Starting phenix.real_space_refine on Fri May 16 11:57:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ipq_35640/05_2025/8ipq_35640.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ipq_35640/05_2025/8ipq_35640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ipq_35640/05_2025/8ipq_35640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ipq_35640/05_2025/8ipq_35640.map" model { file = "/net/cci-nas-00/data/ceres_data/8ipq_35640/05_2025/8ipq_35640.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ipq_35640/05_2025/8ipq_35640.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 9180 2.51 5 N 2608 2.21 5 O 2610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14456 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3679 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 31, 'TRANS': 473} Chain breaks: 1 Chain: "A" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3549 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 29, 'TRANS': 463} Chain breaks: 1 Chain: "C" Number of atoms: 3679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3679 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 31, 'TRANS': 473} Chain breaks: 1 Chain: "D" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3549 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 29, 'TRANS': 463} Chain breaks: 1 Time building chain proxies: 8.73, per 1000 atoms: 0.60 Number of scatterers: 14456 At special positions: 0 Unit cell: (89.024, 137.28, 188.032, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 2610 8.00 N 2608 7.00 C 9180 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: 3.43 Conformation dependent library (CDL) restraints added in 2.1 seconds 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3644 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 8 sheets defined 70.6% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'B' and resid -5 through 24 removed outlier: 3.584A pdb=" N SER B 10 " --> pdb=" O CYS B 6 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN B 24 " --> pdb=" O GLY B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 80 removed outlier: 3.603A pdb=" N GLY B 38 " --> pdb=" O ASP B 34 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 39 " --> pdb=" O TRP B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 98 removed outlier: 3.908A pdb=" N LEU B 87 " --> pdb=" O SER B 83 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA B 89 " --> pdb=" O ARG B 85 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASP B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N SER B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 105 through 112 removed outlier: 3.731A pdb=" N TYR B 112 " --> pdb=" O TYR B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 134 removed outlier: 3.802A pdb=" N THR B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 134 through 145 removed outlier: 3.623A pdb=" N ALA B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 159 Processing helix chain 'B' and resid 161 through 183 removed outlier: 3.657A pdb=" N ALA B 165 " --> pdb=" O GLU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 189 removed outlier: 3.684A pdb=" N ALA B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 219 removed outlier: 3.594A pdb=" N ILE B 200 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU B 202 " --> pdb=" O GLN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 245 removed outlier: 4.126A pdb=" N VAL B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 276 Proline residue: B 262 - end of helix Proline residue: B 267 - end of helix removed outlier: 4.311A pdb=" N HIS B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 290 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.712A pdb=" N GLY B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 391 Processing helix chain 'B' and resid 399 through 408 Processing helix chain 'B' and resid 409 through 416 removed outlier: 3.585A pdb=" N GLU B 415 " --> pdb=" O GLU B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 446 removed outlier: 3.679A pdb=" N GLY B 446 " --> pdb=" O VAL B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 479 Processing helix chain 'B' and resid 489 through 494 Processing helix chain 'A' and resid 7 through 16 Processing helix chain 'A' and resid 20 through 54 removed outlier: 3.877A pdb=" N PHE A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 54 " --> pdb=" O THR A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 105 removed outlier: 4.225A pdb=" N VAL A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 126 Processing helix chain 'A' and resid 126 through 135 removed outlier: 3.588A pdb=" N ASP A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 161 removed outlier: 3.732A pdb=" N VAL A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 160 " --> pdb=" O VAL A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 193 Proline residue: A 180 - end of helix removed outlier: 3.538A pdb=" N THR A 192 " --> pdb=" O HIS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.849A pdb=" N ASP A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 removed outlier: 4.095A pdb=" N SER A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 244 removed outlier: 4.137A pdb=" N HIS A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 270 removed outlier: 4.341A pdb=" N VAL A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA A 249 " --> pdb=" O PRO A 245 " (cutoff:3.500A) Proline residue: A 253 - end of helix removed outlier: 3.648A pdb=" N ALA A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 287 through 290 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 299 through 317 removed outlier: 3.679A pdb=" N LEU A 317 " --> pdb=" O ARG A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 363 Processing helix chain 'A' and resid 385 through 391 Processing helix chain 'A' and resid 398 through 410 Processing helix chain 'A' and resid 411 through 417 Processing helix chain 'A' and resid 420 through 424 removed outlier: 3.783A pdb=" N THR A 424 " --> pdb=" O GLY A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 433 removed outlier: 3.538A pdb=" N ALA A 431 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 449 Processing helix chain 'A' and resid 467 through 477 Processing helix chain 'C' and resid -4 through 24 removed outlier: 3.584A pdb=" N SER C 10 " --> pdb=" O CYS C 6 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN C 24 " --> pdb=" O GLY C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 80 removed outlier: 3.604A pdb=" N GLY C 38 " --> pdb=" O ASP C 34 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 39 " --> pdb=" O TRP C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 98 removed outlier: 3.908A pdb=" N LEU C 87 " --> pdb=" O SER C 83 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA C 89 " --> pdb=" O ARG C 85 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASP C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N SER C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 105 through 112 removed outlier: 3.731A pdb=" N TYR C 112 " --> pdb=" O TYR C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 134 removed outlier: 3.802A pdb=" N THR C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 134 through 145 removed outlier: 3.622A pdb=" N ALA C 138 " --> pdb=" O ASP C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 159 Processing helix chain 'C' and resid 161 through 183 removed outlier: 3.657A pdb=" N ALA C 165 " --> pdb=" O GLU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 189 removed outlier: 3.684A pdb=" N ALA C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 219 removed outlier: 3.594A pdb=" N ILE C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 201 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU C 202 " --> pdb=" O GLN C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 245 removed outlier: 4.125A pdb=" N VAL C 233 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 276 Proline residue: C 262 - end of helix Proline residue: C 267 - end of helix removed outlier: 4.310A pdb=" N HIS C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 290 Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.713A pdb=" N GLY C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 399 through 408 Processing helix chain 'C' and resid 409 through 416 removed outlier: 3.585A pdb=" N GLU C 415 " --> pdb=" O GLU C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 446 removed outlier: 3.680A pdb=" N GLY C 446 " --> pdb=" O VAL C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 479 Processing helix chain 'C' and resid 489 through 494 Processing helix chain 'D' and resid 7 through 16 Processing helix chain 'D' and resid 20 through 54 removed outlier: 3.877A pdb=" N PHE D 24 " --> pdb=" O ARG D 20 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA D 27 " --> pdb=" O ARG D 23 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN D 54 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 105 removed outlier: 4.225A pdb=" N VAL D 63 " --> pdb=" O LEU D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 126 Processing helix chain 'D' and resid 126 through 135 removed outlier: 3.588A pdb=" N ASP D 130 " --> pdb=" O GLY D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 161 removed outlier: 3.732A pdb=" N VAL D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D 160 " --> pdb=" O VAL D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 193 Proline residue: D 180 - end of helix removed outlier: 3.538A pdb=" N THR D 192 " --> pdb=" O HIS D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.849A pdb=" N ASP D 202 " --> pdb=" O ARG D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 218 removed outlier: 4.095A pdb=" N SER D 218 " --> pdb=" O GLU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 244 removed outlier: 4.137A pdb=" N HIS D 231 " --> pdb=" O THR D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 270 removed outlier: 4.342A pdb=" N VAL D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA D 249 " --> pdb=" O PRO D 245 " (cutoff:3.500A) Proline residue: D 253 - end of helix removed outlier: 3.648A pdb=" N ALA D 270 " --> pdb=" O ILE D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 286 Processing helix chain 'D' and resid 287 through 290 Processing helix chain 'D' and resid 293 through 297 Processing helix chain 'D' and resid 299 through 317 removed outlier: 3.678A pdb=" N LEU D 317 " --> pdb=" O ARG D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 363 Processing helix chain 'D' and resid 385 through 391 Processing helix chain 'D' and resid 398 through 410 Processing helix chain 'D' and resid 411 through 417 Processing helix chain 'D' and resid 420 through 424 removed outlier: 3.783A pdb=" N THR D 424 " --> pdb=" O GLY D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 433 removed outlier: 3.538A pdb=" N ALA D 431 " --> pdb=" O GLY D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 449 Processing helix chain 'D' and resid 467 through 477 Processing sheet with id=AA1, first strand: chain 'B' and resid 318 through 320 removed outlier: 3.549A pdb=" N LEU B 355 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 373 through 376 removed outlier: 3.518A pdb=" N LEU B 453 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL B 325 " --> pdb=" O HIS B 498 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N VAL B 500 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 327 " --> pdb=" O VAL B 500 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 385 through 386 Processing sheet with id=AA4, first strand: chain 'A' and resid 339 through 340 removed outlier: 3.503A pdb=" N LEU A 455 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 318 through 320 removed outlier: 3.549A pdb=" N LEU C 355 " --> pdb=" O GLU C 312 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 373 through 376 removed outlier: 3.518A pdb=" N LEU C 453 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL C 325 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N VAL C 500 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL C 327 " --> pdb=" O VAL C 500 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 385 through 386 Processing sheet with id=AA8, first strand: chain 'D' and resid 339 through 340 removed outlier: 3.504A pdb=" N LEU D 455 " --> pdb=" O ALA D 373 " (cutoff:3.500A) 994 hydrogen bonds defined for protein. 2922 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: 4.49 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2978 1.33 - 1.45: 2963 1.45 - 1.58: 8661 1.58 - 1.70: 0 1.70 - 1.82: 98 Bond restraints: 14700 Sorted by residual: bond pdb=" C GLU C 294 " pdb=" N PRO C 295 " ideal model delta sigma weight residual 1.331 1.389 -0.057 1.20e-02 6.94e+03 2.30e+01 bond pdb=" C GLU B 294 " pdb=" N PRO B 295 " ideal model delta sigma weight residual 1.331 1.389 -0.057 1.20e-02 6.94e+03 2.29e+01 bond pdb=" CA GLU B 456 " pdb=" C GLU B 456 " ideal model delta sigma weight residual 1.524 1.570 -0.046 1.26e-02 6.30e+03 1.32e+01 bond pdb=" C GLU B 456 " pdb=" N PRO B 457 " ideal model delta sigma weight residual 1.336 1.380 -0.044 1.25e-02 6.40e+03 1.26e+01 bond pdb=" N PHE C 219 " pdb=" CA PHE C 219 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.26e-02 6.30e+03 7.37e+00 ... (remaining 14695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 19719 2.26 - 4.52: 283 4.52 - 6.78: 77 6.78 - 9.04: 22 9.04 - 11.30: 11 Bond angle restraints: 20112 Sorted by residual: angle pdb=" N LEU C 344 " pdb=" CA LEU C 344 " pdb=" C LEU C 344 " ideal model delta sigma weight residual 113.28 104.57 8.71 1.22e+00 6.72e-01 5.10e+01 angle pdb=" N LEU B 344 " pdb=" CA LEU B 344 " pdb=" C LEU B 344 " ideal model delta sigma weight residual 113.28 104.58 8.70 1.22e+00 6.72e-01 5.09e+01 angle pdb=" C PHE C 219 " pdb=" CA PHE C 219 " pdb=" CB PHE C 219 " ideal model delta sigma weight residual 110.56 101.08 9.48 1.69e+00 3.50e-01 3.15e+01 angle pdb=" N PRO C 295 " pdb=" CA PRO C 295 " pdb=" C PRO C 295 " ideal model delta sigma weight residual 111.03 119.55 -8.52 1.54e+00 4.22e-01 3.06e+01 angle pdb=" N PRO B 295 " pdb=" CA PRO B 295 " pdb=" C PRO B 295 " ideal model delta sigma weight residual 111.03 119.53 -8.50 1.54e+00 4.22e-01 3.05e+01 ... (remaining 20107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 7632 17.21 - 34.42: 942 34.42 - 51.63: 260 51.63 - 68.84: 20 68.84 - 86.05: 10 Dihedral angle restraints: 8864 sinusoidal: 3220 harmonic: 5644 Sorted by residual: dihedral pdb=" C THR B 299 " pdb=" N THR B 299 " pdb=" CA THR B 299 " pdb=" CB THR B 299 " ideal model delta harmonic sigma weight residual -122.00 -134.61 12.61 0 2.50e+00 1.60e-01 2.55e+01 dihedral pdb=" C THR C 299 " pdb=" N THR C 299 " pdb=" CA THR C 299 " pdb=" CB THR C 299 " ideal model delta harmonic sigma weight residual -122.00 -134.60 12.60 0 2.50e+00 1.60e-01 2.54e+01 dihedral pdb=" N THR B 299 " pdb=" C THR B 299 " pdb=" CA THR B 299 " pdb=" CB THR B 299 " ideal model delta harmonic sigma weight residual 123.40 135.58 -12.18 0 2.50e+00 1.60e-01 2.37e+01 ... (remaining 8861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 2414 0.099 - 0.198: 102 0.198 - 0.296: 2 0.296 - 0.395: 0 0.395 - 0.494: 2 Chirality restraints: 2520 Sorted by residual: chirality pdb=" CA THR B 299 " pdb=" N THR B 299 " pdb=" C THR B 299 " pdb=" CB THR B 299 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.49 2.00e-01 2.50e+01 6.10e+00 chirality pdb=" CA THR C 299 " pdb=" N THR C 299 " pdb=" C THR C 299 " pdb=" CB THR C 299 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.49 2.00e-01 2.50e+01 6.10e+00 chirality pdb=" CA PRO B 295 " pdb=" N PRO B 295 " pdb=" C PRO B 295 " pdb=" CB PRO B 295 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2517 not shown) Planarity restraints: 2588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 343 " 0.016 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C ILE B 343 " -0.058 2.00e-02 2.50e+03 pdb=" O ILE B 343 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU B 344 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 343 " -0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C ILE C 343 " 0.058 2.00e-02 2.50e+03 pdb=" O ILE C 343 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU C 344 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 126 " 0.044 5.00e-02 4.00e+02 6.69e-02 7.15e+00 pdb=" N PRO A 127 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 127 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 127 " 0.037 5.00e-02 4.00e+02 ... (remaining 2585 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1903 2.75 - 3.29: 14730 3.29 - 3.82: 25155 3.82 - 4.36: 26136 4.36 - 4.90: 46398 Nonbonded interactions: 114322 Sorted by model distance: nonbonded pdb=" O ALA B 182 " pdb=" OG SER A 118 " model vdw 2.209 3.040 nonbonded pdb=" O LEU B 393 " pdb=" NE ARG A 220 " model vdw 2.230 3.120 nonbonded pdb=" O LEU C 393 " pdb=" NE ARG D 220 " model vdw 2.231 3.120 nonbonded pdb=" OD1 ASP C 134 " pdb=" NH2 ARG C 243 " model vdw 2.243 3.120 nonbonded pdb=" OD1 ASP B 134 " pdb=" NH2 ARG B 243 " model vdw 2.243 3.120 ... (remaining 114317 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.150 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: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.420 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 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 : 0.004 0.057 14700 Z= 0.200 Angle : 0.774 11.295 20112 Z= 0.393 Chirality : 0.045 0.494 2520 Planarity : 0.006 0.107 2588 Dihedral : 16.068 86.048 5220 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.17 % Favored : 92.73 % Rotamer: Outliers : 0.61 % Allowed : 28.28 % Favored : 71.11 % Cbeta Deviations : 0.11 % 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: 0.55 (0.20), residues: 1980 helix: 1.51 (0.15), residues: 1304 sheet: 0.16 (0.52), residues: 120 loop : -2.46 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 375 HIS 0.005 0.001 HIS A 211 PHE 0.016 0.001 PHE A 24 TYR 0.010 0.001 TYR B 133 ARG 0.002 0.000 ARG B 85 Details of bonding type rmsd hydrogen bonds : bond 0.14755 ( 994) hydrogen bonds : angle 4.92878 ( 2922) covalent geometry : bond 0.00387 (14700) covalent geometry : angle 0.77352 (20112) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 266 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B -4 TYR cc_start: 0.5522 (OUTLIER) cc_final: 0.5067 (t80) REVERT: B 212 MET cc_start: 0.8675 (tpp) cc_final: 0.8415 (tpt) REVERT: A 355 MET cc_start: 0.7854 (ptp) cc_final: 0.7559 (ptp) REVERT: C 70 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7245 (tm-30) REVERT: D 215 LEU cc_start: 0.9255 (tp) cc_final: 0.8884 (tp) REVERT: D 231 HIS cc_start: 0.7020 (m170) cc_final: 0.6574 (m170) REVERT: D 299 ASP cc_start: 0.8494 (p0) cc_final: 0.6445 (t70) REVERT: D 350 LYS cc_start: 0.5662 (mtpt) cc_final: 0.5346 (mptt) REVERT: D 351 THR cc_start: 0.7983 (m) cc_final: 0.7361 (p) REVERT: D 440 ARG cc_start: 0.9002 (mtt90) cc_final: 0.8723 (ttm170) REVERT: D 456 LEU cc_start: 0.8556 (mm) cc_final: 0.8349 (mt) outliers start: 9 outliers final: 1 residues processed: 273 average time/residue: 0.3070 time to fit residues: 115.9903 Evaluate side-chains 183 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 181 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -4 TYR Chi-restraints excluded: chain A residue 135 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.178287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.108044 restraints weight = 24392.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.107560 restraints weight = 14466.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.107149 restraints weight = 10013.740| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14700 Z= 0.184 Angle : 0.732 10.097 20112 Z= 0.352 Chirality : 0.043 0.227 2520 Planarity : 0.006 0.072 2588 Dihedral : 4.411 49.574 2151 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.78 % Favored : 92.12 % Rotamer: Outliers : 4.51 % Allowed : 26.91 % Favored : 68.58 % 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: 0.57 (0.20), residues: 1980 helix: 1.56 (0.15), residues: 1308 sheet: -0.01 (0.49), residues: 126 loop : -2.55 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 370 HIS 0.006 0.001 HIS B 378 PHE 0.020 0.001 PHE C 409 TYR 0.017 0.002 TYR D 102 ARG 0.007 0.000 ARG B 405 Details of bonding type rmsd hydrogen bonds : bond 0.05484 ( 994) hydrogen bonds : angle 4.31523 ( 2922) covalent geometry : bond 0.00415 (14700) covalent geometry : angle 0.73152 (20112) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 180 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B -4 TYR cc_start: 0.5530 (OUTLIER) cc_final: 0.4907 (t80) REVERT: B 100 ARG cc_start: 0.7816 (mtt90) cc_final: 0.7536 (mpt180) REVERT: A 211 HIS cc_start: 0.7021 (OUTLIER) cc_final: 0.6714 (t-170) REVERT: C 177 MET cc_start: 0.8346 (mmm) cc_final: 0.8071 (tpt) REVERT: C 390 ASN cc_start: 0.6801 (OUTLIER) cc_final: 0.6570 (m-40) REVERT: D 220 ARG cc_start: 0.8956 (mmt180) cc_final: 0.8528 (mmt90) REVERT: D 305 MET cc_start: 0.8262 (mmp) cc_final: 0.7935 (mmt) REVERT: D 329 VAL cc_start: 0.1957 (OUTLIER) cc_final: 0.0899 (m) outliers start: 66 outliers final: 30 residues processed: 231 average time/residue: 0.2556 time to fit residues: 86.0128 Evaluate side-chains 191 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -4 TYR Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 488 HIS Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 329 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 197 optimal weight: 10.0000 chunk 88 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 163 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 180 optimal weight: 7.9990 chunk 30 optimal weight: 40.0000 chunk 186 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 91 optimal weight: 0.0000 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN C 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.179650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.105930 restraints weight = 23614.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.108812 restraints weight = 11149.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.110486 restraints weight = 7274.799| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14700 Z= 0.141 Angle : 0.693 10.516 20112 Z= 0.326 Chirality : 0.042 0.237 2520 Planarity : 0.005 0.070 2588 Dihedral : 4.337 51.531 2151 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.22 % Favored : 92.68 % Rotamer: Outliers : 4.30 % Allowed : 27.19 % Favored : 68.51 % 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: 0.56 (0.20), residues: 1980 helix: 1.58 (0.14), residues: 1304 sheet: -0.44 (0.49), residues: 126 loop : -2.49 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 375 HIS 0.005 0.001 HIS A 211 PHE 0.016 0.001 PHE D 24 TYR 0.017 0.002 TYR C 108 ARG 0.005 0.000 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.04826 ( 994) hydrogen bonds : angle 4.17492 ( 2922) covalent geometry : bond 0.00313 (14700) covalent geometry : angle 0.69252 (20112) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 170 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B -4 TYR cc_start: 0.5541 (OUTLIER) cc_final: 0.4935 (t80) REVERT: B 158 LEU cc_start: 0.9198 (tp) cc_final: 0.8973 (tt) REVERT: B 372 ARG cc_start: 0.7055 (ttm-80) cc_final: 0.6748 (ptm160) REVERT: B 378 HIS cc_start: 0.8051 (m90) cc_final: 0.7825 (m90) REVERT: A 82 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8492 (tm-30) REVERT: A 138 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7501 (mmt90) REVERT: A 211 HIS cc_start: 0.6911 (OUTLIER) cc_final: 0.6499 (t-170) REVERT: C 336 LYS cc_start: 0.6848 (mttp) cc_final: 0.6364 (mttt) REVERT: C 390 ASN cc_start: 0.6687 (OUTLIER) cc_final: 0.6411 (m-40) REVERT: C 409 PHE cc_start: 0.7593 (t80) cc_final: 0.7119 (t80) REVERT: D 220 ARG cc_start: 0.8849 (mmt180) cc_final: 0.8536 (mmt90) REVERT: D 305 MET cc_start: 0.8117 (mmp) cc_final: 0.7822 (mmt) REVERT: D 353 MET cc_start: 0.8027 (mmm) cc_final: 0.7826 (mmp) REVERT: D 355 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.7009 (ppp) REVERT: D 359 ASP cc_start: 0.8696 (t70) cc_final: 0.8263 (m-30) REVERT: D 380 HIS cc_start: 0.7170 (t70) cc_final: 0.6777 (t70) outliers start: 63 outliers final: 31 residues processed: 222 average time/residue: 0.2594 time to fit residues: 84.0130 Evaluate side-chains 187 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -4 TYR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 HIS Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 355 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 21 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 195 optimal weight: 9.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN C 56 GLN ** C 488 HIS ** 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 = 0.4509 r_free = 0.4509 target = 0.179453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.105265 restraints weight = 23739.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.108024 restraints weight = 11660.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.109649 restraints weight = 7761.424| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14700 Z= 0.143 Angle : 0.682 10.022 20112 Z= 0.321 Chirality : 0.041 0.200 2520 Planarity : 0.005 0.074 2588 Dihedral : 4.299 53.707 2151 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.47 % Favored : 92.42 % Rotamer: Outliers : 4.85 % Allowed : 27.05 % Favored : 68.10 % 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: 0.59 (0.20), residues: 1980 helix: 1.58 (0.14), residues: 1316 sheet: -0.51 (0.50), residues: 122 loop : -2.46 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 375 HIS 0.010 0.001 HIS D 211 PHE 0.022 0.001 PHE C 55 TYR 0.021 0.002 TYR D 102 ARG 0.004 0.000 ARG D 115 Details of bonding type rmsd hydrogen bonds : bond 0.04697 ( 994) hydrogen bonds : angle 4.10436 ( 2922) covalent geometry : bond 0.00323 (14700) covalent geometry : angle 0.68198 (20112) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 162 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B -4 TYR cc_start: 0.5539 (OUTLIER) cc_final: 0.4955 (t80) REVERT: B 113 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8397 (mp) REVERT: B 158 LEU cc_start: 0.9212 (tp) cc_final: 0.8981 (tt) REVERT: B 372 ARG cc_start: 0.7078 (ttm-80) cc_final: 0.6813 (ptm160) REVERT: B 376 MET cc_start: 0.8576 (tmm) cc_final: 0.7771 (tmm) REVERT: B 460 HIS cc_start: 0.4085 (OUTLIER) cc_final: 0.3131 (m170) REVERT: A 82 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8480 (tm-30) REVERT: A 211 HIS cc_start: 0.6927 (OUTLIER) cc_final: 0.6462 (t-170) REVERT: C 74 GLN cc_start: 0.7706 (mm110) cc_final: 0.7384 (mm110) REVERT: D 182 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7478 (tp) REVERT: D 220 ARG cc_start: 0.8854 (mmt180) cc_final: 0.8492 (mmt90) REVERT: D 305 MET cc_start: 0.8119 (mmp) cc_final: 0.7861 (mmt) REVERT: D 353 MET cc_start: 0.8085 (mmm) cc_final: 0.7773 (mmm) REVERT: D 355 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6981 (ppp) REVERT: D 359 ASP cc_start: 0.8712 (t70) cc_final: 0.8292 (m-30) REVERT: D 380 HIS cc_start: 0.7215 (t70) cc_final: 0.6808 (t70) REVERT: D 439 ARG cc_start: 0.8493 (tpp80) cc_final: 0.7972 (tpp80) outliers start: 71 outliers final: 45 residues processed: 221 average time/residue: 0.2374 time to fit residues: 78.7146 Evaluate side-chains 206 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 154 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -4 TYR Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 HIS Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 313 ARG Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 504 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 54 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 153 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.179250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.104958 restraints weight = 24036.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.107794 restraints weight = 11408.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.109493 restraints weight = 7454.344| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14700 Z= 0.138 Angle : 0.677 12.705 20112 Z= 0.317 Chirality : 0.041 0.144 2520 Planarity : 0.005 0.074 2588 Dihedral : 4.250 55.269 2151 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.32 % Favored : 92.58 % Rotamer: Outliers : 4.30 % Allowed : 28.21 % Favored : 67.49 % 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: 0.62 (0.20), residues: 1980 helix: 1.64 (0.14), residues: 1304 sheet: -0.60 (0.49), residues: 122 loop : -2.44 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP C 370 HIS 0.009 0.001 HIS D 211 PHE 0.021 0.001 PHE C 409 TYR 0.020 0.002 TYR D 102 ARG 0.009 0.000 ARG C 468 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 994) hydrogen bonds : angle 4.03918 ( 2922) covalent geometry : bond 0.00313 (14700) covalent geometry : angle 0.67724 (20112) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 156 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B -4 TYR cc_start: 0.5499 (OUTLIER) cc_final: 0.4990 (t80) REVERT: B 113 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8398 (mp) REVERT: B 158 LEU cc_start: 0.9239 (tp) cc_final: 0.9007 (tt) REVERT: B 372 ARG cc_start: 0.7070 (ttm-80) cc_final: 0.6804 (ptm160) REVERT: B 376 MET cc_start: 0.8559 (tmm) cc_final: 0.7914 (tmm) REVERT: B 378 HIS cc_start: 0.7990 (m90) cc_final: 0.7746 (m90) REVERT: B 460 HIS cc_start: 0.4013 (OUTLIER) cc_final: 0.3025 (m170) REVERT: A 82 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8473 (tm-30) REVERT: A 211 HIS cc_start: 0.6911 (OUTLIER) cc_final: 0.6486 (t-170) REVERT: C 157 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8459 (mp) REVERT: D 182 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7451 (tp) REVERT: D 220 ARG cc_start: 0.8905 (mmt180) cc_final: 0.8555 (mmt90) REVERT: D 305 MET cc_start: 0.8091 (mmp) cc_final: 0.7832 (mmt) REVERT: D 353 MET cc_start: 0.7858 (mmm) cc_final: 0.7555 (mmm) REVERT: D 355 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.7028 (ppp) REVERT: D 359 ASP cc_start: 0.8706 (t70) cc_final: 0.8303 (m-30) REVERT: D 380 HIS cc_start: 0.7210 (t70) cc_final: 0.6796 (t70) REVERT: D 440 ARG cc_start: 0.8903 (mtt90) cc_final: 0.8647 (ttm170) outliers start: 63 outliers final: 45 residues processed: 207 average time/residue: 0.2492 time to fit residues: 76.9387 Evaluate side-chains 201 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 148 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -4 TYR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 HIS Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 504 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 168 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 196 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 117 optimal weight: 0.4980 chunk 173 optimal weight: 0.9980 chunk 172 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 0 ASN B 56 GLN ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.175868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.099467 restraints weight = 24719.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.102175 restraints weight = 12256.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.103798 restraints weight = 8227.633| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14700 Z= 0.200 Angle : 0.731 11.423 20112 Z= 0.349 Chirality : 0.044 0.319 2520 Planarity : 0.006 0.086 2588 Dihedral : 4.391 59.866 2151 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.47 % Favored : 92.42 % Rotamer: Outliers : 6.15 % Allowed : 27.53 % Favored : 66.33 % 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: 0.41 (0.20), residues: 1980 helix: 1.35 (0.14), residues: 1328 sheet: -0.61 (0.50), residues: 122 loop : -2.33 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP C 370 HIS 0.009 0.001 HIS D 211 PHE 0.029 0.002 PHE C 409 TYR 0.019 0.003 TYR D 102 ARG 0.007 0.000 ARG C 388 Details of bonding type rmsd hydrogen bonds : bond 0.05292 ( 994) hydrogen bonds : angle 4.16174 ( 2922) covalent geometry : bond 0.00476 (14700) covalent geometry : angle 0.73087 (20112) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 148 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B -4 TYR cc_start: 0.5494 (OUTLIER) cc_final: 0.4887 (t80) REVERT: B 113 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8489 (mp) REVERT: B 133 TYR cc_start: 0.8423 (m-80) cc_final: 0.7242 (m-80) REVERT: B 158 LEU cc_start: 0.9285 (tp) cc_final: 0.9043 (tt) REVERT: B 372 ARG cc_start: 0.7258 (ttm-80) cc_final: 0.7050 (ptm160) REVERT: B 376 MET cc_start: 0.8538 (tmm) cc_final: 0.7831 (tmm) REVERT: B 378 HIS cc_start: 0.8006 (m90) cc_final: 0.7803 (m90) REVERT: B 460 HIS cc_start: 0.4149 (OUTLIER) cc_final: 0.2989 (m170) REVERT: A 82 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8467 (tm-30) REVERT: C 157 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8315 (mt) REVERT: C 212 MET cc_start: 0.9058 (mmm) cc_final: 0.8743 (tpt) REVERT: C 376 MET cc_start: 0.7909 (tmm) cc_final: 0.7685 (tmm) REVERT: C 390 ASN cc_start: 0.6685 (OUTLIER) cc_final: 0.6350 (m-40) REVERT: C 435 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.6996 (tp40) REVERT: D 182 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7618 (tp) REVERT: D 220 ARG cc_start: 0.8998 (mmt180) cc_final: 0.8563 (mmt90) REVERT: D 353 MET cc_start: 0.7766 (mmm) cc_final: 0.7529 (mmm) REVERT: D 355 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.7050 (ppp) REVERT: D 359 ASP cc_start: 0.8831 (t70) cc_final: 0.8352 (m-30) REVERT: D 380 HIS cc_start: 0.7295 (t70) cc_final: 0.6881 (t70) REVERT: D 439 ARG cc_start: 0.8557 (tpp80) cc_final: 0.8022 (tpp80) outliers start: 90 outliers final: 60 residues processed: 223 average time/residue: 0.2352 time to fit residues: 79.2557 Evaluate side-chains 212 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 143 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -4 TYR Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 369 TRP Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 HIS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 504 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 10 optimal weight: 0.9990 chunk 129 optimal weight: 0.2980 chunk 72 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 111 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.176882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.101030 restraints weight = 24755.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.103778 restraints weight = 12036.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.105484 restraints weight = 8001.129| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14700 Z= 0.157 Angle : 0.712 13.036 20112 Z= 0.333 Chirality : 0.042 0.250 2520 Planarity : 0.005 0.086 2588 Dihedral : 4.332 58.731 2151 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.42 % Favored : 92.47 % Rotamer: Outliers : 4.99 % Allowed : 29.10 % Favored : 65.92 % 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: 0.48 (0.20), residues: 1980 helix: 1.42 (0.15), residues: 1324 sheet: -0.67 (0.50), residues: 122 loop : -2.30 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP C 370 HIS 0.008 0.001 HIS D 211 PHE 0.028 0.001 PHE C 409 TYR 0.019 0.002 TYR C 108 ARG 0.006 0.000 ARG C 388 Details of bonding type rmsd hydrogen bonds : bond 0.04919 ( 994) hydrogen bonds : angle 4.08308 ( 2922) covalent geometry : bond 0.00365 (14700) covalent geometry : angle 0.71247 (20112) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 151 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B -4 TYR cc_start: 0.5596 (OUTLIER) cc_final: 0.4914 (t80) REVERT: B 113 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8605 (mp) REVERT: B 133 TYR cc_start: 0.8349 (m-80) cc_final: 0.7012 (m-80) REVERT: B 158 LEU cc_start: 0.9253 (tp) cc_final: 0.9018 (tt) REVERT: B 372 ARG cc_start: 0.7257 (ttm-80) cc_final: 0.7009 (ptm160) REVERT: B 376 MET cc_start: 0.8500 (tmm) cc_final: 0.7980 (tmm) REVERT: B 460 HIS cc_start: 0.4209 (OUTLIER) cc_final: 0.2833 (m170) REVERT: A 82 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8472 (tm-30) REVERT: A 426 LEU cc_start: 0.7444 (tt) cc_final: 0.7037 (pp) REVERT: C 157 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8451 (mp) REVERT: C 212 MET cc_start: 0.9070 (mmm) cc_final: 0.8699 (tpt) REVERT: C 376 MET cc_start: 0.7816 (tmm) cc_final: 0.7574 (tmm) REVERT: C 435 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.7031 (tp40) REVERT: D 182 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7621 (tp) REVERT: D 215 LEU cc_start: 0.9139 (tp) cc_final: 0.8905 (mt) REVERT: D 220 ARG cc_start: 0.8961 (mmt180) cc_final: 0.8436 (mmt90) REVERT: D 355 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7139 (ppp) REVERT: D 359 ASP cc_start: 0.8845 (t70) cc_final: 0.8388 (m-30) REVERT: D 362 ASN cc_start: 0.8458 (m-40) cc_final: 0.7620 (t0) REVERT: D 380 HIS cc_start: 0.7211 (t70) cc_final: 0.6845 (t70) outliers start: 73 outliers final: 55 residues processed: 214 average time/residue: 0.2341 time to fit residues: 76.1917 Evaluate side-chains 208 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 145 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -4 TYR Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 HIS Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 504 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 81 optimal weight: 30.0000 chunk 57 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 191 optimal weight: 6.9990 chunk 133 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 49 optimal weight: 30.0000 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 GLN ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.175498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.099878 restraints weight = 24174.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.102457 restraints weight = 12256.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.103974 restraints weight = 8321.903| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14700 Z= 0.189 Angle : 0.743 13.401 20112 Z= 0.352 Chirality : 0.043 0.331 2520 Planarity : 0.006 0.087 2588 Dihedral : 4.371 54.323 2151 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.22 % Favored : 92.68 % Rotamer: Outliers : 5.81 % Allowed : 28.42 % Favored : 65.78 % 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: 0.39 (0.20), residues: 1980 helix: 1.34 (0.15), residues: 1322 sheet: -0.54 (0.51), residues: 114 loop : -2.32 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP C 370 HIS 0.007 0.001 HIS D 211 PHE 0.023 0.001 PHE D 24 TYR 0.021 0.002 TYR C 108 ARG 0.010 0.000 ARG C 388 Details of bonding type rmsd hydrogen bonds : bond 0.05140 ( 994) hydrogen bonds : angle 4.14878 ( 2922) covalent geometry : bond 0.00450 (14700) covalent geometry : angle 0.74271 (20112) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 144 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B -4 TYR cc_start: 0.5688 (OUTLIER) cc_final: 0.4906 (t80) REVERT: B 39 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8640 (mp) REVERT: B 133 TYR cc_start: 0.8438 (m-80) cc_final: 0.7183 (m-80) REVERT: B 158 LEU cc_start: 0.9260 (tp) cc_final: 0.9022 (tt) REVERT: B 376 MET cc_start: 0.8535 (tmm) cc_final: 0.7273 (tmm) REVERT: B 460 HIS cc_start: 0.4184 (OUTLIER) cc_final: 0.2912 (m170) REVERT: A 82 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8492 (tm-30) REVERT: A 426 LEU cc_start: 0.7585 (tt) cc_final: 0.7127 (pp) REVERT: A 499 PHE cc_start: 0.5486 (OUTLIER) cc_final: 0.4780 (t80) REVERT: C 157 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8349 (mt) REVERT: C 320 MET cc_start: 0.3268 (OUTLIER) cc_final: 0.2263 (ttt) REVERT: C 376 MET cc_start: 0.7740 (tmm) cc_final: 0.7521 (tmm) REVERT: C 435 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7006 (tp40) REVERT: C 497 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.6312 (p0) REVERT: D 118 SER cc_start: 0.7633 (p) cc_final: 0.7363 (p) REVERT: D 182 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7689 (tp) REVERT: D 215 LEU cc_start: 0.9139 (tp) cc_final: 0.8925 (mt) REVERT: D 353 MET cc_start: 0.7949 (mmm) cc_final: 0.7648 (mmp) REVERT: D 362 ASN cc_start: 0.8410 (m-40) cc_final: 0.7633 (t0) REVERT: D 380 HIS cc_start: 0.7366 (t70) cc_final: 0.7005 (t70) REVERT: D 439 ARG cc_start: 0.8449 (tpp80) cc_final: 0.8157 (tpp80) REVERT: D 440 ARG cc_start: 0.8905 (mtt90) cc_final: 0.8666 (ttm170) outliers start: 85 outliers final: 63 residues processed: 220 average time/residue: 0.2324 time to fit residues: 78.2456 Evaluate side-chains 216 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 143 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -4 TYR Chi-restraints excluded: chain B residue 1 VAL Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 HIS Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 504 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 43 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 155 optimal weight: 0.5980 chunk 197 optimal weight: 0.0170 chunk 72 optimal weight: 7.9990 chunk 180 optimal weight: 0.0050 chunk 107 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 overall best weight: 0.9236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.177524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.102080 restraints weight = 24486.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.104864 restraints weight = 11789.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.106542 restraints weight = 7814.937| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14700 Z= 0.138 Angle : 0.715 13.013 20112 Z= 0.330 Chirality : 0.042 0.286 2520 Planarity : 0.005 0.082 2588 Dihedral : 4.256 52.982 2151 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.22 % Favored : 92.68 % Rotamer: Outliers : 4.44 % Allowed : 29.44 % Favored : 66.12 % 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: 0.52 (0.20), residues: 1980 helix: 1.48 (0.14), residues: 1316 sheet: -0.61 (0.49), residues: 124 loop : -2.34 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP C 370 HIS 0.008 0.001 HIS D 211 PHE 0.022 0.001 PHE D 24 TYR 0.024 0.002 TYR D 102 ARG 0.007 0.000 ARG C 388 Details of bonding type rmsd hydrogen bonds : bond 0.04635 ( 994) hydrogen bonds : angle 4.02401 ( 2922) covalent geometry : bond 0.00314 (14700) covalent geometry : angle 0.71526 (20112) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 151 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B -4 TYR cc_start: 0.5518 (OUTLIER) cc_final: 0.4971 (t80) REVERT: B 39 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8629 (mp) REVERT: B 133 TYR cc_start: 0.8319 (m-80) cc_final: 0.6933 (m-80) REVERT: B 158 LEU cc_start: 0.9246 (tp) cc_final: 0.9022 (tt) REVERT: B 376 MET cc_start: 0.8550 (tmm) cc_final: 0.7266 (tmm) REVERT: B 460 HIS cc_start: 0.4175 (OUTLIER) cc_final: 0.2943 (m170) REVERT: A 82 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8475 (tm-30) REVERT: A 88 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.7742 (t70) REVERT: A 305 MET cc_start: 0.8075 (mmm) cc_final: 0.7659 (mmt) REVERT: A 426 LEU cc_start: 0.7614 (tt) cc_final: 0.7171 (pp) REVERT: A 499 PHE cc_start: 0.5627 (OUTLIER) cc_final: 0.4915 (t80) REVERT: C 212 MET cc_start: 0.8995 (mmm) cc_final: 0.8592 (mmm) REVERT: C 250 THR cc_start: 0.7987 (OUTLIER) cc_final: 0.7693 (p) REVERT: C 320 MET cc_start: 0.3657 (OUTLIER) cc_final: 0.3337 (tpp) REVERT: C 376 MET cc_start: 0.7634 (tmm) cc_final: 0.7402 (tmm) REVERT: C 435 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7017 (tp40) REVERT: D 118 SER cc_start: 0.7662 (p) cc_final: 0.7120 (t) REVERT: D 182 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7626 (tp) REVERT: D 215 LEU cc_start: 0.9137 (tp) cc_final: 0.8930 (mt) REVERT: D 353 MET cc_start: 0.7808 (mmm) cc_final: 0.7594 (mmm) REVERT: D 362 ASN cc_start: 0.8510 (m-40) cc_final: 0.7755 (t0) REVERT: D 380 HIS cc_start: 0.7193 (t70) cc_final: 0.6852 (t70) REVERT: D 439 ARG cc_start: 0.8391 (tpp80) cc_final: 0.8076 (tpp80) outliers start: 65 outliers final: 51 residues processed: 206 average time/residue: 0.2353 time to fit residues: 73.4489 Evaluate side-chains 208 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 147 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -4 TYR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 HIS Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 296 HIS Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 313 ARG Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 504 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 183 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 83 optimal weight: 0.4980 chunk 189 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.178545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.104490 restraints weight = 23909.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.107245 restraints weight = 11722.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.108848 restraints weight = 7817.775| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14700 Z= 0.133 Angle : 0.708 13.141 20112 Z= 0.327 Chirality : 0.042 0.318 2520 Planarity : 0.005 0.080 2588 Dihedral : 4.178 50.785 2151 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.87 % Favored : 93.03 % Rotamer: Outliers : 4.17 % Allowed : 30.19 % Favored : 65.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.61 (0.20), residues: 1980 helix: 1.57 (0.14), residues: 1304 sheet: -0.44 (0.52), residues: 114 loop : -2.30 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP C 370 HIS 0.008 0.001 HIS D 211 PHE 0.021 0.001 PHE D 24 TYR 0.023 0.002 TYR D 102 ARG 0.007 0.000 ARG C 388 Details of bonding type rmsd hydrogen bonds : bond 0.04418 ( 994) hydrogen bonds : angle 3.97965 ( 2922) covalent geometry : bond 0.00298 (14700) covalent geometry : angle 0.70779 (20112) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 146 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B -4 TYR cc_start: 0.5519 (OUTLIER) cc_final: 0.4976 (t80) REVERT: B 158 LEU cc_start: 0.9249 (tp) cc_final: 0.9027 (tt) REVERT: B 170 MET cc_start: 0.8213 (ttp) cc_final: 0.7994 (ttm) REVERT: B 376 MET cc_start: 0.8618 (tmm) cc_final: 0.7325 (tmm) REVERT: B 460 HIS cc_start: 0.4093 (OUTLIER) cc_final: 0.2809 (m170) REVERT: A 82 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8492 (tm-30) REVERT: A 305 MET cc_start: 0.8004 (mmm) cc_final: 0.7626 (mmt) REVERT: A 355 MET cc_start: 0.7887 (ptp) cc_final: 0.7579 (ptp) REVERT: A 426 LEU cc_start: 0.7759 (tt) cc_final: 0.7297 (pp) REVERT: A 499 PHE cc_start: 0.5433 (OUTLIER) cc_final: 0.4700 (t80) REVERT: C 212 MET cc_start: 0.8987 (mmm) cc_final: 0.8622 (mmm) REVERT: C 250 THR cc_start: 0.7915 (OUTLIER) cc_final: 0.7567 (p) REVERT: C 320 MET cc_start: 0.3510 (OUTLIER) cc_final: 0.3220 (tpp) REVERT: C 375 TRP cc_start: 0.7469 (t-100) cc_final: 0.6720 (t-100) REVERT: C 435 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.6973 (tp40) REVERT: D 118 SER cc_start: 0.7709 (p) cc_final: 0.7226 (t) REVERT: D 182 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7566 (tp) REVERT: D 215 LEU cc_start: 0.9107 (tp) cc_final: 0.8904 (mt) REVERT: D 353 MET cc_start: 0.7785 (mmm) cc_final: 0.7561 (mmm) REVERT: D 362 ASN cc_start: 0.8525 (m-40) cc_final: 0.7875 (t0) REVERT: D 380 HIS cc_start: 0.7196 (t70) cc_final: 0.6865 (t70) REVERT: D 439 ARG cc_start: 0.8380 (tpp80) cc_final: 0.8126 (tpp80) outliers start: 61 outliers final: 51 residues processed: 198 average time/residue: 0.2317 time to fit residues: 70.2325 Evaluate side-chains 200 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 141 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -4 TYR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 HIS Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 435 GLN Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 504 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 178 optimal weight: 0.9990 chunk 193 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 154 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 chunk 149 optimal weight: 0.4980 chunk 170 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.7164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 378 HIS ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.178851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.104061 restraints weight = 24476.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.106963 restraints weight = 11709.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.108541 restraints weight = 7691.466| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14700 Z= 0.131 Angle : 0.713 13.768 20112 Z= 0.327 Chirality : 0.041 0.308 2520 Planarity : 0.005 0.080 2588 Dihedral : 4.144 49.735 2151 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.02 % Favored : 92.88 % Rotamer: Outliers : 3.96 % Allowed : 30.19 % Favored : 65.85 % 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: 0.68 (0.20), residues: 1980 helix: 1.65 (0.14), residues: 1292 sheet: -0.40 (0.52), residues: 114 loop : -2.24 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP C 370 HIS 0.008 0.001 HIS A 211 PHE 0.021 0.001 PHE D 24 TYR 0.023 0.002 TYR D 102 ARG 0.007 0.000 ARG C 388 Details of bonding type rmsd hydrogen bonds : bond 0.04328 ( 994) hydrogen bonds : angle 3.94976 ( 2922) covalent geometry : bond 0.00295 (14700) covalent geometry : angle 0.71298 (20112) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5583.16 seconds wall clock time: 98 minutes 2.16 seconds (5882.16 seconds total)