Starting phenix.real_space_refine on Sat Jan 18 22:29:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z9a_39858/01_2025/8z9a_39858_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z9a_39858/01_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_39858/01_2025/8z9a_39858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z9a_39858/01_2025/8z9a_39858.map" model { file = "/net/cci-nas-00/data/ceres_data/8z9a_39858/01_2025/8z9a_39858_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z9a_39858/01_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-5571/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: 7.60, per 1000 atoms: 0.58 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: 3.62 Conformation dependent library (CDL) restraints added in 1.7 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: 1.38 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: 4.35 Time building geometry restraints manager: 4.08 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: 0.600 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.140 Find NCS groups from input model: 0.550 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:14.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.100 ------------------------------------------------------------------------------- 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= 0.341 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 *********************** 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 : 1.320 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: 1.0655 time to fit residues: 221.5640 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 : 1.346 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105033 restraints weight = 15129.317| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.09 r_work: 0.2981 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 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 0.032 13359 Z= 0.235 Angle : 0.475 7.549 18084 Z= 0.251 Chirality : 0.038 0.160 2063 Planarity : 0.004 0.076 2140 Dihedral : 11.767 77.802 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 *********************** 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 : 1.419 Fit side-chains REVERT: A 312 ARG cc_start: 0.8322 (ttt180) cc_final: 0.8044 (ttt-90) REVERT: B 42 LYS cc_start: 0.7669 (mtpt) cc_final: 0.7076 (mmtt) REVERT: B 178 ARG cc_start: 0.8536 (ttm170) cc_final: 0.8294 (ttm170) REVERT: C 136 ILE cc_start: 0.6511 (OUTLIER) cc_final: 0.5957 (pp) REVERT: C 178 ARG cc_start: 0.6323 (ttm-80) cc_final: 0.5961 (ttt180) REVERT: D 5 ASP cc_start: 0.6945 (t0) cc_final: 0.6588 (t0) REVERT: D 309 LYS cc_start: 0.8902 (tmtt) cc_final: 0.8409 (tptt) outliers start: 47 outliers final: 19 residues processed: 203 average time/residue: 1.1075 time to fit residues: 248.4325 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 : 1.358 ------------------------------------------------------------------------------- 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: 0.3980 chunk 42 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.153054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.106999 restraints weight = 15221.210| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.11 r_work: 0.2934 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13359 Z= 0.164 Angle : 0.434 7.685 18084 Z= 0.230 Chirality : 0.036 0.156 2063 Planarity : 0.003 0.067 2140 Dihedral : 11.125 77.002 2021 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.83 % Allowed : 15.57 % Favored : 81.60 % 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: 3.03 (0.22), residues: 1541 helix: 2.73 (0.14), residues: 1216 sheet: 1.68 (1.04), residues: 24 loop : -1.20 (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 212 PHE 0.017 0.001 PHE A 385 TYR 0.021 0.001 TYR C 53 ARG 0.007 0.000 ARG A 178 *********************** 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 211 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 1.383 Fit side-chains REVERT: A 312 ARG cc_start: 0.8049 (ttt180) cc_final: 0.7745 (mtp180) REVERT: A 395 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8146 (tp30) REVERT: B 42 LYS cc_start: 0.7316 (mtpt) cc_final: 0.6768 (mmtt) REVERT: B 178 ARG cc_start: 0.8228 (ttm170) cc_final: 0.7875 (ttm170) REVERT: C 136 ILE cc_start: 0.6368 (OUTLIER) cc_final: 0.5909 (pp) REVERT: C 178 ARG cc_start: 0.6460 (ttm-80) cc_final: 0.6006 (ttt180) REVERT: C 401 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7389 (mm-30) REVERT: D 5 ASP cc_start: 0.6800 (t0) cc_final: 0.6469 (t0) outliers start: 40 outliers final: 14 residues processed: 196 average time/residue: 1.1479 time to fit residues: 247.9894 Evaluate side-chains 166 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR 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 137 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: 0.9990 chunk 143 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 68 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.147288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.101541 restraints weight = 15205.201| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.07 r_work: 0.2834 rms_B_bonded: 2.90 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: 0.7614 moved from start: 0.1240 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= 0.366 Angle : 0.536 8.655 18084 Z= 0.279 Chirality : 0.041 0.160 2063 Planarity : 0.004 0.062 2140 Dihedral : 11.497 87.489 2019 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.18 % Allowed : 15.85 % Favored : 79.97 % 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: 2.71 (0.21), residues: 1541 helix: 2.48 (0.14), residues: 1214 sheet: 1.67 (1.01), residues: 24 loop : -1.18 (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 B 233 PHE 0.030 0.002 PHE B 385 TYR 0.023 0.002 TYR C 53 ARG 0.006 0.001 ARG C 102 *********************** 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 227 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 168 time to evaluate : 1.353 Fit side-chains REVERT: A 312 ARG cc_start: 0.8121 (ttt180) cc_final: 0.7775 (mtp180) REVERT: B 178 ARG cc_start: 0.8317 (ttm170) cc_final: 0.7877 (ttm170) REVERT: C 21 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.7021 (mt) REVERT: C 136 ILE cc_start: 0.6444 (OUTLIER) cc_final: 0.5934 (pp) REVERT: C 178 ARG cc_start: 0.6730 (ttm-80) cc_final: 0.6216 (ttt90) REVERT: C 216 MET cc_start: 0.7775 (mmp) cc_final: 0.7417 (mmt) REVERT: C 401 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7601 (mm-30) REVERT: D 5 ASP cc_start: 0.6782 (t0) cc_final: 0.6424 (t0) outliers start: 59 outliers final: 25 residues processed: 206 average time/residue: 1.0780 time to fit residues: 245.5980 Evaluate side-chains 183 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 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 66 VAL 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: 7.9990 chunk 64 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.148504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.102679 restraints weight = 15375.930| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.09 r_work: 0.2850 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13359 Z= 0.283 Angle : 0.497 9.448 18084 Z= 0.260 Chirality : 0.039 0.154 2063 Planarity : 0.003 0.058 2140 Dihedral : 11.334 89.144 2019 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.11 % Allowed : 17.76 % Favored : 79.12 % 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: 2.80 (0.21), residues: 1541 helix: 2.55 (0.14), residues: 1213 sheet: 1.74 (1.01), residues: 24 loop : -1.20 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 13 HIS 0.011 0.001 HIS B 407 PHE 0.024 0.001 PHE B 385 TYR 0.019 0.001 TYR C 53 ARG 0.007 0.001 ARG A 178 *********************** 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: 44 poor density : 169 time to evaluate : 1.413 Fit side-chains REVERT: A 312 ARG cc_start: 0.8079 (ttt180) cc_final: 0.7747 (mtp180) REVERT: B 42 LYS cc_start: 0.7390 (mtpt) cc_final: 0.6834 (mmtt) REVERT: B 178 ARG cc_start: 0.8232 (ttm170) cc_final: 0.7774 (ttm170) REVERT: C 21 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.7041 (mt) REVERT: C 136 ILE cc_start: 0.6538 (OUTLIER) cc_final: 0.6048 (pp) REVERT: C 178 ARG cc_start: 0.6957 (ttm-80) cc_final: 0.6668 (ttt90) REVERT: C 216 MET cc_start: 0.7778 (mmp) cc_final: 0.7577 (mmt) REVERT: C 401 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7585 (mm-30) REVERT: D 5 ASP cc_start: 0.6790 (t0) cc_final: 0.6437 (t0) outliers start: 44 outliers final: 19 residues processed: 199 average time/residue: 1.1277 time to fit residues: 248.2736 Evaluate side-chains 180 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 1.436 ------------------------------------------------------------------------------- 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 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 366 VAL Chi-restraints excluded: chain C residue 21 LEU 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 137 ILE Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain D residue 43 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 51 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.150854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.105025 restraints weight = 15327.946| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.10 r_work: 0.3019 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1328 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= 0.197 Angle : 0.459 9.835 18084 Z= 0.240 Chirality : 0.037 0.150 2063 Planarity : 0.003 0.056 2140 Dihedral : 10.998 89.776 2019 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.90 % Allowed : 18.54 % Favored : 78.56 % 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: 3.06 (0.22), residues: 1541 helix: 2.75 (0.14), residues: 1212 sheet: 1.91 (1.01), residues: 24 loop : -1.15 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 13 HIS 0.003 0.001 HIS A 233 PHE 0.018 0.001 PHE A 385 TYR 0.017 0.001 TYR C 53 ARG 0.006 0.000 ARG C 102 *********************** 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 209 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 1.228 Fit side-chains REVERT: A 312 ARG cc_start: 0.8321 (ttt180) cc_final: 0.7966 (mtp180) REVERT: B 42 LYS cc_start: 0.7716 (mtpt) cc_final: 0.7118 (mmtt) REVERT: B 178 ARG cc_start: 0.8486 (ttm170) cc_final: 0.8091 (ttm170) REVERT: B 462 LEU cc_start: 0.7444 (tt) cc_final: 0.7053 (mp) REVERT: C 21 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7236 (mt) REVERT: C 136 ILE cc_start: 0.7001 (OUTLIER) cc_final: 0.6590 (pp) REVERT: C 178 ARG cc_start: 0.7099 (ttm-80) cc_final: 0.6737 (ttt180) REVERT: C 216 MET cc_start: 0.8050 (mmp) cc_final: 0.7656 (mmt) REVERT: D 5 ASP cc_start: 0.6832 (t0) cc_final: 0.6518 (t0) REVERT: D 86 GLN cc_start: 0.8215 (tp-100) cc_final: 0.7969 (tp-100) outliers start: 41 outliers final: 21 residues processed: 196 average time/residue: 1.1426 time to fit residues: 247.9079 Evaluate side-chains 180 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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 B residue 324 HIS Chi-restraints excluded: chain B residue 366 VAL 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 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 245 SER Chi-restraints excluded: chain C residue 315 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: 0.9990 chunk 80 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 110 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.150823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.104810 restraints weight = 15271.042| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.11 r_work: 0.2878 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13359 Z= 0.207 Angle : 0.465 10.627 18084 Z= 0.243 Chirality : 0.037 0.147 2063 Planarity : 0.003 0.055 2140 Dihedral : 10.976 89.600 2019 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.33 % Allowed : 18.19 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.11 (0.22), residues: 1541 helix: 2.77 (0.14), residues: 1213 sheet: 1.93 (1.02), residues: 24 loop : -1.08 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 13 HIS 0.004 0.001 HIS A 233 PHE 0.019 0.001 PHE B 385 TYR 0.020 0.001 TYR D 160 ARG 0.007 0.000 ARG C 102 *********************** 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 214 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 167 time to evaluate : 1.476 Fit side-chains REVERT: A 229 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: A 312 ARG cc_start: 0.8035 (ttt180) cc_final: 0.7695 (mtp180) REVERT: A 395 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7834 (tt0) REVERT: B 42 LYS cc_start: 0.7272 (mtpt) cc_final: 0.6720 (mmtt) REVERT: B 178 ARG cc_start: 0.8184 (ttm170) cc_final: 0.7872 (ttm170) REVERT: B 461 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6387 (tp40) REVERT: B 462 LEU cc_start: 0.7158 (tt) cc_final: 0.6859 (mp) REVERT: C 21 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6937 (mt) REVERT: C 63 MET cc_start: 0.7557 (ttp) cc_final: 0.7346 (ttp) REVERT: C 126 LYS cc_start: 0.5345 (tppt) cc_final: 0.5106 (tppt) REVERT: C 129 SER cc_start: 0.6612 (t) cc_final: 0.6300 (m) REVERT: C 136 ILE cc_start: 0.6604 (OUTLIER) cc_final: 0.6244 (pp) REVERT: C 178 ARG cc_start: 0.7068 (ttm-80) cc_final: 0.6633 (ttm-80) REVERT: C 216 MET cc_start: 0.7768 (mmp) cc_final: 0.7521 (mmt) REVERT: C 401 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7345 (mm-30) REVERT: D 5 ASP cc_start: 0.6757 (t0) cc_final: 0.6469 (t0) outliers start: 47 outliers final: 27 residues processed: 200 average time/residue: 1.1438 time to fit residues: 251.9053 Evaluate side-chains 189 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 1.384 ------------------------------------------------------------------------------- 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 366 VAL Chi-restraints excluded: chain B residue 407 HIS 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 54 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 228 CYS Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 315 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: 4.9990 chunk 25 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 145 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 390 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.152514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.106488 restraints weight = 15184.386| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.11 r_work: 0.3040 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13359 Z= 0.164 Angle : 0.452 11.396 18084 Z= 0.235 Chirality : 0.036 0.138 2063 Planarity : 0.003 0.054 2140 Dihedral : 10.729 89.664 2019 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.41 % Allowed : 19.32 % Favored : 78.27 % 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: 3.26 (0.22), residues: 1541 helix: 2.88 (0.14), residues: 1213 sheet: 1.91 (1.00), residues: 24 loop : -1.08 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 408 HIS 0.003 0.001 HIS B 407 PHE 0.016 0.001 PHE A 385 TYR 0.022 0.001 TYR D 160 ARG 0.007 0.000 ARG A 178 *********************** 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 203 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 1.488 Fit side-chains REVERT: A 312 ARG cc_start: 0.8309 (ttt180) cc_final: 0.7937 (mtp180) REVERT: A 395 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8145 (tt0) REVERT: A 436 LYS cc_start: 0.8576 (mttp) cc_final: 0.8330 (mttt) REVERT: B 42 LYS cc_start: 0.7676 (mtpt) cc_final: 0.7107 (mmtt) REVERT: B 178 ARG cc_start: 0.8475 (ttm170) cc_final: 0.8261 (ttm170) REVERT: B 199 PHE cc_start: 0.8654 (t80) cc_final: 0.8383 (t80) REVERT: B 462 LEU cc_start: 0.7383 (tt) cc_final: 0.7104 (mp) REVERT: C 21 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7318 (mt) REVERT: C 129 SER cc_start: 0.7068 (t) cc_final: 0.6754 (m) REVERT: C 136 ILE cc_start: 0.6992 (OUTLIER) cc_final: 0.6545 (pp) REVERT: C 178 ARG cc_start: 0.7157 (ttm-80) cc_final: 0.6737 (ttm-80) REVERT: C 216 MET cc_start: 0.8070 (mmp) cc_final: 0.7824 (mmt) REVERT: D 5 ASP cc_start: 0.6963 (t0) cc_final: 0.6623 (t0) outliers start: 34 outliers final: 21 residues processed: 194 average time/residue: 1.1322 time to fit residues: 242.9609 Evaluate side-chains 182 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 366 VAL 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 54 SER Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 228 CYS 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 309 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 89 optimal weight: 6.9990 chunk 127 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.152575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106512 restraints weight = 15183.983| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.12 r_work: 0.2981 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13359 Z= 0.169 Angle : 0.465 11.984 18084 Z= 0.240 Chirality : 0.037 0.137 2063 Planarity : 0.003 0.053 2140 Dihedral : 10.378 89.910 2019 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.24 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: 3.31 (0.22), residues: 1541 helix: 2.93 (0.14), residues: 1213 sheet: 1.93 (1.00), residues: 24 loop : -1.07 (0.37), residues: 304 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 0.016 0.001 PHE B 385 TYR 0.026 0.001 TYR B 92 ARG 0.007 0.000 ARG C 102 *********************** 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 197 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 1.391 Fit side-chains REVERT: A 98 LYS cc_start: 0.8136 (mptm) cc_final: 0.7609 (mmtt) REVERT: A 229 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: A 312 ARG cc_start: 0.8305 (ttt180) cc_final: 0.7921 (mtp180) REVERT: A 395 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8075 (tt0) REVERT: B 42 LYS cc_start: 0.7648 (mtpt) cc_final: 0.7088 (mmtt) REVERT: B 178 ARG cc_start: 0.8447 (ttm170) cc_final: 0.8232 (ttm170) REVERT: B 199 PHE cc_start: 0.8614 (t80) cc_final: 0.8338 (t80) REVERT: B 462 LEU cc_start: 0.7427 (tt) cc_final: 0.7142 (mp) REVERT: C 136 ILE cc_start: 0.6925 (OUTLIER) cc_final: 0.6511 (pp) REVERT: C 178 ARG cc_start: 0.7174 (ttm-80) cc_final: 0.6750 (ttm-80) REVERT: C 216 MET cc_start: 0.8051 (mmp) cc_final: 0.7792 (mmt) REVERT: C 244 LEU cc_start: 0.8218 (tt) cc_final: 0.7903 (pp) REVERT: D 5 ASP cc_start: 0.6905 (t0) cc_final: 0.6592 (t0) outliers start: 32 outliers final: 23 residues processed: 189 average time/residue: 1.1220 time to fit residues: 234.1356 Evaluate side-chains 185 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 1.653 ------------------------------------------------------------------------------- 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 243 GLU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain B residue 366 VAL 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 136 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 228 CYS 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 309 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 75 optimal weight: 0.2980 chunk 7 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 48 optimal weight: 0.4980 chunk 151 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.154031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.108122 restraints weight = 15152.230| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.12 r_work: 0.3062 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1649 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= 0.142 Angle : 0.454 13.078 18084 Z= 0.233 Chirality : 0.036 0.140 2063 Planarity : 0.003 0.053 2140 Dihedral : 10.186 89.588 2019 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.12 % Allowed : 19.60 % Favored : 78.27 % 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: 3.44 (0.22), residues: 1541 helix: 3.02 (0.14), residues: 1212 sheet: 2.01 (0.99), residues: 24 loop : -1.03 (0.37), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 408 HIS 0.004 0.001 HIS B 407 PHE 0.014 0.001 PHE A 385 TYR 0.026 0.001 TYR D 160 ARG 0.007 0.000 ARG C 102 ********************** 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 193 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 1.357 Fit side-chains REVERT: A 98 LYS cc_start: 0.8191 (mptm) cc_final: 0.7672 (mmtt) REVERT: A 229 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: A 395 GLU cc_start: 0.8367 (tp30) cc_final: 0.8084 (tt0) REVERT: B 42 LYS cc_start: 0.7673 (mtpt) cc_final: 0.7121 (mmtt) REVERT: B 178 ARG cc_start: 0.8515 (ttm170) cc_final: 0.8310 (ttm170) REVERT: B 199 PHE cc_start: 0.8658 (t80) cc_final: 0.8382 (t80) REVERT: B 462 LEU cc_start: 0.7409 (tt) cc_final: 0.7162 (mp) REVERT: C 87 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7211 (mmt) REVERT: C 129 SER cc_start: 0.7062 (t) cc_final: 0.6699 (m) REVERT: C 136 ILE cc_start: 0.6980 (OUTLIER) cc_final: 0.6595 (pp) REVERT: C 178 ARG cc_start: 0.7167 (ttm-80) cc_final: 0.6748 (ttm-80) REVERT: C 216 MET cc_start: 0.8050 (mmp) cc_final: 0.7727 (mmt) REVERT: C 244 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7909 (pp) REVERT: C 401 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7692 (mm-30) REVERT: D 5 ASP cc_start: 0.6891 (t0) cc_final: 0.6570 (t0) outliers start: 30 outliers final: 21 residues processed: 185 average time/residue: 1.1286 time to fit residues: 230.1570 Evaluate side-chains 181 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 1.322 ------------------------------------------------------------------------------- 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 425 GLN Chi-restraints excluded: chain B residue 115 LEU 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 87 MET Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 228 CYS Chi-restraints excluded: chain C residue 244 LEU 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: 0.0370 chunk 41 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.5664 ------------------------------------------------------------------------------- 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 424 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 = 0.3749 r_free = 0.3749 target = 0.149979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.103928 restraints weight = 15284.278| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.10 r_work: 0.2867 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1527 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= 0.258 Angle : 0.509 12.968 18084 Z= 0.260 Chirality : 0.039 0.144 2063 Planarity : 0.003 0.054 2140 Dihedral : 10.453 87.866 2019 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.48 % Allowed : 19.60 % Favored : 77.92 % 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: 1.96 (1.00), residues: 24 loop : -1.09 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 13 HIS 0.006 0.001 HIS B 407 PHE 0.023 0.001 PHE B 385 TYR 0.028 0.001 TYR D 160 ARG 0.007 0.000 ARG C 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9088.53 seconds wall clock time: 161 minutes 37.66 seconds (9697.66 seconds total)