Starting phenix.real_space_refine on Tue Jun 17 16:07:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u8a_20686/06_2025/6u8a_20686.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u8a_20686/06_2025/6u8a_20686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6u8a_20686/06_2025/6u8a_20686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u8a_20686/06_2025/6u8a_20686.map" model { file = "/net/cci-nas-00/data/ceres_data/6u8a_20686/06_2025/6u8a_20686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u8a_20686/06_2025/6u8a_20686.cif" } resolution = 3.4 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= -0.000 sd= 0.005 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 116 5.16 5 C 13172 2.51 5 N 3324 2.21 5 O 3420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20032 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4985 Classifications: {'peptide': 617} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 594} Chain breaks: 4 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'P0T': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 11.42, per 1000 atoms: 0.57 Number of scatterers: 20032 At special positions: 0 Unit cell: (126.14, 126.14, 111.3, 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 116 16.00 O 3420 8.00 N 3324 7.00 C 13172 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: 4.28 Conformation dependent library (CDL) restraints added in 2.2 seconds 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4672 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 61.6% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 95 through 102 removed outlier: 3.576A pdb=" N ARG A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 112 removed outlier: 3.618A pdb=" N THR A 112 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 135 through 145 Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 176 through 185 Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.566A pdb=" N ILE A 290 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.624A pdb=" N PHE A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 324 removed outlier: 4.363A pdb=" N TYR A 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 377 through 413 removed outlier: 5.328A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 471 through 492 removed outlier: 3.968A pdb=" N LEU A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 4.266A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 removed outlier: 3.836A pdb=" N THR A 516 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY A 518 " --> pdb=" O TYR A 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 518' Processing helix chain 'A' and resid 519 through 529 Processing helix chain 'A' and resid 533 through 559 removed outlier: 3.706A pdb=" N PHE A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 Processing helix chain 'A' and resid 618 through 649 Processing helix chain 'A' and resid 655 through 672 Processing helix chain 'A' and resid 711 through 718 Processing helix chain 'B' and resid 76 through 87 Processing helix chain 'B' and resid 95 through 102 removed outlier: 3.576A pdb=" N ARG B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 112 removed outlier: 3.618A pdb=" N THR B 112 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 135 through 145 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 176 through 185 Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 282 Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.566A pdb=" N ILE B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.624A pdb=" N PHE B 311 " --> pdb=" O LYS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 324 removed outlier: 4.363A pdb=" N TYR B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 377 through 413 removed outlier: 5.328A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 471 through 492 removed outlier: 3.968A pdb=" N LEU B 475 " --> pdb=" O TYR B 471 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 4.266A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 removed outlier: 3.836A pdb=" N THR B 516 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY B 518 " --> pdb=" O TYR B 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 513 through 518' Processing helix chain 'B' and resid 519 through 529 Processing helix chain 'B' and resid 533 through 559 removed outlier: 3.706A pdb=" N PHE B 540 " --> pdb=" O ASP B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 618 through 649 Processing helix chain 'B' and resid 655 through 672 Processing helix chain 'B' and resid 711 through 718 Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'C' and resid 95 through 102 removed outlier: 3.577A pdb=" N ARG C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN C 102 " --> pdb=" O TYR C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 112 removed outlier: 3.619A pdb=" N THR C 112 " --> pdb=" O SER C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 135 through 145 Processing helix chain 'C' and resid 166 through 174 removed outlier: 4.037A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 185 Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 282 Processing helix chain 'C' and resid 286 through 290 removed outlier: 3.566A pdb=" N ILE C 290 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.624A pdb=" N PHE C 311 " --> pdb=" O LYS C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 324 removed outlier: 4.363A pdb=" N TYR C 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 377 through 413 removed outlier: 5.329A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 471 through 492 removed outlier: 3.968A pdb=" N LEU C 475 " --> pdb=" O TYR C 471 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 512 removed outlier: 4.266A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 518 removed outlier: 3.837A pdb=" N THR C 516 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY C 518 " --> pdb=" O TYR C 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 513 through 518' Processing helix chain 'C' and resid 519 through 529 Processing helix chain 'C' and resid 533 through 559 removed outlier: 3.705A pdb=" N PHE C 540 " --> pdb=" O ASP C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 Processing helix chain 'C' and resid 618 through 649 Processing helix chain 'C' and resid 655 through 672 Processing helix chain 'C' and resid 711 through 718 Processing helix chain 'D' and resid 76 through 87 Processing helix chain 'D' and resid 95 through 102 removed outlier: 3.577A pdb=" N ARG D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN D 102 " --> pdb=" O TYR D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 112 removed outlier: 3.618A pdb=" N THR D 112 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 135 through 145 Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 176 through 185 Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 212 through 219 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 282 Processing helix chain 'D' and resid 286 through 290 removed outlier: 3.566A pdb=" N ILE D 290 " --> pdb=" O LEU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 305 Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.623A pdb=" N PHE D 311 " --> pdb=" O LYS D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 324 removed outlier: 4.363A pdb=" N TYR D 323 " --> pdb=" O SER D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 368 through 372 Processing helix chain 'D' and resid 377 through 413 removed outlier: 5.328A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 471 through 492 removed outlier: 3.968A pdb=" N LEU D 475 " --> pdb=" O TYR D 471 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 477 " --> pdb=" O GLU D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 512 removed outlier: 4.266A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 removed outlier: 3.836A pdb=" N THR D 516 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY D 518 " --> pdb=" O TYR D 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 513 through 518' Processing helix chain 'D' and resid 519 through 529 Processing helix chain 'D' and resid 533 through 559 removed outlier: 3.706A pdb=" N PHE D 540 " --> pdb=" O ASP D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 602 Processing helix chain 'D' and resid 618 through 649 Processing helix chain 'D' and resid 655 through 672 Processing helix chain 'D' and resid 711 through 718 Processing sheet with id=AA1, first strand: chain 'A' and resid 330 through 335 removed outlier: 6.660A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 330 through 335 removed outlier: 6.660A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 330 through 335 removed outlier: 6.661A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 330 through 335 removed outlier: 6.659A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) 1072 hydrogen bonds defined for protein. 3108 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: 5.69 Time building geometry restraints manager: 5.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6137 1.34 - 1.46: 5115 1.46 - 1.58: 9112 1.58 - 1.71: 0 1.71 - 1.83: 180 Bond restraints: 20544 Sorted by residual: bond pdb=" C12 P0T C1001 " pdb=" O02 P0T C1001 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" C12 P0T A1002 " pdb=" O02 P0T A1002 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" C12 P0T D1001 " pdb=" O02 P0T D1001 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.64e+00 bond pdb=" C12 P0T A1001 " pdb=" O02 P0T A1001 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.63e+00 bond pdb=" C11 P0T A1001 " pdb=" O01 P0T A1001 " ideal model delta sigma weight residual 1.352 1.403 -0.051 2.00e-02 2.50e+03 6.41e+00 ... (remaining 20539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 26945 2.34 - 4.67: 796 4.67 - 7.01: 83 7.01 - 9.34: 36 9.34 - 11.68: 16 Bond angle restraints: 27876 Sorted by residual: angle pdb=" N ILE D 529 " pdb=" CA ILE D 529 " pdb=" C ILE D 529 " ideal model delta sigma weight residual 111.91 108.09 3.82 8.90e-01 1.26e+00 1.84e+01 angle pdb=" N ILE B 529 " pdb=" CA ILE B 529 " pdb=" C ILE B 529 " ideal model delta sigma weight residual 111.91 108.11 3.80 8.90e-01 1.26e+00 1.83e+01 angle pdb=" N ILE C 529 " pdb=" CA ILE C 529 " pdb=" C ILE C 529 " ideal model delta sigma weight residual 111.91 108.11 3.80 8.90e-01 1.26e+00 1.82e+01 angle pdb=" N ILE A 529 " pdb=" CA ILE A 529 " pdb=" C ILE A 529 " ideal model delta sigma weight residual 111.91 108.11 3.80 8.90e-01 1.26e+00 1.82e+01 angle pdb=" C03 P0T A1001 " pdb=" C04 P0T A1001 " pdb=" C08 P0T A1001 " ideal model delta sigma weight residual 111.12 122.80 -11.68 3.00e+00 1.11e-01 1.52e+01 ... (remaining 27871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.27: 10837 19.27 - 38.53: 1023 38.53 - 57.80: 196 57.80 - 77.07: 32 77.07 - 96.33: 12 Dihedral angle restraints: 12100 sinusoidal: 4880 harmonic: 7220 Sorted by residual: dihedral pdb=" CA ASN C 655 " pdb=" C ASN C 655 " pdb=" N SER C 656 " pdb=" CA SER C 656 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ASN A 655 " pdb=" C ASN A 655 " pdb=" N SER A 656 " pdb=" CA SER A 656 " ideal model delta harmonic sigma weight residual 180.00 -160.81 -19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ASN B 655 " pdb=" C ASN B 655 " pdb=" N SER B 656 " pdb=" CA SER B 656 " ideal model delta harmonic sigma weight residual -180.00 -160.82 -19.18 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 12097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1999 0.045 - 0.090: 861 0.090 - 0.135: 212 0.135 - 0.180: 68 0.180 - 0.225: 8 Chirality restraints: 3148 Sorted by residual: chirality pdb=" C03 P0T A1002 " pdb=" C04 P0T A1002 " pdb=" C05 P0T A1002 " pdb=" C10 P0T A1002 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C03 P0T C1001 " pdb=" C04 P0T C1001 " pdb=" C05 P0T C1001 " pdb=" C10 P0T C1001 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C03 P0T A1001 " pdb=" C04 P0T A1001 " pdb=" C05 P0T A1001 " pdb=" C10 P0T A1001 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3145 not shown) Planarity restraints: 3420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 137 " -0.045 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO B 138 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 138 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 138 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 137 " -0.045 5.00e-02 4.00e+02 6.66e-02 7.11e+00 pdb=" N PRO A 138 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 138 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 138 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 137 " -0.045 5.00e-02 4.00e+02 6.66e-02 7.10e+00 pdb=" N PRO D 138 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 138 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 138 " -0.037 5.00e-02 4.00e+02 ... (remaining 3417 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6104 2.82 - 3.34: 17959 3.34 - 3.86: 33559 3.86 - 4.38: 37894 4.38 - 4.90: 66133 Nonbonded interactions: 161649 Sorted by model distance: nonbonded pdb=" O GLU C 90 " pdb=" OG1 THR C 93 " model vdw 2.296 3.040 nonbonded pdb=" O GLU D 90 " pdb=" OG1 THR D 93 " model vdw 2.296 3.040 nonbonded pdb=" O GLU A 90 " pdb=" OG1 THR A 93 " model vdw 2.297 3.040 nonbonded pdb=" O GLU B 90 " pdb=" OG1 THR B 93 " model vdw 2.297 3.040 nonbonded pdb=" O ILE A 529 " pdb=" ND2 ASN B 639 " model vdw 2.302 3.120 ... (remaining 161644 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 32 through 719) selection = chain 'B' selection = (chain 'C' and resid 32 through 719) selection = (chain 'D' and resid 32 through 719) } 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: 0.010 Normalize map: mean=0, sd=1: 1.940 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: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 41.010 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.040 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 : 0.008 0.065 20544 Z= 0.343 Angle : 0.966 11.681 27876 Z= 0.497 Chirality : 0.054 0.225 3148 Planarity : 0.007 0.067 3420 Dihedral : 15.898 96.335 7428 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.37 % Allowed : 8.94 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.12), residues: 2428 helix: -2.38 (0.09), residues: 1460 sheet: -2.79 (0.43), residues: 92 loop : -2.72 (0.16), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 333 HIS 0.006 0.002 HIS D 251 PHE 0.019 0.003 PHE B 161 TYR 0.013 0.002 TYR D 111 ARG 0.004 0.001 ARG D 392 Details of bonding type rmsd hydrogen bonds : bond 0.14053 ( 1072) hydrogen bonds : angle 6.14329 ( 3108) covalent geometry : bond 0.00806 (20544) covalent geometry : angle 0.96569 (27876) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 405 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LEU cc_start: 0.7255 (mm) cc_final: 0.6674 (pp) REVERT: A 113 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6692 (mt-10) REVERT: A 173 GLU cc_start: 0.8400 (tp30) cc_final: 0.8198 (tp30) REVERT: A 541 LEU cc_start: 0.9104 (tp) cc_final: 0.8896 (tp) REVERT: B 255 MET cc_start: 0.8120 (mmm) cc_final: 0.7902 (mmm) REVERT: B 372 MET cc_start: 0.9125 (mtt) cc_final: 0.8903 (mtt) REVERT: B 383 GLN cc_start: 0.7898 (tp40) cc_final: 0.7604 (tt0) REVERT: B 404 MET cc_start: 0.8670 (mmp) cc_final: 0.8460 (mmt) REVERT: B 541 LEU cc_start: 0.9052 (tp) cc_final: 0.8787 (tp) REVERT: B 640 MET cc_start: 0.8412 (ttp) cc_final: 0.8069 (ttp) REVERT: C 113 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7058 (mt-10) REVERT: C 235 GLN cc_start: 0.7661 (mt0) cc_final: 0.7435 (mt0) REVERT: C 255 MET cc_start: 0.8176 (mmm) cc_final: 0.7930 (mmt) REVERT: C 464 TRP cc_start: 0.6065 (m100) cc_final: 0.5829 (m100) REVERT: D 113 GLU cc_start: 0.7296 (mt-10) cc_final: 0.7088 (mt-10) REVERT: D 255 MET cc_start: 0.8169 (mmm) cc_final: 0.7959 (mmt) REVERT: D 305 GLU cc_start: 0.7603 (tt0) cc_final: 0.7064 (mt-10) REVERT: D 464 TRP cc_start: 0.6079 (m100) cc_final: 0.5860 (m100) REVERT: D 473 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7529 (mp0) REVERT: D 528 MET cc_start: 0.8073 (ttt) cc_final: 0.7569 (ttt) REVERT: D 536 ASP cc_start: 0.7392 (t70) cc_final: 0.7190 (t0) outliers start: 8 outliers final: 0 residues processed: 405 average time/residue: 0.3158 time to fit residues: 200.3024 Evaluate side-chains 270 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 98 optimal weight: 0.5980 chunk 191 optimal weight: 5.9990 chunk 74 optimal weight: 0.3980 chunk 116 optimal weight: 7.9990 chunk 142 optimal weight: 0.9980 chunk 221 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 186 ASN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN A 316 GLN A 414 GLN A 487 GLN B 163 GLN B 186 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 ASN B 316 GLN C 186 ASN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN C 316 GLN D 186 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN D 316 GLN D 487 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.154667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.126555 restraints weight = 27195.094| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.83 r_work: 0.3289 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20544 Z= 0.119 Angle : 0.527 7.673 27876 Z= 0.268 Chirality : 0.037 0.191 3148 Planarity : 0.005 0.063 3420 Dihedral : 6.981 54.962 2772 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.91 % Allowed : 13.55 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.27 (0.16), residues: 2428 helix: -0.03 (0.12), residues: 1476 sheet: -2.14 (0.47), residues: 92 loop : -2.03 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 715 HIS 0.005 0.001 HIS B 251 PHE 0.017 0.001 PHE D 467 TYR 0.016 0.001 TYR D 455 ARG 0.005 0.000 ARG B 706 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 1072) hydrogen bonds : angle 4.10317 ( 3108) covalent geometry : bond 0.00273 (20544) covalent geometry : angle 0.52736 (27876) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 353 time to evaluate : 2.222 Fit side-chains REVERT: A 92 LEU cc_start: 0.7411 (mm) cc_final: 0.6525 (pp) REVERT: A 454 TRP cc_start: 0.8155 (t-100) cc_final: 0.7844 (t60) REVERT: A 519 PHE cc_start: 0.8516 (m-80) cc_final: 0.8269 (m-80) REVERT: A 536 ASP cc_start: 0.7671 (t70) cc_final: 0.7459 (t0) REVERT: B 111 TYR cc_start: 0.6026 (m-80) cc_final: 0.5819 (m-80) REVERT: B 324 GLN cc_start: 0.8351 (tm-30) cc_final: 0.8138 (tm-30) REVERT: B 383 GLN cc_start: 0.8445 (tp40) cc_final: 0.8241 (tp40) REVERT: B 455 TYR cc_start: 0.9144 (t80) cc_final: 0.8908 (t80) REVERT: B 473 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8165 (mp0) REVERT: B 645 MET cc_start: 0.8255 (tmm) cc_final: 0.7892 (tmm) REVERT: C 111 TYR cc_start: 0.6204 (m-80) cc_final: 0.5747 (m-80) REVERT: C 113 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7214 (mt-10) REVERT: C 118 LYS cc_start: 0.8433 (ttpt) cc_final: 0.8083 (tttt) REVERT: C 305 GLU cc_start: 0.8384 (tt0) cc_final: 0.8024 (mt-10) REVERT: C 454 TRP cc_start: 0.8259 (t-100) cc_final: 0.7958 (t60) REVERT: C 455 TYR cc_start: 0.9230 (t80) cc_final: 0.8998 (t80) REVERT: D 111 TYR cc_start: 0.6083 (m-80) cc_final: 0.5729 (m-80) REVERT: D 113 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7212 (mt-10) REVERT: D 118 LYS cc_start: 0.8426 (ttpt) cc_final: 0.8034 (tttt) REVERT: D 178 GLN cc_start: 0.7954 (mt0) cc_final: 0.7552 (mp10) REVERT: D 255 MET cc_start: 0.8764 (mmm) cc_final: 0.8415 (mmt) REVERT: D 305 GLU cc_start: 0.8169 (tt0) cc_final: 0.7646 (mt-10) REVERT: D 446 ILE cc_start: 0.9179 (tp) cc_final: 0.8872 (tp) REVERT: D 454 TRP cc_start: 0.8176 (t-100) cc_final: 0.7917 (t60) REVERT: D 457 TRP cc_start: 0.8256 (t-100) cc_final: 0.7986 (t-100) REVERT: D 464 TRP cc_start: 0.6409 (m100) cc_final: 0.6198 (m100) REVERT: D 519 PHE cc_start: 0.8489 (m-80) cc_final: 0.8255 (m-80) REVERT: D 687 ARG cc_start: 0.7480 (ttm110) cc_final: 0.7265 (mtm110) outliers start: 41 outliers final: 21 residues processed: 382 average time/residue: 0.3017 time to fit residues: 184.0559 Evaluate side-chains 305 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 284 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 316 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 429 PHE Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 316 GLN Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 672 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 46 optimal weight: 8.9990 chunk 2 optimal weight: 0.0370 chunk 48 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 195 optimal weight: 5.9990 overall best weight: 1.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN B 487 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN C 487 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.153854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.124889 restraints weight = 26840.417| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.86 r_work: 0.3268 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20544 Z= 0.116 Angle : 0.523 9.859 27876 Z= 0.256 Chirality : 0.036 0.196 3148 Planarity : 0.004 0.058 3420 Dihedral : 6.596 58.228 2772 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.54 % Allowed : 16.34 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.17), residues: 2428 helix: 0.97 (0.13), residues: 1456 sheet: -1.72 (0.49), residues: 92 loop : -1.64 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 715 HIS 0.005 0.001 HIS B 313 PHE 0.017 0.001 PHE B 467 TYR 0.012 0.001 TYR D 455 ARG 0.003 0.000 ARG C 317 Details of bonding type rmsd hydrogen bonds : bond 0.03237 ( 1072) hydrogen bonds : angle 3.86205 ( 3108) covalent geometry : bond 0.00269 (20544) covalent geometry : angle 0.52270 (27876) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 315 time to evaluate : 2.670 Fit side-chains REVERT: A 92 LEU cc_start: 0.7390 (mm) cc_final: 0.6413 (pp) REVERT: A 178 GLN cc_start: 0.7977 (mt0) cc_final: 0.7593 (mp10) REVERT: A 269 HIS cc_start: 0.7924 (t70) cc_final: 0.7590 (t70) REVERT: A 305 GLU cc_start: 0.8276 (mt-10) cc_final: 0.8076 (tt0) REVERT: A 536 ASP cc_start: 0.7755 (t70) cc_final: 0.7506 (t0) REVERT: B 111 TYR cc_start: 0.5774 (m-80) cc_final: 0.5570 (m-80) REVERT: B 383 GLN cc_start: 0.8452 (tp40) cc_final: 0.8002 (tt0) REVERT: B 455 TYR cc_start: 0.9191 (t80) cc_final: 0.8943 (t80) REVERT: B 645 MET cc_start: 0.8374 (tmm) cc_final: 0.7708 (tmm) REVERT: B 687 ARG cc_start: 0.7905 (ttm110) cc_final: 0.7657 (mtm-85) REVERT: C 111 TYR cc_start: 0.6029 (m-80) cc_final: 0.5584 (m-80) REVERT: C 113 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7026 (mt-10) REVERT: C 178 GLN cc_start: 0.8009 (mt0) cc_final: 0.7561 (mp10) REVERT: C 305 GLU cc_start: 0.8311 (tt0) cc_final: 0.7879 (mt-10) REVERT: C 634 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: D 111 TYR cc_start: 0.6064 (m-80) cc_final: 0.5668 (m-80) REVERT: D 113 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7184 (mt-10) REVERT: D 118 LYS cc_start: 0.8357 (ttpt) cc_final: 0.7994 (tttt) REVERT: D 178 GLN cc_start: 0.7928 (mt0) cc_final: 0.7511 (mp10) REVERT: D 255 MET cc_start: 0.8763 (mmm) cc_final: 0.8391 (mmt) REVERT: D 269 HIS cc_start: 0.7940 (t70) cc_final: 0.7589 (t70) REVERT: D 305 GLU cc_start: 0.8155 (tt0) cc_final: 0.7637 (mt-10) REVERT: D 454 TRP cc_start: 0.8201 (t-100) cc_final: 0.7925 (t60) REVERT: D 464 TRP cc_start: 0.6374 (m100) cc_final: 0.6101 (m100) outliers start: 33 outliers final: 17 residues processed: 337 average time/residue: 0.3434 time to fit residues: 185.2943 Evaluate side-chains 294 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 276 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 644 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 157 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 22 optimal weight: 0.0970 chunk 4 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 202 optimal weight: 0.0670 chunk 56 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.153888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.125096 restraints weight = 26977.881| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.87 r_work: 0.3266 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20544 Z= 0.111 Angle : 0.500 7.163 27876 Z= 0.248 Chirality : 0.036 0.174 3148 Planarity : 0.004 0.055 3420 Dihedral : 6.323 59.832 2772 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.51 % Allowed : 16.90 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.46 (0.17), residues: 2428 helix: 1.42 (0.14), residues: 1472 sheet: -1.56 (0.50), residues: 92 loop : -1.46 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 715 HIS 0.006 0.001 HIS A 313 PHE 0.019 0.001 PHE A 467 TYR 0.013 0.001 TYR C 455 ARG 0.002 0.000 ARG D 706 Details of bonding type rmsd hydrogen bonds : bond 0.03105 ( 1072) hydrogen bonds : angle 3.69738 ( 3108) covalent geometry : bond 0.00256 (20544) covalent geometry : angle 0.49973 (27876) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 314 time to evaluate : 2.592 Fit side-chains REVERT: A 39 PHE cc_start: 0.7115 (OUTLIER) cc_final: 0.5984 (p90) REVERT: A 92 LEU cc_start: 0.7282 (mm) cc_final: 0.6343 (pp) REVERT: A 178 GLN cc_start: 0.8040 (mt0) cc_final: 0.7625 (mp10) REVERT: A 269 HIS cc_start: 0.8047 (t70) cc_final: 0.7686 (t70) REVERT: A 545 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9297 (mt) REVERT: B 39 PHE cc_start: 0.7242 (OUTLIER) cc_final: 0.5932 (p90) REVERT: B 383 GLN cc_start: 0.8380 (tp40) cc_final: 0.7988 (tt0) REVERT: B 634 TYR cc_start: 0.8344 (OUTLIER) cc_final: 0.7486 (m-80) REVERT: B 645 MET cc_start: 0.8437 (tmm) cc_final: 0.7686 (tmm) REVERT: B 687 ARG cc_start: 0.7950 (ttm110) cc_final: 0.7745 (mtm110) REVERT: C 111 TYR cc_start: 0.5825 (m-80) cc_final: 0.5419 (m-80) REVERT: C 235 GLN cc_start: 0.7846 (mt0) cc_final: 0.7603 (mt0) REVERT: C 305 GLU cc_start: 0.8259 (tt0) cc_final: 0.7728 (mt-10) REVERT: C 634 TYR cc_start: 0.8287 (OUTLIER) cc_final: 0.7363 (m-80) REVERT: D 111 TYR cc_start: 0.5921 (m-80) cc_final: 0.5472 (m-80) REVERT: D 178 GLN cc_start: 0.8060 (mt0) cc_final: 0.7635 (mp10) REVERT: D 235 GLN cc_start: 0.7822 (mt0) cc_final: 0.7546 (mt0) REVERT: D 255 MET cc_start: 0.8811 (mmm) cc_final: 0.8415 (mmt) REVERT: D 269 HIS cc_start: 0.7982 (t70) cc_final: 0.7704 (t70) REVERT: D 305 GLU cc_start: 0.8195 (tt0) cc_final: 0.7688 (mt-10) outliers start: 54 outliers final: 27 residues processed: 354 average time/residue: 0.3985 time to fit residues: 225.7537 Evaluate side-chains 309 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 277 time to evaluate : 2.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 670 GLU Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 105 optimal weight: 0.7980 chunk 96 optimal weight: 0.2980 chunk 213 optimal weight: 0.8980 chunk 238 optimal weight: 8.9990 chunk 223 optimal weight: 0.6980 chunk 228 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 224 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 HIS B 163 GLN C 163 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN D 163 GLN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.155409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.127452 restraints weight = 27016.670| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.84 r_work: 0.3286 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20544 Z= 0.096 Angle : 0.479 6.419 27876 Z= 0.238 Chirality : 0.036 0.158 3148 Planarity : 0.003 0.050 3420 Dihedral : 6.112 59.380 2772 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.84 % Allowed : 17.13 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.85 (0.17), residues: 2428 helix: 1.75 (0.14), residues: 1476 sheet: -1.54 (0.51), residues: 92 loop : -1.32 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 715 HIS 0.004 0.000 HIS B 313 PHE 0.020 0.001 PHE B 467 TYR 0.014 0.001 TYR B 455 ARG 0.004 0.000 ARG A 687 Details of bonding type rmsd hydrogen bonds : bond 0.02936 ( 1072) hydrogen bonds : angle 3.58107 ( 3108) covalent geometry : bond 0.00214 (20544) covalent geometry : angle 0.47943 (27876) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 318 time to evaluate : 3.595 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.7072 (OUTLIER) cc_final: 0.5862 (p90) REVERT: A 92 LEU cc_start: 0.7004 (mm) cc_final: 0.6139 (pp) REVERT: A 178 GLN cc_start: 0.8035 (mt0) cc_final: 0.7607 (mp10) REVERT: A 269 HIS cc_start: 0.7906 (t-90) cc_final: 0.7580 (t-90) REVERT: B 383 GLN cc_start: 0.8335 (tp40) cc_final: 0.7953 (tt0) REVERT: B 634 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.7476 (m-80) REVERT: B 687 ARG cc_start: 0.7706 (ttm110) cc_final: 0.7492 (mtm110) REVERT: C 39 PHE cc_start: 0.7202 (OUTLIER) cc_final: 0.5552 (p90) REVERT: C 113 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7086 (mt-10) REVERT: C 178 GLN cc_start: 0.8086 (mt0) cc_final: 0.7685 (mp10) REVERT: C 235 GLN cc_start: 0.7770 (mt0) cc_final: 0.7539 (mt0) REVERT: C 269 HIS cc_start: 0.7961 (t70) cc_final: 0.7627 (t70) REVERT: C 634 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.7355 (m-80) REVERT: D 39 PHE cc_start: 0.7048 (OUTLIER) cc_final: 0.5648 (p90) REVERT: D 92 LEU cc_start: 0.7692 (mt) cc_final: 0.6208 (pp) REVERT: D 111 TYR cc_start: 0.5577 (m-80) cc_final: 0.5167 (m-80) REVERT: D 178 GLN cc_start: 0.8004 (mt0) cc_final: 0.7582 (mp10) REVERT: D 235 GLN cc_start: 0.7831 (mt0) cc_final: 0.7559 (mt0) REVERT: D 269 HIS cc_start: 0.7899 (t70) cc_final: 0.7570 (t70) outliers start: 61 outliers final: 30 residues processed: 359 average time/residue: 0.4040 time to fit residues: 233.9102 Evaluate side-chains 315 residues out of total 2200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 280 time to evaluate : 4.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 670 GLU Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 520 GLN Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 672 GLU Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- 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: 67.6118 > 50: distance: 11 - 25: 3.097 distance: 16 - 33: 7.745 distance: 20 - 45: 11.116 distance: 23 - 25: 4.841 distance: 24 - 51: 15.109 distance: 25 - 26: 4.818 distance: 26 - 27: 8.420 distance: 26 - 29: 5.850 distance: 27 - 28: 12.573 distance: 27 - 33: 9.571 distance: 28 - 58: 32.365 distance: 29 - 30: 12.020 distance: 29 - 31: 21.796 distance: 30 - 32: 8.172 distance: 33 - 34: 8.621 distance: 34 - 35: 12.442 distance: 34 - 37: 6.752 distance: 35 - 36: 5.879 distance: 35 - 45: 13.089 distance: 36 - 66: 25.070 distance: 37 - 38: 10.475 distance: 38 - 39: 16.967 distance: 38 - 40: 14.144 distance: 39 - 41: 6.437 distance: 40 - 42: 13.360 distance: 41 - 43: 17.088 distance: 42 - 43: 6.117 distance: 43 - 44: 7.862 distance: 45 - 46: 16.350 distance: 46 - 47: 18.966 distance: 46 - 49: 15.809 distance: 47 - 48: 4.507 distance: 47 - 51: 9.963 distance: 49 - 50: 8.010 distance: 51 - 52: 10.678 distance: 52 - 53: 7.120 distance: 52 - 55: 13.010 distance: 53 - 54: 15.325 distance: 53 - 58: 11.037 distance: 55 - 56: 23.229 distance: 55 - 57: 3.189 distance: 58 - 59: 16.110 distance: 59 - 60: 16.581 distance: 59 - 62: 6.628 distance: 60 - 66: 4.171 distance: 62 - 63: 21.691 distance: 63 - 64: 19.460 distance: 64 - 65: 33.753 distance: 66 - 67: 6.034 distance: 67 - 68: 10.429 distance: 67 - 70: 4.817 distance: 68 - 69: 7.965 distance: 68 - 74: 6.818 distance: 70 - 71: 4.304 distance: 70 - 72: 30.210 distance: 71 - 73: 12.086 distance: 74 - 75: 3.523 distance: 75 - 76: 11.126 distance: 75 - 78: 7.952 distance: 76 - 77: 14.925 distance: 76 - 83: 16.225 distance: 78 - 79: 15.401 distance: 79 - 80: 3.664 distance: 80 - 81: 10.568 distance: 80 - 82: 18.700 distance: 83 - 84: 14.399 distance: 84 - 85: 3.222 distance: 84 - 87: 9.966 distance: 85 - 86: 18.454 distance: 85 - 92: 12.048 distance: 87 - 88: 38.686 distance: 88 - 89: 12.662 distance: 89 - 90: 3.666 distance: 90 - 91: 38.208 distance: 92 - 93: 4.056 distance: 93 - 94: 31.231 distance: 93 - 96: 18.070 distance: 94 - 95: 26.083 distance: 94 - 99: 47.323 distance: 96 - 97: 20.110 distance: 96 - 98: 33.687 distance: 99 - 100: 11.753 distance: 100 - 101: 15.194 distance: 100 - 103: 24.339 distance: 101 - 102: 11.769 distance: 101 - 107: 17.277 distance: 102 - 126: 17.648 distance: 104 - 106: 39.725