Starting phenix.real_space_refine on Sun Nov 17 18:56:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipq_35640/11_2024/8ipq_35640.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipq_35640/11_2024/8ipq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipq_35640/11_2024/8ipq_35640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipq_35640/11_2024/8ipq_35640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipq_35640/11_2024/8ipq_35640.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ipq_35640/11_2024/8ipq_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 8.81, per 1000 atoms: 0.61 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: 3.60 Conformation dependent library (CDL) restraints added in 2.0 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: 1.32 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: 4.30 Time building geometry restraints manager: 4.14 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: 0.00 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.710 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.050 ------------------------------------------------------------------------------- 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= 0.261 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 *********************** 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 : 1.550 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: 0.3207 time to fit residues: 121.6980 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 : 1.544 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 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= 0.275 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 *********************** 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 : 1.467 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: 0.5655 (OUTLIER) cc_final: 0.5054 (t80) REVERT: B 100 ARG cc_start: 0.7756 (mtt90) cc_final: 0.7500 (mpt180) REVERT: A 211 HIS cc_start: 0.6993 (OUTLIER) cc_final: 0.6665 (t-170) REVERT: C 177 MET cc_start: 0.8359 (mmm) cc_final: 0.8047 (tpt) REVERT: C 390 ASN cc_start: 0.6808 (OUTLIER) cc_final: 0.6573 (m-40) REVERT: D 220 ARG cc_start: 0.8755 (mmt180) cc_final: 0.8418 (mmt90) REVERT: D 305 MET cc_start: 0.8098 (mmp) cc_final: 0.7794 (mmt) REVERT: D 329 VAL cc_start: 0.1460 (OUTLIER) cc_final: 0.0344 (m) outliers start: 66 outliers final: 30 residues processed: 231 average time/residue: 0.2660 time to fit residues: 90.0053 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 : 1.511 ------------------------------------------------------------------------------- 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 99 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 160 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 144 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 24 ASN C 56 GLN C 287 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 14700 Z= 0.424 Angle : 0.800 11.896 20112 Z= 0.390 Chirality : 0.046 0.286 2520 Planarity : 0.006 0.090 2588 Dihedral : 4.672 55.587 2151 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.83 % Favored : 92.07 % Rotamer: Outliers : 7.51 % Allowed : 25.55 % Favored : 66.94 % 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: 0.17 (0.20), residues: 1980 helix: 1.16 (0.14), residues: 1312 sheet: -0.37 (0.50), residues: 122 loop : -2.40 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 375 HIS 0.006 0.001 HIS A 232 PHE 0.022 0.002 PHE D 24 TYR 0.019 0.003 TYR C 108 ARG 0.008 0.001 ARG D 115 *********************** 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 281 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 171 time to evaluate : 1.493 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: 0.5744 (OUTLIER) cc_final: 0.4989 (t80) REVERT: B 56 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7816 (tm-30) REVERT: B 113 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8465 (mp) REVERT: B 133 TYR cc_start: 0.8468 (m-80) cc_final: 0.7580 (m-80) REVERT: B 460 HIS cc_start: 0.3956 (OUTLIER) cc_final: 0.2955 (m170) REVERT: A 138 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7141 (mpt180) REVERT: A 149 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8513 (mm) REVERT: C 80 THR cc_start: 0.8685 (t) cc_final: 0.8453 (t) REVERT: C 212 MET cc_start: 0.8656 (mmm) cc_final: 0.8445 (mmm) REVERT: C 250 THR cc_start: 0.8182 (OUTLIER) cc_final: 0.7958 (p) REVERT: C 376 MET cc_start: 0.7835 (tmm) cc_final: 0.7627 (tmm) REVERT: C 390 ASN cc_start: 0.6626 (OUTLIER) cc_final: 0.6268 (m-40) REVERT: C 409 PHE cc_start: 0.7842 (t80) cc_final: 0.7638 (t80) REVERT: D 182 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7577 (tp) REVERT: D 215 LEU cc_start: 0.8829 (tp) cc_final: 0.8623 (tp) REVERT: D 220 ARG cc_start: 0.8858 (mmt180) cc_final: 0.8474 (mmt90) REVERT: D 375 PHE cc_start: 0.7187 (m-80) cc_final: 0.6953 (m-80) REVERT: D 380 HIS cc_start: 0.6950 (t70) cc_final: 0.6487 (t-90) REVERT: D 439 ARG cc_start: 0.8495 (tpp80) cc_final: 0.8295 (tpp80) outliers start: 110 outliers final: 62 residues processed: 265 average time/residue: 0.2548 time to fit residues: 100.1354 Evaluate side-chains 217 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 146 time to evaluate : 1.577 ------------------------------------------------------------------------------- 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 56 GLN Chi-restraints excluded: chain B residue 65 THR 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 167 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 304 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 65 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 78 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 138 ARG Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 149 LEU 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 224 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 283 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 65 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 128 VAL 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 250 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 77 VAL 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 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 282 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 0.5980 chunk 135 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 180 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 171 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN C 56 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 14700 Z= 0.403 Angle : 0.784 11.855 20112 Z= 0.379 Chirality : 0.045 0.192 2520 Planarity : 0.006 0.094 2588 Dihedral : 4.700 58.662 2151 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.03 % Favored : 91.87 % Rotamer: Outliers : 7.24 % Allowed : 27.94 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1980 helix: 1.08 (0.14), residues: 1314 sheet: -0.48 (0.52), residues: 112 loop : -2.55 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 369 HIS 0.006 0.001 HIS A 211 PHE 0.023 0.002 PHE D 24 TYR 0.019 0.003 TYR C 108 ARG 0.005 0.001 ARG C 73 *********************** 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 252 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 146 time to evaluate : 1.604 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: 0.5657 (OUTLIER) cc_final: 0.4847 (t80) REVERT: B 133 TYR cc_start: 0.8504 (m-80) cc_final: 0.7447 (m-80) REVERT: B 376 MET cc_start: 0.8612 (tmm) cc_final: 0.7887 (tmm) REVERT: B 460 HIS cc_start: 0.3964 (OUTLIER) cc_final: 0.2907 (m170) REVERT: A 426 LEU cc_start: 0.7328 (tt) cc_final: 0.6949 (pp) REVERT: C 147 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8286 (mp) REVERT: C 390 ASN cc_start: 0.6559 (OUTLIER) cc_final: 0.6194 (m-40) REVERT: C 409 PHE cc_start: 0.7865 (t80) cc_final: 0.7613 (t80) REVERT: D 115 ARG cc_start: 0.7985 (mtm-85) cc_final: 0.7494 (ptp-170) REVERT: D 182 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7651 (tp) REVERT: D 380 HIS cc_start: 0.6880 (t70) cc_final: 0.6439 (t-90) outliers start: 106 outliers final: 71 residues processed: 237 average time/residue: 0.2561 time to fit residues: 90.1807 Evaluate side-chains 219 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 143 time to evaluate : 1.567 ------------------------------------------------------------------------------- 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 65 THR 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 167 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 286 GLU 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 34 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 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 145 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 174 VAL 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 240 ASP Chi-restraints excluded: chain A residue 269 ILE 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 C residue 97 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 147 LEU 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 286 GLU Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 372 ARG 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 D residue 16 LEU Chi-restraints excluded: chain D residue 37 SER 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 135 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 506 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 0.0870 chunk 108 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 142 optimal weight: 8.9990 chunk 78 optimal weight: 0.1980 chunk 163 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 171 optimal weight: 4.9990 chunk 48 optimal weight: 30.0000 overall best weight: 1.2162 ------------------------------------------------------------------------------- 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** C 24 ASN C 56 GLN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3268 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= 0.219 Angle : 0.717 13.250 20112 Z= 0.334 Chirality : 0.042 0.169 2520 Planarity : 0.006 0.082 2588 Dihedral : 4.524 57.013 2151 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.88 % Favored : 92.02 % Rotamer: Outliers : 4.44 % Allowed : 30.74 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.20), residues: 1980 helix: 1.32 (0.15), residues: 1316 sheet: -0.60 (0.52), residues: 112 loop : -2.48 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP C 370 HIS 0.017 0.001 HIS D 211 PHE 0.020 0.001 PHE D 24 TYR 0.018 0.002 TYR C 108 ARG 0.004 0.000 ARG B 86 *********************** 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 220 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 155 time to evaluate : 1.576 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: symmetry clash REVERT: B -4 TYR cc_start: 0.5417 (OUTLIER) cc_final: 0.4799 (t80) REVERT: B 133 TYR cc_start: 0.8351 (m-80) cc_final: 0.7034 (m-80) REVERT: B 158 LEU cc_start: 0.9201 (tp) cc_final: 0.8974 (tt) REVERT: B 376 MET cc_start: 0.8560 (tmm) cc_final: 0.8360 (tmm) REVERT: B 460 HIS cc_start: 0.3887 (OUTLIER) cc_final: 0.2664 (m170) REVERT: A 426 LEU cc_start: 0.7256 (tt) cc_final: 0.6783 (pp) REVERT: C 147 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8207 (mp) REVERT: C 376 MET cc_start: 0.7899 (tmm) cc_final: 0.7692 (tmm) REVERT: C 409 PHE cc_start: 0.7758 (t80) cc_final: 0.7507 (t80) REVERT: D 82 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8498 (tm-30) REVERT: D 115 ARG cc_start: 0.7931 (mtm-85) cc_final: 0.7527 (ptp-170) REVERT: D 380 HIS cc_start: 0.6813 (t70) cc_final: 0.6429 (t70) REVERT: D 439 ARG cc_start: 0.8455 (tpp80) cc_final: 0.8251 (tpp80) outliers start: 65 outliers final: 40 residues processed: 212 average time/residue: 0.2534 time to fit residues: 80.3269 Evaluate side-chains 189 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 1.525 ------------------------------------------------------------------------------- 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 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 451 VAL Chi-restraints excluded: chain B residue 460 HIS Chi-restraints excluded: chain A residue 34 SER 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 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 309 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 375 PHE 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 147 LEU 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 286 GLU 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 82 GLN 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 228 PHE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 506 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 191 optimal weight: 3.9990 chunk 159 optimal weight: 0.0770 chunk 88 optimal weight: 20.0000 chunk 15 optimal weight: 4.9990 chunk 63 optimal weight: 0.0370 chunk 100 optimal weight: 2.9990 overall best weight: 1.6222 ------------------------------------------------------------------------------- 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 ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3397 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= 0.246 Angle : 0.715 11.438 20112 Z= 0.336 Chirality : 0.042 0.178 2520 Planarity : 0.005 0.084 2588 Dihedral : 4.449 54.406 2151 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.88 % Favored : 92.02 % Rotamer: Outliers : 4.92 % Allowed : 30.60 % Favored : 64.48 % 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: 0.33 (0.20), residues: 1980 helix: 1.32 (0.15), residues: 1316 sheet: -0.62 (0.52), residues: 112 loop : -2.36 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 370 HIS 0.006 0.001 HIS A 211 PHE 0.020 0.001 PHE D 24 TYR 0.021 0.002 TYR D 102 ARG 0.008 0.000 ARG D 83 *********************** 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 223 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 151 time to evaluate : 1.548 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: 0.5525 (OUTLIER) cc_final: 0.4833 (t80) REVERT: B 113 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8597 (mp) REVERT: B 133 TYR cc_start: 0.8375 (m-80) cc_final: 0.6993 (m-80) REVERT: B 158 LEU cc_start: 0.9229 (tp) cc_final: 0.9007 (tt) REVERT: B 376 MET cc_start: 0.8632 (tmm) cc_final: 0.7411 (tmm) REVERT: B 460 HIS cc_start: 0.3876 (OUTLIER) cc_final: 0.2750 (m170) REVERT: A 229 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8022 (tm-30) REVERT: A 355 MET cc_start: 0.7900 (ptp) cc_final: 0.7677 (ptp) REVERT: A 426 LEU cc_start: 0.7559 (tt) cc_final: 0.6972 (pp) REVERT: A 499 PHE cc_start: 0.5730 (OUTLIER) cc_final: 0.4972 (t80) REVERT: C 147 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8224 (mp) REVERT: C 320 MET cc_start: 0.3862 (OUTLIER) cc_final: 0.3441 (tpp) REVERT: C 376 MET cc_start: 0.7798 (tmm) cc_final: 0.7579 (tmm) REVERT: C 409 PHE cc_start: 0.7812 (t80) cc_final: 0.7543 (t80) REVERT: D 18 ARG cc_start: 0.5946 (OUTLIER) cc_final: 0.5217 (ttp80) REVERT: D 115 ARG cc_start: 0.8012 (mtm-85) cc_final: 0.7671 (ptp-170) REVERT: D 182 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7694 (tp) REVERT: D 215 LEU cc_start: 0.9098 (tp) cc_final: 0.8815 (mt) REVERT: D 362 ASN cc_start: 0.8487 (m-40) cc_final: 0.7740 (t0) REVERT: D 380 HIS cc_start: 0.6843 (t70) cc_final: 0.6460 (t70) outliers start: 72 outliers final: 53 residues processed: 211 average time/residue: 0.2629 time to fit residues: 83.5208 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 : 1.555 ------------------------------------------------------------------------------- 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 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 382 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 78 LEU 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 140 LEU 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 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 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 51 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 147 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 286 GLU Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 372 ARG 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 12 LEU Chi-restraints excluded: chain D residue 18 ARG 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 221 LEU Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 506 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 190 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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** A 494 HIS C 24 ASN ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14700 Z= 0.271 Angle : 0.725 10.635 20112 Z= 0.342 Chirality : 0.043 0.164 2520 Planarity : 0.006 0.081 2588 Dihedral : 4.425 50.460 2151 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.88 % Favored : 92.02 % Rotamer: Outliers : 5.94 % Allowed : 29.10 % Favored : 64.96 % 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: 0.35 (0.20), residues: 1980 helix: 1.34 (0.15), residues: 1310 sheet: -0.57 (0.51), residues: 114 loop : -2.32 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 370 HIS 0.007 0.001 HIS A 211 PHE 0.022 0.001 PHE D 24 TYR 0.020 0.002 TYR C 108 ARG 0.004 0.000 ARG B 86 *********************** 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 237 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 150 time to evaluate : 1.524 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: 0.5584 (OUTLIER) cc_final: 0.4869 (t80) REVERT: B 39 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8567 (mp) REVERT: B 133 TYR cc_start: 0.8426 (m-80) cc_final: 0.7006 (m-80) REVERT: B 158 LEU cc_start: 0.9243 (tp) cc_final: 0.9027 (tt) REVERT: B 376 MET cc_start: 0.8656 (tmm) cc_final: 0.7423 (tmm) REVERT: B 460 HIS cc_start: 0.3943 (OUTLIER) cc_final: 0.2765 (m170) REVERT: A 82 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8547 (tm-30) REVERT: A 426 LEU cc_start: 0.7746 (tt) cc_final: 0.7130 (pp) REVERT: A 499 PHE cc_start: 0.5638 (OUTLIER) cc_final: 0.4833 (t80) REVERT: C 135 TRP cc_start: 0.7603 (p-90) cc_final: 0.7402 (p-90) REVERT: C 147 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8231 (mp) REVERT: C 250 THR cc_start: 0.8101 (OUTLIER) cc_final: 0.7867 (p) REVERT: C 320 MET cc_start: 0.4096 (OUTLIER) cc_final: 0.3667 (tpt) REVERT: C 375 TRP cc_start: 0.7434 (t-100) cc_final: 0.6986 (t-100) REVERT: C 409 PHE cc_start: 0.7673 (t80) cc_final: 0.7379 (t80) REVERT: D 18 ARG cc_start: 0.6078 (OUTLIER) cc_final: 0.5310 (ttp80) REVERT: D 81 CYS cc_start: 0.8503 (t) cc_final: 0.8015 (m) REVERT: D 115 ARG cc_start: 0.8051 (mtm-85) cc_final: 0.7670 (ptp-170) REVERT: D 118 SER cc_start: 0.7398 (p) cc_final: 0.7110 (p) REVERT: D 182 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7709 (tp) REVERT: D 215 LEU cc_start: 0.9182 (tp) cc_final: 0.8862 (tt) REVERT: D 362 ASN cc_start: 0.8568 (m-40) cc_final: 0.7861 (t0) REVERT: D 380 HIS cc_start: 0.6883 (t70) cc_final: 0.6527 (t70) outliers start: 87 outliers final: 61 residues processed: 223 average time/residue: 0.2492 time to fit residues: 83.8441 Evaluate side-chains 214 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 143 time to evaluate : 1.699 ------------------------------------------------------------------------------- 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 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 250 THR 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 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 140 LEU 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 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 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 51 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 147 LEU 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 250 THR Chi-restraints excluded: chain C residue 286 GLU 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 C residue 497 ASP Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 71 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 221 LEU Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 506 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 57 optimal weight: 0.0470 chunk 37 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 130 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 150 optimal weight: 0.0980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3677 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= 0.191 Angle : 0.722 10.930 20112 Z= 0.333 Chirality : 0.042 0.187 2520 Planarity : 0.005 0.078 2588 Dihedral : 4.291 48.511 2151 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.63 % Favored : 92.27 % Rotamer: Outliers : 4.23 % Allowed : 30.74 % Favored : 65.03 % 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: 0.47 (0.20), residues: 1980 helix: 1.47 (0.15), residues: 1304 sheet: -0.58 (0.52), residues: 112 loop : -2.34 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP C 370 HIS 0.007 0.001 HIS A 211 PHE 0.019 0.001 PHE D 24 TYR 0.023 0.002 TYR D 102 ARG 0.004 0.000 ARG B 86 *********************** 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 221 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 159 time to evaluate : 1.598 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: 0.5484 (OUTLIER) cc_final: 0.4968 (t80) REVERT: B 39 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8616 (mp) REVERT: B 158 LEU cc_start: 0.9242 (tp) cc_final: 0.9027 (tt) REVERT: B 170 MET cc_start: 0.8244 (ttp) cc_final: 0.8018 (ttm) REVERT: B 372 ARG cc_start: 0.7350 (ttm-80) cc_final: 0.7074 (ptm160) REVERT: B 376 MET cc_start: 0.8649 (tmm) cc_final: 0.7416 (tmm) REVERT: B 460 HIS cc_start: 0.3876 (OUTLIER) cc_final: 0.2721 (m170) REVERT: A 82 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8547 (tm-30) REVERT: A 88 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.7699 (t70) REVERT: A 499 PHE cc_start: 0.5675 (OUTLIER) cc_final: 0.4866 (t80) REVERT: C 320 MET cc_start: 0.4325 (OUTLIER) cc_final: 0.4011 (tpt) REVERT: C 375 TRP cc_start: 0.7358 (t-100) cc_final: 0.6771 (t-100) REVERT: C 409 PHE cc_start: 0.7699 (t80) cc_final: 0.7409 (t80) REVERT: D 115 ARG cc_start: 0.7971 (mtm-85) cc_final: 0.7609 (ptp-170) REVERT: D 118 SER cc_start: 0.7445 (p) cc_final: 0.6841 (t) REVERT: D 182 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7685 (tp) REVERT: D 362 ASN cc_start: 0.8604 (m-40) cc_final: 0.7899 (t0) REVERT: D 380 HIS cc_start: 0.6771 (t70) cc_final: 0.6420 (t70) REVERT: D 440 ARG cc_start: 0.8950 (mtt90) cc_final: 0.8699 (ttm170) outliers start: 62 outliers final: 45 residues processed: 212 average time/residue: 0.2674 time to fit residues: 83.9671 Evaluate side-chains 207 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 154 time to evaluate : 1.447 ------------------------------------------------------------------------------- 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 200 ILE Chi-restraints excluded: chain B residue 264 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 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 140 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 182 LEU 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 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 157 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 286 GLU 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 439 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 34 SER 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 182 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 506 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 3.9990 chunk 182 optimal weight: 30.0000 chunk 166 optimal weight: 0.6980 chunk 177 optimal weight: 0.5980 chunk 107 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 139 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 168 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3775 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= 0.213 Angle : 0.731 14.027 20112 Z= 0.337 Chirality : 0.042 0.154 2520 Planarity : 0.005 0.076 2588 Dihedral : 4.241 46.015 2151 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.42 % Favored : 92.47 % Rotamer: Outliers : 4.03 % Allowed : 31.56 % Favored : 64.41 % 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: 0.51 (0.20), residues: 1980 helix: 1.50 (0.15), residues: 1304 sheet: -0.49 (0.52), residues: 114 loop : -2.34 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP C 370 HIS 0.007 0.001 HIS A 211 PHE 0.020 0.001 PHE D 24 TYR 0.021 0.002 TYR D 102 ARG 0.008 0.000 ARG C 388 *********************** 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 211 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 152 time to evaluate : 1.570 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 39 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8673 (mp) REVERT: B 157 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8400 (tt) REVERT: B 158 LEU cc_start: 0.9241 (tp) cc_final: 0.9029 (tt) REVERT: B 170 MET cc_start: 0.8207 (ttp) cc_final: 0.7985 (ttm) REVERT: B 372 ARG cc_start: 0.7331 (ttm-80) cc_final: 0.7058 (ptm160) REVERT: B 376 MET cc_start: 0.8649 (tmm) cc_final: 0.7288 (tmm) REVERT: B 460 HIS cc_start: 0.3834 (OUTLIER) cc_final: 0.2654 (m170) REVERT: A 82 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8526 (tm-30) REVERT: A 229 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7890 (tm-30) REVERT: A 355 MET cc_start: 0.7866 (ptp) cc_final: 0.7454 (pmm) REVERT: A 499 PHE cc_start: 0.5722 (OUTLIER) cc_final: 0.4936 (t80) REVERT: C 320 MET cc_start: 0.4399 (OUTLIER) cc_final: 0.4084 (tpt) REVERT: C 375 TRP cc_start: 0.7371 (t-100) cc_final: 0.6789 (t-100) REVERT: C 409 PHE cc_start: 0.7660 (t80) cc_final: 0.7355 (t80) REVERT: D 18 ARG cc_start: 0.6001 (OUTLIER) cc_final: 0.5209 (ttp80) REVERT: D 115 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7612 (ptp-170) REVERT: D 118 SER cc_start: 0.7557 (p) cc_final: 0.6991 (t) REVERT: D 182 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7656 (tp) REVERT: D 211 HIS cc_start: 0.8318 (t70) cc_final: 0.8062 (t70) REVERT: D 222 ASP cc_start: 0.7679 (m-30) cc_final: 0.7195 (p0) REVERT: D 362 ASN cc_start: 0.8638 (m-40) cc_final: 0.8020 (t0) REVERT: D 380 HIS cc_start: 0.6821 (t70) cc_final: 0.6448 (t70) outliers start: 59 outliers final: 48 residues processed: 204 average time/residue: 0.2602 time to fit residues: 79.2206 Evaluate side-chains 204 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 148 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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 264 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 HIS Chi-restraints excluded: chain B residue 488 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 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 140 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 182 LEU 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 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 385 THR 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 157 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 286 GLU 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 439 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 71 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 228 PHE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 506 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 130 optimal weight: 20.0000 chunk 197 optimal weight: 0.0770 chunk 181 optimal weight: 0.7980 chunk 157 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 121 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- 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 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14700 Z= 0.203 Angle : 0.731 13.640 20112 Z= 0.335 Chirality : 0.042 0.192 2520 Planarity : 0.005 0.078 2588 Dihedral : 4.184 43.412 2151 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.42 % Favored : 92.47 % Rotamer: Outliers : 4.03 % Allowed : 31.56 % Favored : 64.41 % 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: 0.53 (0.20), residues: 1980 helix: 1.52 (0.15), residues: 1304 sheet: -0.48 (0.53), residues: 114 loop : -2.35 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP C 370 HIS 0.007 0.001 HIS A 211 PHE 0.020 0.001 PHE D 24 TYR 0.024 0.002 TYR D 102 ARG 0.008 0.000 ARG C 388 ********************** 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 216 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 157 time to evaluate : 1.489 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 100 ARG cc_start: 0.7672 (mmt180) cc_final: 0.7352 (mmt180) REVERT: B 157 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8404 (tt) REVERT: B 158 LEU cc_start: 0.9223 (tp) cc_final: 0.9010 (tt) REVERT: B 376 MET cc_start: 0.8647 (tmm) cc_final: 0.7258 (tmm) REVERT: B 460 HIS cc_start: 0.3772 (OUTLIER) cc_final: 0.2553 (m170) REVERT: A 82 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8520 (tm-30) REVERT: A 88 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.7721 (t70) REVERT: A 355 MET cc_start: 0.7882 (ptp) cc_final: 0.7485 (pmm) REVERT: A 455 LEU cc_start: 0.5844 (mp) cc_final: 0.5351 (tt) REVERT: A 499 PHE cc_start: 0.5612 (OUTLIER) cc_final: 0.4822 (t80) REVERT: C 70 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6735 (tp30) REVERT: C 157 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8349 (mp) REVERT: C 320 MET cc_start: 0.4345 (OUTLIER) cc_final: 0.3774 (tpp) REVERT: C 375 TRP cc_start: 0.7269 (t-100) cc_final: 0.6801 (t-100) REVERT: C 409 PHE cc_start: 0.7654 (t80) cc_final: 0.7351 (t80) REVERT: D 18 ARG cc_start: 0.5964 (OUTLIER) cc_final: 0.5179 (ttp80) REVERT: D 115 ARG cc_start: 0.7895 (mtm-85) cc_final: 0.7595 (ptp-170) REVERT: D 118 SER cc_start: 0.7630 (p) cc_final: 0.7082 (t) REVERT: D 211 HIS cc_start: 0.8349 (t70) cc_final: 0.8105 (t70) REVERT: D 222 ASP cc_start: 0.7671 (m-30) cc_final: 0.6254 (t0) REVERT: D 355 MET cc_start: 0.7703 (ppp) cc_final: 0.7077 (mtm) REVERT: D 362 ASN cc_start: 0.8639 (m-40) cc_final: 0.8005 (t0) REVERT: D 380 HIS cc_start: 0.6762 (t70) cc_final: 0.6387 (t70) REVERT: D 440 ARG cc_start: 0.8911 (mtt90) cc_final: 0.8677 (ttm170) outliers start: 59 outliers final: 40 residues processed: 210 average time/residue: 0.2885 time to fit residues: 91.1969 Evaluate side-chains 196 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 148 time to evaluate : 1.460 ------------------------------------------------------------------------------- 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 304 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 HIS Chi-restraints excluded: chain B residue 488 HIS 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 125 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 182 LEU 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 309 VAL Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 385 THR 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 157 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 286 GLU 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 D residue 12 LEU Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 504 VAL Chi-restraints excluded: chain D residue 506 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.0040 chunk 48 optimal weight: 20.0000 chunk 144 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 43 optimal weight: 8.9990 chunk 157 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 28 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 ** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.179083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.104951 restraints weight = 23911.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.107715 restraints weight = 11797.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.109356 restraints weight = 7856.886| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14700 Z= 0.192 Angle : 0.726 13.186 20112 Z= 0.331 Chirality : 0.042 0.224 2520 Planarity : 0.005 0.074 2588 Dihedral : 4.127 42.163 2151 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.32 % Favored : 92.58 % Rotamer: Outliers : 3.55 % Allowed : 31.90 % Favored : 64.55 % 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: 0.51 (0.20), residues: 1980 helix: 1.48 (0.14), residues: 1326 sheet: -0.52 (0.54), residues: 112 loop : -2.44 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP C 370 HIS 0.008 0.001 HIS A 211 PHE 0.019 0.001 PHE D 24 TYR 0.024 0.002 TYR D 102 ARG 0.007 0.000 ARG C 388 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3006.29 seconds wall clock time: 55 minutes 42.04 seconds (3342.04 seconds total)