Starting phenix.real_space_refine on Tue Sep 24 22:37:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4x_17429/09_2024/8p4x_17429.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4x_17429/09_2024/8p4x_17429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4x_17429/09_2024/8p4x_17429.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4x_17429/09_2024/8p4x_17429.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4x_17429/09_2024/8p4x_17429.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4x_17429/09_2024/8p4x_17429.cif" } resolution = 2.57 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= -0.001 sd= 0.189 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 78 5.16 5 C 5564 2.51 5 N 1456 2.21 5 O 1652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8756 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4282 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 39, 'TRANS': 486} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' MG': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Restraints were copied for chains: B Time building chain proxies: 8.50, per 1000 atoms: 0.97 Number of scatterers: 8756 At special positions: 0 Unit cell: (95.682, 104.302, 95.682, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 4 15.00 Mg 2 11.99 O 1652 8.00 N 1456 7.00 C 5564 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: 2.41 Conformation dependent library (CDL) restraints added in 1.0 seconds 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 2 sheets defined 56.7% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 77 through 99 removed outlier: 3.626A pdb=" N LYS A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N HIS A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 121 removed outlier: 4.228A pdb=" N LYS A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 135 through 148 removed outlier: 3.663A pdb=" N ASP A 139 " --> pdb=" O TRP A 135 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 141 " --> pdb=" O PRO A 137 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 171 Processing helix chain 'A' and resid 178 through 190 removed outlier: 3.871A pdb=" N LEU A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.762A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 225 removed outlier: 3.528A pdb=" N GLY A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.710A pdb=" N GLU A 234 " --> pdb=" O CYS A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 265 Processing helix chain 'A' and resid 283 through 290 Processing helix chain 'A' and resid 293 through 309 removed outlier: 3.559A pdb=" N HIS A 302 " --> pdb=" O TYR A 298 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.646A pdb=" N LEU A 317 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 318 " --> pdb=" O GLY A 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 314 through 318' Processing helix chain 'A' and resid 319 through 331 removed outlier: 3.880A pdb=" N TRP A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG A 324 " --> pdb=" O GLN A 320 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET A 330 " --> pdb=" O TYR A 326 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 368 through 381 removed outlier: 3.555A pdb=" N CYS A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 397 Processing helix chain 'A' and resid 404 through 416 removed outlier: 3.845A pdb=" N GLY A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A 411 " --> pdb=" O ASP A 407 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 432 removed outlier: 4.093A pdb=" N ALA A 425 " --> pdb=" O TRP A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 442 removed outlier: 3.909A pdb=" N CYS A 442 " --> pdb=" O CYS A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 456 Processing helix chain 'A' and resid 459 through 466 removed outlier: 3.614A pdb=" N TYR A 465 " --> pdb=" O PHE A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 470 Processing helix chain 'A' and resid 479 through 483 removed outlier: 3.625A pdb=" N ALA A 483 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 492 Processing helix chain 'A' and resid 505 through 524 removed outlier: 3.588A pdb=" N SER A 511 " --> pdb=" O LYS A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 544 removed outlier: 3.536A pdb=" N VAL A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 Processing helix chain 'B' and resid 77 through 99 removed outlier: 3.627A pdb=" N LYS B 97 " --> pdb=" O ASP B 93 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N HIS B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 121 removed outlier: 4.228A pdb=" N LYS B 114 " --> pdb=" O ASP B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 135 through 148 removed outlier: 3.663A pdb=" N ASP B 139 " --> pdb=" O TRP B 135 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA B 141 " --> pdb=" O PRO B 137 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 171 Processing helix chain 'B' and resid 178 through 190 removed outlier: 3.871A pdb=" N LEU B 188 " --> pdb=" O GLN B 184 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 removed outlier: 3.763A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 225 removed outlier: 3.528A pdb=" N GLY B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 removed outlier: 3.709A pdb=" N GLU B 234 " --> pdb=" O CYS B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 265 Processing helix chain 'B' and resid 283 through 290 Processing helix chain 'B' and resid 293 through 309 removed outlier: 3.559A pdb=" N HIS B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 308 " --> pdb=" O ASN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 318 removed outlier: 3.646A pdb=" N LEU B 317 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 318 " --> pdb=" O GLY B 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 314 through 318' Processing helix chain 'B' and resid 319 through 331 removed outlier: 3.881A pdb=" N TRP B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG B 324 " --> pdb=" O GLN B 320 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET B 330 " --> pdb=" O TYR B 326 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER B 331 " --> pdb=" O PHE B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 368 through 381 removed outlier: 3.556A pdb=" N CYS B 374 " --> pdb=" O TRP B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 397 Processing helix chain 'B' and resid 404 through 416 removed outlier: 3.844A pdb=" N GLY B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 410 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 432 removed outlier: 4.093A pdb=" N ALA B 425 " --> pdb=" O TRP B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 442 removed outlier: 3.909A pdb=" N CYS B 442 " --> pdb=" O CYS B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 456 Processing helix chain 'B' and resid 459 through 466 removed outlier: 3.615A pdb=" N TYR B 465 " --> pdb=" O PHE B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 470 Processing helix chain 'B' and resid 479 through 483 removed outlier: 3.625A pdb=" N ALA B 483 " --> pdb=" O PRO B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 492 Processing helix chain 'B' and resid 505 through 524 removed outlier: 3.587A pdb=" N SER B 511 " --> pdb=" O LYS B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 544 removed outlier: 3.537A pdb=" N VAL B 540 " --> pdb=" O ASP B 536 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 106 removed outlier: 6.299A pdb=" N VAL A 33 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N THR A 126 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A 35 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N GLU A 128 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N TRP A 37 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 103 through 106 removed outlier: 6.300A pdb=" N VAL B 33 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N THR B 126 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B 35 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N GLU B 128 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N TRP B 37 " --> pdb=" O GLU B 128 " (cutoff:3.500A) 340 hydrogen bonds defined for protein. 996 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: 2.47 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2744 1.34 - 1.46: 2088 1.46 - 1.58: 4014 1.58 - 1.69: 4 1.69 - 1.81: 114 Bond restraints: 8964 Sorted by residual: bond pdb=" O3P FAD A 601 " pdb=" P FAD A 601 " ideal model delta sigma weight residual 1.660 1.585 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" O3P FAD B 601 " pdb=" P FAD B 601 " ideal model delta sigma weight residual 1.660 1.585 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" O5' FAD B 601 " pdb=" P FAD B 601 " ideal model delta sigma weight residual 1.637 1.574 0.063 2.00e-02 2.50e+03 9.95e+00 bond pdb=" O5' FAD A 601 " pdb=" P FAD A 601 " ideal model delta sigma weight residual 1.637 1.574 0.063 2.00e-02 2.50e+03 9.95e+00 bond pdb=" O5B FAD A 601 " pdb=" PA FAD A 601 " ideal model delta sigma weight residual 1.634 1.572 0.062 2.00e-02 2.50e+03 9.49e+00 ... (remaining 8959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 11902 1.48 - 2.96: 221 2.96 - 4.44: 60 4.44 - 5.93: 5 5.93 - 7.41: 6 Bond angle restraints: 12194 Sorted by residual: angle pdb=" O1P FAD B 601 " pdb=" P FAD B 601 " pdb=" O2P FAD B 601 " ideal model delta sigma weight residual 122.50 115.09 7.41 3.00e+00 1.11e-01 6.10e+00 angle pdb=" O1P FAD A 601 " pdb=" P FAD A 601 " pdb=" O2P FAD A 601 " ideal model delta sigma weight residual 122.50 115.10 7.40 3.00e+00 1.11e-01 6.08e+00 angle pdb=" O1A FAD B 601 " pdb=" PA FAD B 601 " pdb=" O5B FAD B 601 " ideal model delta sigma weight residual 104.10 111.17 -7.07 3.00e+00 1.11e-01 5.55e+00 angle pdb=" O1A FAD A 601 " pdb=" PA FAD A 601 " pdb=" O5B FAD A 601 " ideal model delta sigma weight residual 104.10 111.16 -7.06 3.00e+00 1.11e-01 5.54e+00 angle pdb=" O1A FAD B 601 " pdb=" PA FAD B 601 " pdb=" O2A FAD B 601 " ideal model delta sigma weight residual 121.20 114.74 6.46 3.00e+00 1.11e-01 4.64e+00 ... (remaining 12189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.12: 5002 18.12 - 36.25: 212 36.25 - 54.37: 62 54.37 - 72.50: 30 72.50 - 90.62: 12 Dihedral angle restraints: 5318 sinusoidal: 2270 harmonic: 3048 Sorted by residual: dihedral pdb=" CA ARG B 39 " pdb=" C ARG B 39 " pdb=" N HIS B 40 " pdb=" CA HIS B 40 " ideal model delta harmonic sigma weight residual 180.00 163.19 16.81 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ARG A 39 " pdb=" C ARG A 39 " pdb=" N HIS A 40 " pdb=" CA HIS A 40 " ideal model delta harmonic sigma weight residual 180.00 163.28 16.72 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" O5' FAD A 601 " pdb=" O3P FAD A 601 " pdb=" P FAD A 601 " pdb=" PA FAD A 601 " ideal model delta sinusoidal sigma weight residual -61.77 -152.39 90.62 1 3.00e+01 1.11e-03 1.08e+01 ... (remaining 5315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 662 0.025 - 0.049: 346 0.049 - 0.074: 114 0.074 - 0.098: 42 0.098 - 0.123: 56 Chirality restraints: 1220 Sorted by residual: chirality pdb=" CA VAL A 76 " pdb=" N VAL A 76 " pdb=" C VAL A 76 " pdb=" CB VAL A 76 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA VAL B 33 " pdb=" N VAL B 33 " pdb=" C VAL B 33 " pdb=" CB VAL B 33 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" C2B FAD A 601 " pdb=" C1B FAD A 601 " pdb=" C3B FAD A 601 " pdb=" O2B FAD A 601 " both_signs ideal model delta sigma weight residual False -2.53 -2.66 0.12 2.00e-01 2.50e+01 3.65e-01 ... (remaining 1217 not shown) Planarity restraints: 1552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 526 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO B 527 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 526 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO A 527 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 533 " 0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO A 534 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 534 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 534 " 0.017 5.00e-02 4.00e+02 ... (remaining 1549 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 120 2.67 - 3.23: 7683 3.23 - 3.78: 12540 3.78 - 4.34: 18624 4.34 - 4.90: 30825 Nonbonded interactions: 69792 Sorted by model distance: nonbonded pdb=" O HOH B 717 " pdb=" O HOH B 740 " model vdw 2.112 3.040 nonbonded pdb=" O HOH A 717 " pdb=" O HOH A 740 " model vdw 2.114 3.040 nonbonded pdb=" OD2 ASP B 420 " pdb=" O HOH B 701 " model vdw 2.116 3.040 nonbonded pdb=" OD2 ASP A 420 " pdb=" O HOH A 701 " model vdw 2.116 3.040 nonbonded pdb=" NH1 ARG A 324 " pdb=" O HOH A 701 " model vdw 2.125 3.120 ... (remaining 69787 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 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.300 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:12.800 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 42.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 0.075 8964 Z= 0.273 Angle : 0.561 7.407 12194 Z= 0.284 Chirality : 0.040 0.123 1220 Planarity : 0.004 0.040 1552 Dihedral : 13.116 90.621 3362 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % 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: -0.11 (0.26), residues: 1048 helix: 0.99 (0.24), residues: 528 sheet: 0.00 (0.58), residues: 70 loop : -1.38 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 430 HIS 0.003 0.001 HIS A 45 PHE 0.012 0.001 PHE B 543 TYR 0.012 0.001 TYR B 326 ARG 0.003 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.056 Fit side-chains REVERT: A 115 GLN cc_start: 0.7079 (tt0) cc_final: 0.6857 (tt0) REVERT: A 200 ASP cc_start: 0.7123 (t70) cc_final: 0.6896 (t0) REVERT: B 115 GLN cc_start: 0.7076 (tt0) cc_final: 0.6854 (tt0) REVERT: B 200 ASP cc_start: 0.7121 (t70) cc_final: 0.6893 (t0) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 1.3783 time to fit residues: 212.2074 Evaluate side-chains 127 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN B 205 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8964 Z= 0.222 Angle : 0.615 7.584 12194 Z= 0.311 Chirality : 0.045 0.165 1220 Planarity : 0.006 0.046 1552 Dihedral : 10.268 90.212 1232 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.86 % Allowed : 8.42 % Favored : 90.71 % 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: 0.19 (0.26), residues: 1048 helix: 1.22 (0.24), residues: 528 sheet: 0.21 (0.58), residues: 70 loop : -1.21 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 430 HIS 0.004 0.001 HIS A 45 PHE 0.014 0.002 PHE B 543 TYR 0.009 0.002 TYR A 326 ARG 0.003 0.001 ARG A 515 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 1.113 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 140 average time/residue: 1.4415 time to fit residues: 213.3027 Evaluate side-chains 126 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain B residue 110 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8964 Z= 0.299 Angle : 0.678 8.607 12194 Z= 0.346 Chirality : 0.048 0.142 1220 Planarity : 0.006 0.045 1552 Dihedral : 10.942 109.508 1232 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.94 % Allowed : 8.53 % Favored : 89.52 % 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: -0.04 (0.25), residues: 1048 helix: 0.87 (0.22), residues: 542 sheet: 0.87 (0.59), residues: 66 loop : -1.31 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 430 HIS 0.005 0.001 HIS B 385 PHE 0.017 0.002 PHE A 543 TYR 0.011 0.002 TYR B 465 ARG 0.003 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 129 time to evaluate : 1.048 Fit side-chains REVERT: A 114 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7514 (ttpt) REVERT: A 118 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7285 (mt-10) REVERT: A 188 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8025 (mp) REVERT: A 341 GLU cc_start: 0.6226 (OUTLIER) cc_final: 0.5275 (mp0) REVERT: B 114 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7521 (ttpt) REVERT: B 118 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: B 188 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8027 (mp) REVERT: B 341 GLU cc_start: 0.6228 (OUTLIER) cc_final: 0.5276 (mp0) outliers start: 18 outliers final: 6 residues processed: 135 average time/residue: 1.5411 time to fit residues: 219.1559 Evaluate side-chains 136 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 490 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 0.0570 chunk 45 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8964 Z= 0.168 Angle : 0.547 6.703 12194 Z= 0.274 Chirality : 0.042 0.120 1220 Planarity : 0.005 0.041 1552 Dihedral : 9.616 106.031 1232 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.38 % Allowed : 9.29 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.26), residues: 1048 helix: 1.22 (0.23), residues: 542 sheet: 1.11 (0.60), residues: 66 loop : -1.21 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 430 HIS 0.004 0.001 HIS A 45 PHE 0.013 0.001 PHE B 543 TYR 0.008 0.001 TYR A 326 ARG 0.002 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 119 time to evaluate : 1.045 Fit side-chains REVERT: A 341 GLU cc_start: 0.6197 (OUTLIER) cc_final: 0.5252 (mp0) REVERT: B 341 GLU cc_start: 0.6197 (OUTLIER) cc_final: 0.5256 (mp0) outliers start: 22 outliers final: 11 residues processed: 129 average time/residue: 1.6209 time to fit residues: 220.0704 Evaluate side-chains 139 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain B residue 535 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 0.4980 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8964 Z= 0.229 Angle : 0.612 7.843 12194 Z= 0.308 Chirality : 0.045 0.140 1220 Planarity : 0.005 0.043 1552 Dihedral : 10.097 111.655 1232 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.48 % Allowed : 10.48 % Favored : 87.04 % 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: 0.24 (0.25), residues: 1048 helix: 1.15 (0.23), residues: 540 sheet: 1.13 (0.61), residues: 66 loop : -1.26 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 430 HIS 0.004 0.001 HIS A 45 PHE 0.014 0.002 PHE A 543 TYR 0.010 0.001 TYR B 326 ARG 0.002 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 0.930 Fit side-chains REVERT: A 118 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7231 (mt-10) REVERT: A 188 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7936 (mp) REVERT: A 341 GLU cc_start: 0.6243 (OUTLIER) cc_final: 0.5266 (mp0) REVERT: B 118 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7238 (mt-10) REVERT: B 188 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7935 (mp) REVERT: B 341 GLU cc_start: 0.6246 (OUTLIER) cc_final: 0.5267 (mp0) outliers start: 23 outliers final: 11 residues processed: 134 average time/residue: 1.5671 time to fit residues: 221.2268 Evaluate side-chains 140 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain B residue 535 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.0270 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 538 ASN B 136 GLN B 538 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8964 Z= 0.214 Angle : 0.600 7.672 12194 Z= 0.301 Chirality : 0.044 0.131 1220 Planarity : 0.005 0.041 1552 Dihedral : 10.076 112.438 1232 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.27 % Allowed : 11.12 % Favored : 86.61 % 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: 0.28 (0.26), residues: 1048 helix: 1.19 (0.23), residues: 540 sheet: 1.17 (0.60), residues: 66 loop : -1.25 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 430 HIS 0.004 0.001 HIS A 45 PHE 0.014 0.002 PHE A 543 TYR 0.009 0.001 TYR A 326 ARG 0.002 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 1.097 Fit side-chains REVERT: A 110 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7476 (p0) REVERT: A 118 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7204 (mt-10) REVERT: A 188 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7937 (mp) REVERT: A 341 GLU cc_start: 0.6248 (OUTLIER) cc_final: 0.5262 (mp0) REVERT: A 526 ASP cc_start: 0.8009 (t0) cc_final: 0.7785 (t0) REVERT: B 110 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7452 (p0) REVERT: B 118 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7209 (mt-10) REVERT: B 188 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7931 (mp) REVERT: B 341 GLU cc_start: 0.6251 (OUTLIER) cc_final: 0.5263 (mp0) outliers start: 21 outliers final: 11 residues processed: 127 average time/residue: 1.6476 time to fit residues: 220.2592 Evaluate side-chains 142 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain B residue 535 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A 538 ASN B 36 HIS B 538 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8964 Z= 0.360 Angle : 0.741 9.612 12194 Z= 0.379 Chirality : 0.050 0.158 1220 Planarity : 0.006 0.045 1552 Dihedral : 11.267 116.168 1232 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.81 % Allowed : 11.23 % Favored : 85.96 % 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: -0.12 (0.25), residues: 1048 helix: 0.80 (0.22), residues: 540 sheet: 1.09 (0.60), residues: 66 loop : -1.37 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 430 HIS 0.007 0.002 HIS A 385 PHE 0.018 0.003 PHE A 543 TYR 0.014 0.002 TYR A 465 ARG 0.005 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 1.071 Fit side-chains REVERT: A 110 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7380 (p0) REVERT: A 118 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7251 (mt-10) REVERT: A 188 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7972 (mp) REVERT: A 341 GLU cc_start: 0.6313 (OUTLIER) cc_final: 0.5579 (mp0) REVERT: A 526 ASP cc_start: 0.8056 (t0) cc_final: 0.7834 (t0) REVERT: B 110 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7381 (p0) REVERT: B 118 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7272 (mt-10) REVERT: B 188 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7970 (mp) REVERT: B 341 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.5578 (mp0) REVERT: B 526 ASP cc_start: 0.8060 (t0) cc_final: 0.7837 (t0) outliers start: 26 outliers final: 12 residues processed: 139 average time/residue: 1.5213 time to fit residues: 222.8098 Evaluate side-chains 144 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 118 GLU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain B residue 497 GLU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 535 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 78 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8964 Z= 0.246 Angle : 0.639 8.024 12194 Z= 0.325 Chirality : 0.045 0.164 1220 Planarity : 0.006 0.042 1552 Dihedral : 10.565 113.664 1232 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.38 % Allowed : 11.88 % Favored : 85.75 % 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: 0.00 (0.25), residues: 1048 helix: 0.93 (0.22), residues: 540 sheet: 1.17 (0.60), residues: 66 loop : -1.37 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 430 HIS 0.004 0.001 HIS B 385 PHE 0.015 0.002 PHE B 543 TYR 0.010 0.002 TYR B 465 ARG 0.002 0.000 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 119 time to evaluate : 1.365 Fit side-chains REVERT: A 110 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7335 (p0) REVERT: A 188 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7945 (mp) REVERT: A 222 LYS cc_start: 0.7539 (mptt) cc_final: 0.6904 (mmmt) REVERT: A 341 GLU cc_start: 0.6273 (OUTLIER) cc_final: 0.5253 (mp0) REVERT: A 526 ASP cc_start: 0.8014 (t0) cc_final: 0.7795 (t0) REVERT: B 110 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7333 (p0) REVERT: B 188 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7942 (mp) REVERT: B 222 LYS cc_start: 0.7539 (mptt) cc_final: 0.6905 (mmmt) REVERT: B 341 GLU cc_start: 0.6273 (OUTLIER) cc_final: 0.5249 (mp0) REVERT: B 526 ASP cc_start: 0.8015 (t0) cc_final: 0.7796 (t0) outliers start: 22 outliers final: 13 residues processed: 130 average time/residue: 1.5787 time to fit residues: 215.9648 Evaluate side-chains 140 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 535 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 ASN B 538 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8964 Z= 0.254 Angle : 0.651 8.341 12194 Z= 0.330 Chirality : 0.046 0.170 1220 Planarity : 0.006 0.042 1552 Dihedral : 10.559 114.708 1232 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.05 % Allowed : 12.42 % Favored : 85.53 % 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: 0.00 (0.25), residues: 1048 helix: 0.94 (0.22), residues: 540 sheet: 1.16 (0.61), residues: 66 loop : -1.38 (0.26), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 430 HIS 0.005 0.001 HIS A 385 PHE 0.015 0.002 PHE A 543 TYR 0.011 0.002 TYR B 326 ARG 0.002 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 1.057 Fit side-chains REVERT: A 110 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7334 (p0) REVERT: A 188 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7943 (mp) REVERT: A 222 LYS cc_start: 0.7474 (mptt) cc_final: 0.6878 (ptpp) REVERT: A 341 GLU cc_start: 0.6280 (OUTLIER) cc_final: 0.5568 (mp0) REVERT: B 110 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7340 (p0) REVERT: B 188 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7942 (mp) REVERT: B 222 LYS cc_start: 0.7474 (mptt) cc_final: 0.6876 (ptpp) REVERT: B 341 GLU cc_start: 0.6277 (OUTLIER) cc_final: 0.5566 (mp0) outliers start: 19 outliers final: 11 residues processed: 130 average time/residue: 1.5504 time to fit residues: 212.4080 Evaluate side-chains 135 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 490 LYS Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 535 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.5283 > 50: distance: 51 - 55: 33.919 distance: 55 - 56: 56.370 distance: 56 - 57: 39.924 distance: 57 - 58: 48.229 distance: 57 - 59: 55.275 distance: 59 - 60: 7.669 distance: 60 - 61: 52.388 distance: 60 - 63: 48.333 distance: 61 - 62: 4.554 distance: 61 - 68: 51.582 distance: 63 - 64: 31.792 distance: 64 - 65: 40.517 distance: 65 - 66: 67.314 distance: 66 - 67: 37.309 distance: 68 - 69: 38.249 distance: 68 - 74: 27.953 distance: 69 - 70: 59.615 distance: 69 - 72: 8.742 distance: 70 - 71: 41.420 distance: 70 - 75: 40.391 distance: 72 - 73: 45.094 distance: 73 - 74: 53.081 distance: 75 - 76: 25.115 distance: 76 - 77: 46.220 distance: 76 - 79: 51.877 distance: 77 - 78: 21.116 distance: 77 - 84: 67.079 distance: 79 - 80: 41.556 distance: 80 - 81: 44.771 distance: 81 - 82: 20.272 distance: 81 - 83: 20.924 distance: 84 - 85: 36.040 distance: 85 - 86: 47.774 distance: 85 - 88: 25.561 distance: 86 - 87: 43.845 distance: 86 - 91: 41.167 distance: 88 - 89: 67.290 distance: 88 - 90: 25.271 distance: 91 - 92: 44.781 distance: 92 - 93: 38.569 distance: 92 - 95: 10.883 distance: 93 - 94: 43.537 distance: 93 - 98: 39.587 distance: 95 - 96: 32.246 distance: 96 - 97: 42.674 distance: 98 - 99: 39.217 distance: 99 - 100: 54.062 distance: 99 - 102: 39.759 distance: 100 - 101: 39.399 distance: 100 - 108: 26.325 distance: 102 - 103: 53.245 distance: 103 - 104: 45.832 distance: 103 - 105: 51.969 distance: 104 - 106: 53.855 distance: 105 - 107: 41.298 distance: 106 - 107: 38.992 distance: 108 - 109: 54.104 distance: 108 - 114: 9.714 distance: 109 - 110: 43.140 distance: 109 - 112: 22.037 distance: 110 - 111: 40.358 distance: 110 - 115: 60.754 distance: 112 - 113: 41.957 distance: 113 - 114: 50.412 distance: 115 - 116: 33.820 distance: 116 - 117: 25.726 distance: 116 - 119: 32.571 distance: 117 - 118: 14.498 distance: 117 - 123: 41.273 distance: 119 - 120: 26.210 distance: 120 - 121: 43.066 distance: 120 - 122: 57.323 distance: 123 - 124: 35.807 distance: 123 - 129: 37.320 distance: 124 - 125: 48.817 distance: 124 - 127: 36.744 distance: 125 - 126: 21.583 distance: 125 - 130: 34.290 distance: 128 - 129: 39.028