Starting phenix.real_space_refine on Thu Jun 12 23:02:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ipq_35640/06_2025/8ipq_35640.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ipq_35640/06_2025/8ipq_35640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ipq_35640/06_2025/8ipq_35640.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ipq_35640/06_2025/8ipq_35640.map" model { file = "/net/cci-nas-00/data/ceres_data/8ipq_35640/06_2025/8ipq_35640.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ipq_35640/06_2025/8ipq_35640.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 9180 2.51 5 N 2608 2.21 5 O 2610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.22, per 1000 atoms: 0.64 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: 3.39 Conformation dependent library (CDL) restraints added in 1.9 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: 1.77 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: 4.80 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2978 1.33 - 1.45: 2963 1.45 - 1.58: 8661 1.58 - 1.70: 0 1.70 - 1.82: 98 Bond restraints: 14700 Sorted by residual: bond pdb=" C GLU C 294 " pdb=" N PRO C 295 " ideal model delta sigma weight residual 1.331 1.389 -0.057 1.20e-02 6.94e+03 2.30e+01 bond pdb=" C GLU B 294 " pdb=" N PRO B 295 " ideal model delta sigma weight residual 1.331 1.389 -0.057 1.20e-02 6.94e+03 2.29e+01 bond pdb=" CA GLU B 456 " pdb=" C GLU B 456 " ideal model delta sigma weight residual 1.524 1.570 -0.046 1.26e-02 6.30e+03 1.32e+01 bond pdb=" C GLU B 456 " pdb=" N PRO B 457 " ideal model delta sigma weight residual 1.336 1.380 -0.044 1.25e-02 6.40e+03 1.26e+01 bond pdb=" N PHE C 219 " pdb=" CA PHE C 219 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.26e-02 6.30e+03 7.37e+00 ... (remaining 14695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 19719 2.26 - 4.52: 283 4.52 - 6.78: 77 6.78 - 9.04: 22 9.04 - 11.30: 11 Bond angle restraints: 20112 Sorted by residual: angle pdb=" N LEU C 344 " pdb=" CA LEU C 344 " pdb=" C LEU C 344 " ideal model delta sigma weight residual 113.28 104.57 8.71 1.22e+00 6.72e-01 5.10e+01 angle pdb=" N LEU B 344 " pdb=" CA LEU B 344 " pdb=" C LEU B 344 " ideal model delta sigma weight residual 113.28 104.58 8.70 1.22e+00 6.72e-01 5.09e+01 angle pdb=" C PHE C 219 " pdb=" CA PHE C 219 " pdb=" CB PHE C 219 " ideal model delta sigma weight residual 110.56 101.08 9.48 1.69e+00 3.50e-01 3.15e+01 angle pdb=" N PRO C 295 " pdb=" CA PRO C 295 " pdb=" C PRO C 295 " ideal model delta sigma weight residual 111.03 119.55 -8.52 1.54e+00 4.22e-01 3.06e+01 angle pdb=" N PRO B 295 " pdb=" CA PRO B 295 " pdb=" C PRO B 295 " ideal model delta sigma weight residual 111.03 119.53 -8.50 1.54e+00 4.22e-01 3.05e+01 ... (remaining 20107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 7632 17.21 - 34.42: 942 34.42 - 51.63: 260 51.63 - 68.84: 20 68.84 - 86.05: 10 Dihedral angle restraints: 8864 sinusoidal: 3220 harmonic: 5644 Sorted by residual: dihedral pdb=" C THR B 299 " pdb=" N THR B 299 " pdb=" CA THR B 299 " pdb=" CB THR B 299 " ideal model delta harmonic sigma weight residual -122.00 -134.61 12.61 0 2.50e+00 1.60e-01 2.55e+01 dihedral pdb=" C THR C 299 " pdb=" N THR C 299 " pdb=" CA THR C 299 " pdb=" CB THR C 299 " ideal model delta harmonic sigma weight residual -122.00 -134.60 12.60 0 2.50e+00 1.60e-01 2.54e+01 dihedral pdb=" N THR B 299 " pdb=" C THR B 299 " pdb=" CA THR B 299 " pdb=" CB THR B 299 " ideal model delta harmonic sigma weight residual 123.40 135.58 -12.18 0 2.50e+00 1.60e-01 2.37e+01 ... (remaining 8861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 2414 0.099 - 0.198: 102 0.198 - 0.296: 2 0.296 - 0.395: 0 0.395 - 0.494: 2 Chirality restraints: 2520 Sorted by residual: chirality pdb=" CA THR B 299 " pdb=" N THR B 299 " pdb=" C THR B 299 " pdb=" CB THR B 299 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.49 2.00e-01 2.50e+01 6.10e+00 chirality pdb=" CA THR C 299 " pdb=" N THR C 299 " pdb=" C THR C 299 " pdb=" CB THR C 299 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.49 2.00e-01 2.50e+01 6.10e+00 chirality pdb=" CA PRO B 295 " pdb=" N PRO B 295 " pdb=" C PRO B 295 " pdb=" CB PRO B 295 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2517 not shown) Planarity restraints: 2588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 343 " 0.016 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C ILE B 343 " -0.058 2.00e-02 2.50e+03 pdb=" O ILE B 343 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU B 344 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 343 " -0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C ILE C 343 " 0.058 2.00e-02 2.50e+03 pdb=" O ILE C 343 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU C 344 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 126 " 0.044 5.00e-02 4.00e+02 6.69e-02 7.15e+00 pdb=" N PRO A 127 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 127 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 127 " 0.037 5.00e-02 4.00e+02 ... (remaining 2585 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1903 2.75 - 3.29: 14730 3.29 - 3.82: 25155 3.82 - 4.36: 26136 4.36 - 4.90: 46398 Nonbonded interactions: 114322 Sorted by model distance: nonbonded pdb=" O ALA B 182 " pdb=" OG SER A 118 " model vdw 2.209 3.040 nonbonded pdb=" O LEU B 393 " pdb=" NE ARG A 220 " model vdw 2.230 3.120 nonbonded pdb=" O LEU C 393 " pdb=" NE ARG D 220 " model vdw 2.231 3.120 nonbonded pdb=" OD1 ASP C 134 " pdb=" NH2 ARG C 243 " model vdw 2.243 3.120 nonbonded pdb=" OD1 ASP B 134 " pdb=" NH2 ARG B 243 " model vdw 2.243 3.120 ... (remaining 114317 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.800 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: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 34.730 Find NCS groups from input model: 0.590 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14700 Z= 0.200 Angle : 0.774 11.295 20112 Z= 0.393 Chirality : 0.045 0.494 2520 Planarity : 0.006 0.107 2588 Dihedral : 16.068 86.048 5220 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.17 % Favored : 92.73 % Rotamer: Outliers : 0.61 % Allowed : 28.28 % Favored : 71.11 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.20), residues: 1980 helix: 1.51 (0.15), residues: 1304 sheet: 0.16 (0.52), residues: 120 loop : -2.46 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 375 HIS 0.005 0.001 HIS A 211 PHE 0.016 0.001 PHE A 24 TYR 0.010 0.001 TYR B 133 ARG 0.002 0.000 ARG B 85 Details of bonding type rmsd hydrogen bonds : bond 0.14755 ( 994) hydrogen bonds : angle 4.92878 ( 2922) covalent geometry : bond 0.00387 (14700) covalent geometry : angle 0.77352 (20112) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 266 time to evaluate : 1.557 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: 0.3448 time to fit residues: 131.6625 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 : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue -4 TYR Chi-restraints excluded: chain A residue 135 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.178354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.107964 restraints weight = 24393.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.107596 restraints weight = 14607.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.106807 restraints weight = 10634.066| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1825 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= 0.178 Angle : 0.732 10.486 20112 Z= 0.351 Chirality : 0.043 0.232 2520 Planarity : 0.006 0.070 2588 Dihedral : 4.411 49.350 2151 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.78 % Favored : 92.12 % Rotamer: Outliers : 4.58 % Allowed : 26.71 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.20), residues: 1980 helix: 1.52 (0.15), residues: 1320 sheet: -0.03 (0.49), residues: 126 loop : -2.57 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 370 HIS 0.006 0.001 HIS B 378 PHE 0.025 0.001 PHE C 409 TYR 0.016 0.002 TYR D 102 ARG 0.007 0.000 ARG B 405 Details of bonding type rmsd hydrogen bonds : bond 0.05496 ( 994) hydrogen bonds : angle 4.32501 ( 2922) covalent geometry : bond 0.00412 (14700) covalent geometry : angle 0.73183 (20112) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 181 time to evaluate : 1.458 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: 0.5506 (OUTLIER) cc_final: 0.4884 (t80) REVERT: B 100 ARG cc_start: 0.7835 (mtt90) cc_final: 0.7556 (mpt180) REVERT: A 211 HIS cc_start: 0.7004 (OUTLIER) cc_final: 0.6713 (t-170) REVERT: C 369 TRP cc_start: 0.8227 (t-100) cc_final: 0.7968 (t60) REVERT: C 390 ASN cc_start: 0.6746 (OUTLIER) cc_final: 0.6506 (m-40) REVERT: C 451 VAL cc_start: 0.8782 (OUTLIER) cc_final: 0.8477 (m) REVERT: D 220 ARG cc_start: 0.8983 (mmt180) cc_final: 0.8552 (mmt90) REVERT: D 305 MET cc_start: 0.8266 (mmp) cc_final: 0.7946 (mmt) REVERT: D 329 VAL cc_start: 0.1956 (OUTLIER) cc_final: 0.0861 (m) outliers start: 67 outliers final: 30 residues processed: 233 average time/residue: 0.2614 time to fit residues: 90.3036 Evaluate side-chains 192 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 2.066 ------------------------------------------------------------------------------- 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 451 VAL Chi-restraints excluded: chain C residue 488 HIS Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 329 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 197 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 30 optimal weight: 40.0000 chunk 186 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN C 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.176598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.100482 restraints weight = 24334.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.103238 restraints weight = 11865.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.104773 restraints weight = 7896.145| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14700 Z= 0.187 Angle : 0.722 10.875 20112 Z= 0.345 Chirality : 0.043 0.256 2520 Planarity : 0.006 0.078 2588 Dihedral : 4.422 52.514 2151 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.58 % Favored : 92.32 % Rotamer: Outliers : 5.46 % Allowed : 26.91 % Favored : 67.62 % 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: 0.44 (0.20), residues: 1980 helix: 1.45 (0.14), residues: 1310 sheet: -0.28 (0.50), residues: 122 loop : -2.49 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 375 HIS 0.005 0.001 HIS A 211 PHE 0.018 0.001 PHE D 24 TYR 0.017 0.002 TYR C 108 ARG 0.005 0.000 ARG B 86 Details of bonding type rmsd hydrogen bonds : bond 0.05283 ( 994) hydrogen bonds : angle 4.28334 ( 2922) covalent geometry : bond 0.00441 (14700) covalent geometry : angle 0.72234 (20112) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3960 Ramachandran restraints generated. 1980 Oldfield, 0 Emsley, 1980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 167 time to evaluate : 1.543 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: 0.5642 (OUTLIER) cc_final: 0.4992 (t80) REVERT: B 376 MET cc_start: 0.8016 (tmm) cc_final: 0.7733 (tmm) REVERT: B 378 HIS cc_start: 0.8103 (m90) cc_final: 0.7880 (m90) REVERT: A 211 HIS cc_start: 0.7238 (OUTLIER) cc_final: 0.6792 (t-170) REVERT: C 336 LYS cc_start: 0.6957 (mttp) cc_final: 0.6740 (mptt) REVERT: C 390 ASN cc_start: 0.6795 (OUTLIER) cc_final: 0.6486 (m-40) REVERT: C 409 PHE cc_start: 0.7783 (t80) cc_final: 0.7435 (t80) REVERT: D 215 LEU cc_start: 0.8864 (tp) cc_final: 0.8304 (mt) REVERT: D 220 ARG cc_start: 0.8936 (mmt180) cc_final: 0.8434 (mmt90) REVERT: D 355 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6960 (ppp) REVERT: D 359 ASP cc_start: 0.8793 (t70) cc_final: 0.8295 (m-30) REVERT: D 375 PHE cc_start: 0.7444 (m-80) cc_final: 0.7107 (m-80) REVERT: D 380 HIS cc_start: 0.7181 (t70) cc_final: 0.6709 (t70) outliers start: 80 outliers final: 44 residues processed: 233 average time/residue: 0.2598 time to fit residues: 92.0276 Evaluate side-chains 198 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 150 time to evaluate : 2.842 ------------------------------------------------------------------------------- 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 123 THR 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 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 369 TRP Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 HIS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 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 170 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 PHE Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 375 PHE 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 242 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 390 ASN Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 228 PHE Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 355 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.7196 > 50: distance: 5 - 17: 3.016 distance: 47 - 65: 6.253 distance: 59 - 65: 5.974 distance: 65 - 66: 19.269 distance: 66 - 67: 30.361 distance: 66 - 69: 33.505 distance: 67 - 68: 44.932 distance: 67 - 72: 23.309 distance: 69 - 70: 22.900 distance: 69 - 71: 22.504 distance: 72 - 73: 9.785 distance: 73 - 74: 26.168 distance: 73 - 76: 32.331 distance: 74 - 75: 8.380 distance: 74 - 80: 38.762 distance: 76 - 77: 36.819 distance: 77 - 78: 28.978 distance: 77 - 79: 42.792 distance: 80 - 81: 10.874 distance: 81 - 84: 45.264 distance: 82 - 87: 51.528 distance: 84 - 85: 34.455 distance: 84 - 86: 20.141 distance: 87 - 88: 11.591 distance: 88 - 89: 40.927 distance: 88 - 91: 40.028 distance: 89 - 90: 51.406 distance: 89 - 98: 22.574 distance: 91 - 92: 23.693 distance: 92 - 93: 43.512 distance: 93 - 94: 14.636 distance: 94 - 95: 21.142 distance: 95 - 96: 37.668 distance: 95 - 97: 31.150 distance: 98 - 99: 26.523 distance: 99 - 100: 8.801 distance: 99 - 102: 20.188 distance: 100 - 101: 56.448 distance: 100 - 103: 31.404 distance: 103 - 104: 20.519 distance: 104 - 105: 16.792 distance: 104 - 107: 31.276 distance: 105 - 106: 24.750 distance: 105 - 111: 21.886 distance: 106 - 134: 26.281 distance: 107 - 108: 22.040 distance: 108 - 109: 17.501 distance: 108 - 110: 19.961 distance: 111 - 112: 20.355 distance: 112 - 113: 31.501 distance: 112 - 115: 37.432 distance: 113 - 114: 13.659 distance: 113 - 119: 23.891 distance: 114 - 141: 11.748 distance: 115 - 116: 34.213 distance: 116 - 117: 6.470 distance: 116 - 118: 46.394 distance: 119 - 120: 4.628 distance: 119 - 125: 40.419 distance: 120 - 121: 15.411 distance: 121 - 122: 39.232 distance: 121 - 126: 49.632 distance: 122 - 148: 22.570 distance: 124 - 125: 39.749 distance: 126 - 127: 7.700 distance: 127 - 128: 37.980 distance: 127 - 130: 47.489 distance: 128 - 129: 40.556 distance: 128 - 134: 37.335 distance: 129 - 153: 27.549 distance: 130 - 131: 11.010 distance: 130 - 132: 9.807 distance: 131 - 133: 23.285 distance: 134 - 135: 26.401 distance: 135 - 136: 33.729 distance: 135 - 138: 25.408 distance: 136 - 137: 29.476 distance: 136 - 141: 20.433 distance: 137 - 158: 30.780 distance: 138 - 139: 41.327 distance: 138 - 140: 32.496