - 0.159: 8 Chirality restraints: 2063 Sorted by residual: chirality pdb=" C2 PC1 B 502 " pdb=" C1 PC1 B 502 " pdb=" C3 PC1 B 502 " pdb=" O21 PC1 B 502 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.16 2.00e-01 2.50e+01 6.34e-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 0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" C2 PC1 A 502 " pdb=" C1 PC1 A 502 " pdb=" C3 PC1 A 502 " pdb=" O21 PC1 A 502 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 2060 not shown) Planarity restraints: 2140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 SOU D 402 " 0.051 2.00e-02 2.50e+03 1.38e-01 2.39e+02 pdb=" C11 SOU D 402 " 0.015 2.00e-02 2.50e+03 pdb=" C12 SOU D 402 " -0.124 2.00e-02 2.50e+03 pdb=" C8 SOU D 402 " -0.165 2.00e-02 2.50e+03 pdb=" C9 SOU D 402 " 0.224 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 SOU D 402 " -0.106 2.00e-02 2.50e+03 8.76e-02 9.59e+01 pdb=" C4 SOU D 402 " 0.137 2.00e-02 2.50e+03 pdb=" C5 SOU D 402 " 0.032 2.00e-02 2.50e+03 pdb=" C6 SOU D 402 " 0.019 2.00e-02 2.50e+03 pdb=" C7 SOU D 402 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 118 " -0.085 5.00e-02 4.00e+02 1.23e-01 2.43e+01 pdb=" N PRO D 119 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " -0.066 5.00e-02 4.00e+02 ... (remaining 2137 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 340 2.71 - 3.26: 13266 3.26 - 3.81: 21982 3.81 - 4.35: 26751 4.35 - 4.90: 46142 Nonbonded interactions: 108481 Sorted by model distance: nonbonded pdb=" O VAL D 116 " pdb=" OH TYR D 157 " model vdw 2.163 3.040 nonbonded pdb=" OE2 GLU A 320 " pdb=" OH TYR C 409 " model vdw 2.180 3.040 nonbonded pdb=" O PHE D 10 " pdb=" OG1 THR D 14 " model vdw 2.185 3.040 nonbonded pdb=" OH TYR B 409 " pdb=" OE2 GLU C 320 " model vdw 2.197 3.040 nonbonded pdb=" OH TYR C 92 " pdb=" OG SER C 338 " model vdw 2.215 3.040 ... (remaining 108476 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 156 or resid 175 through 463 or resid 501)) selection = (chain 'B' and (resid 5 through 156 or resid 175 through 463 or resid 501)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 33.940 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.005 0.093 13359 Z= 0.245 Angle : 0.835 14.611 18084 Z= 0.361 Chirality : 0.039 0.159 2063 Planarity : 0.006 0.138 2140 Dihedral : 16.754 88.562 4832 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.56 % Allowed : 17.41 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.22), residues: 1541 helix: 2.10 (0.15), residues: 1209 sheet: 1.55 (1.04), residues: 24 loop : -1.28 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 13 HIS 0.004 0.001 HIS A 388 PHE 0.020 0.001 PHE B 385 TYR 0.021 0.001 TYR C 44 ARG 0.007 0.001 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.12246 ( 960) hydrogen bonds : angle 4.88103 ( 2862) covalent geometry : bond 0.00517 (13359) covalent geometry : angle 0.83510 (18084) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 1.327 Fit side-chains revert: symmetry clash REVERT: D 5 ASP cc_start: 0.7007 (t0) cc_final: 0.6762 (t0) outliers start: 22 outliers final: 19 residues processed: 188 average time/residue: 1.0533 time to fit residues: 219.3433 Evaluate side-chains 175 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 15 ASN Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 275 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS A 322 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN C 72 GLN C 214 ASN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.150850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105038 restraints weight = 15129.966| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.09 r_work: 0.2982 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13359 Z= 0.155 Angle : 0.475 7.551 18084 Z= 0.251 Chirality : 0.038 0.160 2063 Planarity : 0.004 0.076 2140 Dihedral : 11.768 77.792 2040 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.33 % Allowed : 14.65 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.22), residues: 1541 helix: 2.47 (0.15), residues: 1217 sheet: 1.69 (1.07), residues: 24 loop : -1.22 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 408 HIS 0.004 0.001 HIS C 343 PHE 0.022 0.001 PHE B 385 TYR 0.018 0.001 TYR C 53 ARG 0.005 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.04698 ( 960) hydrogen bonds : angle 3.51065 ( 2862) covalent geometry : bond 0.00365 (13359) covalent geometry : angle 0.47535 (18084) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 176 time to evaluate : 1.466 Fit side-chains REVERT: A 312 ARG cc_start: 0.8322 (ttt180) cc_final: 0.8044 (ttt-90) REVERT: B 42 LYS cc_start: 0.7670 (mtpt) cc_final: 0.7078 (mmtt) REVERT: B 178 ARG cc_start: 0.8536 (ttm170) cc_final: 0.8294 (ttm170) REVERT: C 136 ILE cc_start: 0.6512 (OUTLIER) cc_final: 0.5957 (pp) REVERT: C 178 ARG cc_start: 0.6321 (ttm-80) cc_final: 0.5958 (ttt180) REVERT: D 5 ASP cc_start: 0.6942 (t0) cc_final: 0.6587 (t0) REVERT: D 309 LYS cc_start: 0.8901 (tmtt) cc_final: 0.8408 (tptt) outliers start: 47 outliers final: 19 residues processed: 203 average time/residue: 1.1445 time to fit residues: 256.6283 Evaluate side-chains 172 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 247 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 55 optimal weight: 0.0980 chunk 42 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.153247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107224 restraints weight = 15217.377| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.11 r_work: 0.2937 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13359 Z= 0.114 Angle : 0.431 7.566 18084 Z= 0.228 Chirality : 0.036 0.155 2063 Planarity : 0.003 0.067 2140 Dihedral : 11.091 76.386 2021 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.55 % Allowed : 15.99 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.22), residues: 1541 helix: 2.74 (0.14), residues: 1216 sheet: 1.69 (1.05), residues: 24 loop : -1.19 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 13 HIS 0.003 0.001 HIS A 388 PHE 0.017 0.001 PHE A 385 TYR 0.020 0.001 TYR C 53 ARG 0.007 0.000 ARG A 178 Details of bonding type rmsd hydrogen bonds : bond 0.04176 ( 960) hydrogen bonds : angle 3.31337 ( 2862) covalent geometry : bond 0.00249 (13359) covalent geometry : angle 0.43128 (18084) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 1.503 Fit side-chains REVERT: A 312 ARG cc_start: 0.8044 (ttt180) cc_final: 0.7740 (mtp180) REVERT: A 395 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8148 (tp30) REVERT: B 42 LYS cc_start: 0.7312 (mtpt) cc_final: 0.6795 (mmtt) REVERT: B 178 ARG cc_start: 0.8226 (ttm170) cc_final: 0.7875 (ttm170) REVERT: C 136 ILE cc_start: 0.6356 (OUTLIER) cc_final: 0.5900 (pp) REVERT: C 178 ARG cc_start: 0.6455 (ttm-80) cc_final: 0.6000 (ttt180) REVERT: C 310 LEU cc_start: 0.7233 (mt) cc_final: 0.7027 (tp) REVERT: C 401 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7254 (mm-30) REVERT: D 5 ASP cc_start: 0.6793 (t0) cc_final: 0.6445 (t0) outliers start: 36 outliers final: 12 residues processed: 191 average time/residue: 1.1071 time to fit residues: 233.3693 Evaluate side-chains 168 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 400 MET Chi-restraints excluded: chain C residue 462 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 152 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 134 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 HIS D 214 GLN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.147471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.101722 restraints weight = 15187.453| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.07 r_work: 0.2835 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 13359 Z= 0.230 Angle : 0.532 8.758 18084 Z= 0.277 Chirality : 0.041 0.158 2063 Planarity : 0.004 0.062 2140 Dihedral : 11.480 87.723 2019 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.10 % Allowed : 16.07 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.21), residues: 1541 helix: 2.49 (0.14), residues: 1214 sheet: 1.63 (1.02), residues: 24 loop : -1.15 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 408 HIS 0.006 0.001 HIS A 233 PHE 0.029 0.002 PHE B 385 TYR 0.023 0.002 TYR C 53 ARG 0.006 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.05197 ( 960) hydrogen bonds : angle 3.52579 ( 2862) covalent geometry : bond 0.00560 (13359) covalent geometry : angle 0.53196 (18084) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 171 time to evaluate : 1.335 Fit side-chains REVERT: A 312 ARG cc_start: 0.8120 (ttt180) cc_final: 0.7774 (mtp180) REVERT: B 178 ARG cc_start: 0.8319 (ttm170) cc_final: 0.7883 (ttm170) REVERT: C 21 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.7029 (mt) REVERT: C 136 ILE cc_start: 0.6459 (OUTLIER) cc_final: 0.5961 (pp) REVERT: C 178 ARG cc_start: 0.6906 (ttm-80) cc_final: 0.6377 (ttt90) REVERT: C 216 MET cc_start: 0.7799 (mmp) cc_final: 0.7434 (mmt) REVERT: C 401 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7597 (mm-30) REVERT: D 5 ASP cc_start: 0.6787 (t0) cc_final: 0.6429 (t0) outliers start: 58 outliers final: 25 residues processed: 207 average time/residue: 1.0562 time to fit residues: 241.5782 Evaluate side-chains 185 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 247 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 95 optimal weight: 8.9990 chunk 64 optimal weight: 0.0050 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 16 optimal weight: 0.0000 chunk 94 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 HIS ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.153191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.107363 restraints weight = 15275.992| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.11 r_work: 0.2942 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13359 Z= 0.105 Angle : 0.430 8.889 18084 Z= 0.226 Chirality : 0.036 0.151 2063 Planarity : 0.003 0.058 2140 Dihedral : 10.874 85.541 2019 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.62 % Allowed : 18.19 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.24 (0.22), residues: 1541 helix: 2.87 (0.14), residues: 1212 sheet: 1.86 (1.01), residues: 24 loop : -1.04 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 13 HIS 0.022 0.001 HIS B 407 PHE 0.016 0.001 PHE A 385 TYR 0.017 0.001 TYR C 53 ARG 0.007 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 960) hydrogen bonds : angle 3.27612 ( 2862) covalent geometry : bond 0.00220 (13359) covalent geometry : angle 0.43013 (18084) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 1.650 Fit side-chains REVERT: A 312 ARG cc_start: 0.8049 (ttt180) cc_final: 0.7725 (mtp180) REVERT: B 42 LYS cc_start: 0.7405 (mtpt) cc_final: 0.6877 (mmtt) REVERT: B 178 ARG cc_start: 0.8265 (ttm170) cc_final: 0.7867 (ttm170) REVERT: B 199 PHE cc_start: 0.8405 (t80) cc_final: 0.8097 (t80) REVERT: B 462 LEU cc_start: 0.7203 (tt) cc_final: 0.6861 (mp) REVERT: C 21 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6870 (mt) REVERT: C 178 ARG cc_start: 0.6874 (ttm-80) cc_final: 0.6456 (ttt180) REVERT: C 401 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7411 (mm-30) REVERT: D 5 ASP cc_start: 0.6831 (t0) cc_final: 0.6535 (t0) outliers start: 37 outliers final: 15 residues processed: 200 average time/residue: 1.1209 time to fit residues: 247.0668 Evaluate side-chains 174 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain D residue 66 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 51 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 114 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 HIS ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.151159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.105172 restraints weight = 15371.689| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.11 r_work: 0.2894 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13359 Z= 0.136 Angle : 0.466 10.020 18084 Z= 0.241 Chirality : 0.037 0.213 2063 Planarity : 0.003 0.057 2140 Dihedral : 10.870 88.353 2019 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.97 % Allowed : 17.98 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.22), residues: 1541 helix: 2.83 (0.14), residues: 1214 sheet: 1.79 (1.01), residues: 24 loop : -1.06 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 13 HIS 0.003 0.001 HIS B 407 PHE 0.019 0.001 PHE B 385 TYR 0.021 0.001 TYR B 92 ARG 0.006 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.04327 ( 960) hydrogen bonds : angle 3.31558 ( 2862) covalent geometry : bond 0.00315 (13359) covalent geometry : angle 0.46574 (18084) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 1.505 Fit side-chains revert: symmetry clash REVERT: A 312 ARG cc_start: 0.8074 (ttt180) cc_final: 0.7746 (mtp180) REVERT: A 395 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7942 (tt0) REVERT: B 42 LYS cc_start: 0.7386 (mtpt) cc_final: 0.6866 (mmtt) REVERT: B 178 ARG cc_start: 0.8258 (ttm170) cc_final: 0.7970 (ttm170) REVERT: B 461 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.6890 (mp10) REVERT: B 462 LEU cc_start: 0.7204 (tt) cc_final: 0.6871 (mp) REVERT: C 21 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6968 (mt) REVERT: C 63 MET cc_start: 0.7611 (ttp) cc_final: 0.7411 (ttp) REVERT: C 136 ILE cc_start: 0.6684 (OUTLIER) cc_final: 0.6323 (pt) REVERT: C 137 ILE cc_start: 0.5557 (OUTLIER) cc_final: 0.5320 (mp) REVERT: C 178 ARG cc_start: 0.7018 (ttm-80) cc_final: 0.6647 (ttt90) REVERT: D 5 ASP cc_start: 0.6844 (t0) cc_final: 0.6527 (t0) outliers start: 42 outliers final: 18 residues processed: 195 average time/residue: 1.1723 time to fit residues: 253.1018 Evaluate side-chains 178 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 66 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 111 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 50 optimal weight: 0.3980 chunk 82 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 HIS C 424 GLN D 86 GLN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.150935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.104840 restraints weight = 15281.505| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.11 r_work: 0.2891 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13359 Z= 0.143 Angle : 0.471 10.824 18084 Z= 0.244 Chirality : 0.038 0.193 2063 Planarity : 0.003 0.056 2140 Dihedral : 10.890 89.388 2019 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.97 % Allowed : 18.26 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.22), residues: 1541 helix: 2.80 (0.14), residues: 1214 sheet: 1.76 (1.00), residues: 24 loop : -1.06 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 13 HIS 0.003 0.001 HIS A 212 PHE 0.020 0.001 PHE B 385 TYR 0.021 0.001 TYR D 160 ARG 0.007 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.04385 ( 960) hydrogen bonds : angle 3.33996 ( 2862) covalent geometry : bond 0.00333 (13359) covalent geometry : angle 0.47058 (18084) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 1.533 Fit side-chains revert: symmetry clash REVERT: A 229 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: A 312 ARG cc_start: 0.8093 (ttt180) cc_final: 0.7748 (mtp180) REVERT: A 395 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7902 (tt0) REVERT: B 42 LYS cc_start: 0.7408 (mtpt) cc_final: 0.6873 (mmtt) REVERT: B 178 ARG cc_start: 0.8244 (ttm170) cc_final: 0.7942 (ttm170) REVERT: B 462 LEU cc_start: 0.7232 (tt) cc_final: 0.6926 (mp) REVERT: C 136 ILE cc_start: 0.6603 (OUTLIER) cc_final: 0.6264 (pt) REVERT: C 137 ILE cc_start: 0.5353 (OUTLIER) cc_final: 0.5070 (mp) REVERT: C 178 ARG cc_start: 0.7087 (ttm-80) cc_final: 0.6690 (ttt180) REVERT: C 216 MET cc_start: 0.7706 (mmp) cc_final: 0.7433 (mmt) REVERT: C 401 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7617 (mm-30) REVERT: D 5 ASP cc_start: 0.6845 (t0) cc_final: 0.6526 (t0) outliers start: 42 outliers final: 23 residues processed: 198 average time/residue: 1.1720 time to fit residues: 255.8202 Evaluate side-chains 182 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 66 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 81 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 HIS ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.152470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.106342 restraints weight = 15190.301| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.12 r_work: 0.2944 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13359 Z= 0.119 Angle : 0.459 11.320 18084 Z= 0.237 Chirality : 0.037 0.186 2063 Planarity : 0.003 0.055 2140 Dihedral : 10.755 88.803 2019 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.26 % Allowed : 19.53 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.22), residues: 1541 helix: 2.89 (0.14), residues: 1215 sheet: 1.77 (1.00), residues: 24 loop : -1.04 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 13 HIS 0.002 0.001 HIS B 233 PHE 0.016 0.001 PHE A 385 TYR 0.024 0.001 TYR D 160 ARG 0.007 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 960) hydrogen bonds : angle 3.27616 ( 2862) covalent geometry : bond 0.00268 (13359) covalent geometry : angle 0.45868 (18084) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 1.298 Fit side-chains revert: symmetry clash REVERT: A 229 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7743 (mp0) REVERT: A 312 ARG cc_start: 0.8102 (ttt180) cc_final: 0.7754 (mtp180) REVERT: A 395 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: A 436 LYS cc_start: 0.8364 (mttp) cc_final: 0.8072 (mttt) REVERT: B 42 LYS cc_start: 0.7438 (mtpt) cc_final: 0.6931 (mmtt) REVERT: B 178 ARG cc_start: 0.8267 (ttm170) cc_final: 0.8004 (ttm170) REVERT: B 199 PHE cc_start: 0.8440 (t80) cc_final: 0.8139 (t80) REVERT: B 462 LEU cc_start: 0.7206 (tt) cc_final: 0.6904 (mp) REVERT: C 178 ARG cc_start: 0.7081 (ttm-80) cc_final: 0.6779 (ttm-80) REVERT: C 216 MET cc_start: 0.7751 (mmp) cc_final: 0.7455 (mmt) REVERT: D 5 ASP cc_start: 0.6821 (t0) cc_final: 0.6504 (t0) outliers start: 32 outliers final: 17 residues processed: 189 average time/residue: 1.0586 time to fit residues: 220.9879 Evaluate side-chains 178 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 22 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 266 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 89 optimal weight: 0.8980 chunk 127 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 407 HIS D 86 GLN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.153368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.107208 restraints weight = 15170.763| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.12 r_work: 0.2958 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13359 Z= 0.113 Angle : 0.451 11.990 18084 Z= 0.233 Chirality : 0.036 0.178 2063 Planarity : 0.003 0.055 2140 Dihedral : 10.336 88.508 2019 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.12 % Allowed : 19.53 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.37 (0.22), residues: 1541 helix: 2.96 (0.14), residues: 1215 sheet: 1.82 (0.99), residues: 24 loop : -1.02 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 13 HIS 0.003 0.001 HIS A 212 PHE 0.017 0.001 PHE B 385 TYR 0.025 0.001 TYR D 160 ARG 0.007 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 960) hydrogen bonds : angle 3.23666 ( 2862) covalent geometry : bond 0.00250 (13359) covalent geometry : angle 0.45110 (18084) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 1.489 Fit side-chains revert: symmetry clash REVERT: A 98 LYS cc_start: 0.7811 (mptm) cc_final: 0.7274 (mmtt) REVERT: A 395 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: B 42 LYS cc_start: 0.7422 (mtpt) cc_final: 0.6925 (mmtt) REVERT: B 178 ARG cc_start: 0.8258 (ttm170) cc_final: 0.8003 (ttm170) REVERT: B 199 PHE cc_start: 0.8432 (t80) cc_final: 0.8126 (t80) REVERT: B 461 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.6250 (tp40) REVERT: B 462 LEU cc_start: 0.7208 (tt) cc_final: 0.6972 (mp) REVERT: C 129 SER cc_start: 0.6768 (t) cc_final: 0.6415 (m) REVERT: C 136 ILE cc_start: 0.6753 (OUTLIER) cc_final: 0.6391 (pt) REVERT: C 178 ARG cc_start: 0.7066 (ttm-80) cc_final: 0.6623 (ttm-80) REVERT: C 216 MET cc_start: 0.7730 (mmp) cc_final: 0.7427 (mmt) REVERT: C 244 LEU cc_start: 0.8045 (tt) cc_final: 0.7718 (pp) REVERT: C 401 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7524 (mm-30) REVERT: D 5 ASP cc_start: 0.6810 (t0) cc_final: 0.6508 (t0) REVERT: D 290 ASP cc_start: 0.8296 (m-30) cc_final: 0.7320 (t0) outliers start: 30 outliers final: 18 residues processed: 188 average time/residue: 1.0394 time to fit residues: 216.2257 Evaluate side-chains 181 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 266 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 48 optimal weight: 0.2980 chunk 151 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS A 307 GLN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 HIS C 390 ASN ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 GLN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.153012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.106852 restraints weight = 15194.490| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.12 r_work: 0.2990 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13359 Z= 0.119 Angle : 0.467 13.052 18084 Z= 0.239 Chirality : 0.037 0.173 2063 Planarity : 0.003 0.054 2140 Dihedral : 10.187 88.878 2019 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.56 % Allowed : 20.38 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.36 (0.22), residues: 1541 helix: 2.95 (0.14), residues: 1214 sheet: 1.89 (0.98), residues: 24 loop : -1.04 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 13 HIS 0.003 0.001 HIS A 212 PHE 0.016 0.001 PHE B 385 TYR 0.027 0.001 TYR D 160 ARG 0.007 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 960) hydrogen bonds : angle 3.25473 ( 2862) covalent geometry : bond 0.00267 (13359) covalent geometry : angle 0.46659 (18084) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 1.368 Fit side-chains REVERT: A 98 LYS cc_start: 0.8009 (mptm) cc_final: 0.7475 (mmtt) REVERT: A 229 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: A 312 ARG cc_start: 0.8188 (ttt180) cc_final: 0.7801 (mtp180) REVERT: A 395 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: A 428 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8271 (mtmp) REVERT: B 42 LYS cc_start: 0.7609 (mtpt) cc_final: 0.7068 (mmtt) REVERT: B 178 ARG cc_start: 0.8388 (ttm170) cc_final: 0.8141 (ttm170) REVERT: B 199 PHE cc_start: 0.8553 (t80) cc_final: 0.8251 (t80) REVERT: B 461 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.6352 (tp40) REVERT: B 462 LEU cc_start: 0.7256 (tt) cc_final: 0.7023 (mp) REVERT: C 129 SER cc_start: 0.6920 (t) cc_final: 0.6560 (m) REVERT: C 178 ARG cc_start: 0.7115 (ttm-80) cc_final: 0.6683 (ttm-80) REVERT: C 216 MET cc_start: 0.7842 (mmp) cc_final: 0.7574 (mmt) REVERT: C 244 LEU cc_start: 0.8203 (tt) cc_final: 0.7888 (pp) REVERT: C 401 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7642 (mm-30) REVERT: D 5 ASP cc_start: 0.6844 (t0) cc_final: 0.6519 (t0) REVERT: D 89 ARG cc_start: 0.7761 (mtm180) cc_final: 0.7500 (mtm-85) REVERT: D 290 ASP cc_start: 0.8363 (m-30) cc_final: 0.7455 (t0) REVERT: D 347 MET cc_start: 0.5458 (tpp) cc_final: 0.5032 (tpt) outliers start: 22 outliers final: 19 residues processed: 178 average time/residue: 1.1864 time to fit residues: 232.2272 Evaluate side-chains 178 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 407 HIS Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 34 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 128 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 56 optimal weight: 0.0010 chunk 64 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 99 optimal weight: 5.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS B 407 HIS ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 GLN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.154509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.108482 restraints weight = 15163.213| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.13 r_work: 0.3065 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13359 Z= 0.105 Angle : 0.456 13.054 18084 Z= 0.234 Chirality : 0.036 0.173 2063 Planarity : 0.003 0.054 2140 Dihedral : 10.037 88.153 2019 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.70 % Allowed : 20.45 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.45 (0.22), residues: 1541 helix: 3.02 (0.14), residues: 1213 sheet: 1.91 (0.98), residues: 24 loop : -1.02 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 408 HIS 0.007 0.001 HIS B 407 PHE 0.014 0.001 PHE C 385 TYR 0.029 0.001 TYR D 160 ARG 0.007 0.000 ARG C 102 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 960) hydrogen bonds : angle 3.23001 ( 2862) covalent geometry : bond 0.00225 (13359) covalent geometry : angle 0.45558 (18084) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9583.73 seconds wall clock time: 165 minutes 3.86 seconds (9903.86 seconds total)