Starting phenix.real_space_refine on Sat Jun 14 13:54:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7epa_31235/06_2025/7epa_31235.cif Found real_map, /net/cci-nas-00/data/ceres_data/7epa_31235/06_2025/7epa_31235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7epa_31235/06_2025/7epa_31235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7epa_31235/06_2025/7epa_31235.map" model { file = "/net/cci-nas-00/data/ceres_data/7epa_31235/06_2025/7epa_31235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7epa_31235/06_2025/7epa_31235.cif" } resolution = 3.6 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= 0.194 sd= 0.754 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6779 atoms to isotropic. 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 62 5.16 5 C 6676 2.51 5 N 1956 2.21 5 O 1941 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10635 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 782, 5310 Classifications: {'peptide': 782} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PTRANS': 38, 'TRANS': 743} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 814 Unresolved non-hydrogen angles: 1054 Unresolved non-hydrogen dihedrals: 684 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 10, 'TYR:plan': 13, 'ASN:plan1': 7, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 15, 'GLU:plan': 22, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 481 Chain: "B" Number of atoms: 5325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 782, 5325 Classifications: {'peptide': 782} Incomplete info: {'truncation_to_alanine': 212} Link IDs: {'PTRANS': 38, 'TRANS': 743} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 799 Unresolved non-hydrogen angles: 1039 Unresolved non-hydrogen dihedrals: 669 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 12, 'TYR:plan': 13, 'ASN:plan1': 5, 'TRP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 15, 'GLU:plan': 22, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 464 Time building chain proxies: 7.86, per 1000 atoms: 0.74 Number of scatterers: 10635 At special positions: 0 Unit cell: (118.9, 77.9, 188.6, 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 62 16.00 O 1941 8.00 N 1956 7.00 C 6676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 362 " distance=2.03 Simple disulfide: pdb=" SG CYS A 400 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 500 " - pdb=" SG CYS A 519 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 537 " distance=2.03 Simple disulfide: pdb=" SG CYS A 540 " - pdb=" SG CYS A 553 " distance=2.03 Simple disulfide: pdb=" SG CYS A 632 " - pdb=" SG CYS A 721 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 362 " distance=2.03 Simple disulfide: pdb=" SG CYS B 400 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 500 " - pdb=" SG CYS B 519 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 522 " distance=2.04 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 537 " distance=2.03 Simple disulfide: pdb=" SG CYS B 540 " - pdb=" SG CYS B 553 " distance=2.03 Simple disulfide: pdb=" SG CYS B 632 " - pdb=" SG CYS B 721 " distance=2.03 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: 2.92 Conformation dependent library (CDL) restraints added in 1.7 seconds 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2908 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 48.5% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'A' and resid 57 through 74 Processing helix chain 'A' and resid 95 through 110 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 144 through 155 Processing helix chain 'A' and resid 169 through 173 removed outlier: 3.919A pdb=" N LEU A 172 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.594A pdb=" N GLN A 191 " --> pdb=" O PRO A 187 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 202 " --> pdb=" O ILE A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 231 removed outlier: 3.536A pdb=" N ARG A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 259 removed outlier: 3.990A pdb=" N PHE A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 286 Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.587A pdb=" N ALA A 305 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.538A pdb=" N ALA A 310 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 311 " --> pdb=" O GLU A 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 307 through 311' Processing helix chain 'A' and resid 324 through 333 removed outlier: 3.567A pdb=" N SER A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 removed outlier: 4.523A pdb=" N GLU A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 365 removed outlier: 3.940A pdb=" N ALA A 364 " --> pdb=" O ASP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 400 Processing helix chain 'A' and resid 414 through 422 removed outlier: 3.753A pdb=" N PHE A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 592 removed outlier: 4.139A pdb=" N GLY A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Proline residue: A 571 - end of helix Processing helix chain 'A' and resid 595 through 600 removed outlier: 3.549A pdb=" N ALA A 600 " --> pdb=" O PRO A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 623 Processing helix chain 'A' and resid 628 through 656 Processing helix chain 'A' and resid 677 through 700 removed outlier: 3.717A pdb=" N ALA A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 748 removed outlier: 3.778A pdb=" N GLY A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 783 Proline residue: A 778 - end of helix Processing helix chain 'A' and resid 788 through 820 Proline residue: A 812 - end of helix Processing helix chain 'B' and resid 57 through 74 Processing helix chain 'B' and resid 95 through 110 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 144 through 155 Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.865A pdb=" N LEU B 172 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 202 removed outlier: 3.552A pdb=" N GLN B 191 " --> pdb=" O PRO B 187 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE B 202 " --> pdb=" O ILE B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 231 removed outlier: 3.550A pdb=" N ARG B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 259 removed outlier: 4.094A pdb=" N PHE B 250 " --> pdb=" O SER B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 286 Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.592A pdb=" N ALA B 305 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 311 removed outlier: 3.555A pdb=" N ALA B 310 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA B 311 " --> pdb=" O GLU B 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 307 through 311' Processing helix chain 'B' and resid 324 through 333 removed outlier: 3.614A pdb=" N SER B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 353 removed outlier: 4.470A pdb=" N GLU B 347 " --> pdb=" O PRO B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 400 Processing helix chain 'B' and resid 407 through 411 removed outlier: 3.515A pdb=" N MET B 410 " --> pdb=" O CYS B 407 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG B 411 " --> pdb=" O ASP B 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 407 through 411' Processing helix chain 'B' and resid 414 through 422 removed outlier: 3.630A pdb=" N PHE B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 592 removed outlier: 4.143A pdb=" N GLY B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) Proline residue: B 571 - end of helix Processing helix chain 'B' and resid 595 through 600 removed outlier: 3.551A pdb=" N ALA B 600 " --> pdb=" O PRO B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 623 Processing helix chain 'B' and resid 628 through 656 Processing helix chain 'B' and resid 677 through 700 removed outlier: 3.758A pdb=" N ALA B 681 " --> pdb=" O ALA B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 747 removed outlier: 3.701A pdb=" N GLY B 730 " --> pdb=" O ALA B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 784 Proline residue: B 778 - end of helix Processing helix chain 'B' and resid 788 through 820 Proline residue: B 812 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.537A pdb=" N LEU A 32 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N HIS A 87 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU A 34 " --> pdb=" O HIS A 87 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU A 89 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLY A 36 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N ILE A 140 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY A 35 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL A 139 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 235 through 241 removed outlier: 7.785A pdb=" N VAL A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N SER A 238 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N THR A 209 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LYS A 240 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA A 211 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ALA A 266 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE A 317 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY A 472 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR A 457 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LYS A 470 " --> pdb=" O THR A 457 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU A 459 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR A 468 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR A 473 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR A 479 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 428 through 429 removed outlier: 4.444A pdb=" N PHE A 428 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 511 through 512 Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 28 removed outlier: 6.601A pdb=" N LEU B 32 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N HIS B 87 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU B 34 " --> pdb=" O HIS B 87 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU B 89 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY B 36 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL B 33 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY B 138 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N ILE B 163 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL B 139 " --> pdb=" O ILE B 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 238 through 241 removed outlier: 3.539A pdb=" N GLU B 239 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ALA B 266 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE B 317 " --> pdb=" O ALA B 293 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY B 472 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR B 457 " --> pdb=" O LYS B 470 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LYS B 470 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU B 459 " --> pdb=" O TYR B 468 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR B 468 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR B 473 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR B 479 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 428 through 429 removed outlier: 4.506A pdb=" N PHE B 428 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 441 " --> pdb=" O PHE B 428 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 511 through 512 571 hydrogen bonds defined for protein. 1671 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: 3.40 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3684 1.35 - 1.46: 2466 1.46 - 1.58: 4617 1.58 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 10847 Sorted by residual: bond pdb=" C ARG A 411 " pdb=" N PRO A 412 " ideal model delta sigma weight residual 1.333 1.348 -0.015 1.01e-02 9.80e+03 2.13e+00 bond pdb=" C GLU A 502 " pdb=" N PRO A 503 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.36e+00 bond pdb=" C GLU B 502 " pdb=" N PRO B 503 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.31e+00 bond pdb=" C GLY A 116 " pdb=" O GLY A 116 " ideal model delta sigma weight residual 1.243 1.235 0.008 9.30e-03 1.16e+04 7.32e-01 bond pdb=" CA ASP B 421 " pdb=" CB ASP B 421 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.69e-02 3.50e+03 6.03e-01 ... (remaining 10842 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 14428 1.28 - 2.56: 320 2.56 - 3.85: 71 3.85 - 5.13: 15 5.13 - 6.41: 5 Bond angle restraints: 14839 Sorted by residual: angle pdb=" C GLY B 130 " pdb=" N ASP B 131 " pdb=" CA ASP B 131 " ideal model delta sigma weight residual 121.54 126.07 -4.53 1.91e+00 2.74e-01 5.62e+00 angle pdb=" N GLN B 42 " pdb=" CA GLN B 42 " pdb=" C GLN B 42 " ideal model delta sigma weight residual 108.34 111.19 -2.85 1.31e+00 5.83e-01 4.72e+00 angle pdb=" N GLU B 502 " pdb=" CA GLU B 502 " pdb=" C GLU B 502 " ideal model delta sigma weight residual 109.81 114.19 -4.38 2.21e+00 2.05e-01 3.94e+00 angle pdb=" N GLU A 502 " pdb=" CA GLU A 502 " pdb=" C GLU A 502 " ideal model delta sigma weight residual 109.81 114.14 -4.33 2.21e+00 2.05e-01 3.84e+00 angle pdb=" C ALA A 230 " pdb=" N ARG A 231 " pdb=" CA ARG A 231 " ideal model delta sigma weight residual 122.76 119.74 3.02 1.63e+00 3.76e-01 3.42e+00 ... (remaining 14834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.08: 5987 16.08 - 32.16: 367 32.16 - 48.24: 91 48.24 - 64.33: 13 64.33 - 80.41: 2 Dihedral angle restraints: 6460 sinusoidal: 1958 harmonic: 4502 Sorted by residual: dihedral pdb=" CB CYS A 234 " pdb=" SG CYS A 234 " pdb=" SG CYS A 518 " pdb=" CB CYS A 518 " ideal model delta sinusoidal sigma weight residual 93.00 14.04 78.96 1 1.00e+01 1.00e-02 7.76e+01 dihedral pdb=" CB CYS A 632 " pdb=" SG CYS A 632 " pdb=" SG CYS A 721 " pdb=" CB CYS A 721 " ideal model delta sinusoidal sigma weight residual -86.00 -21.68 -64.32 1 1.00e+01 1.00e-02 5.44e+01 dihedral pdb=" CB CYS B 234 " pdb=" SG CYS B 234 " pdb=" SG CYS B 518 " pdb=" CB CYS B 518 " ideal model delta sinusoidal sigma weight residual 93.00 29.55 63.45 1 1.00e+01 1.00e-02 5.31e+01 ... (remaining 6457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 964 0.024 - 0.049: 476 0.049 - 0.073: 172 0.073 - 0.098: 76 0.098 - 0.122: 42 Chirality restraints: 1730 Sorted by residual: chirality pdb=" CA ILE B 317 " pdb=" N ILE B 317 " pdb=" C ILE B 317 " pdb=" CB ILE B 317 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 chirality pdb=" CA ILE B 140 " pdb=" N ILE B 140 " pdb=" C ILE B 140 " pdb=" CB ILE B 140 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.59e-01 chirality pdb=" CA ILE B 315 " pdb=" N ILE B 315 " pdb=" C ILE B 315 " pdb=" CB ILE B 315 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.56e-01 ... (remaining 1727 not shown) Planarity restraints: 1976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 523 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO B 524 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 524 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 524 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 523 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO A 524 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 524 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 524 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 502 " 0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO A 503 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 503 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 503 " 0.018 5.00e-02 4.00e+02 ... (remaining 1973 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2872 2.80 - 3.32: 9937 3.32 - 3.85: 17382 3.85 - 4.37: 17184 4.37 - 4.90: 30790 Nonbonded interactions: 78165 Sorted by model distance: nonbonded pdb=" OG SER B 356 " pdb=" OE1 GLN B 359 " model vdw 2.274 3.040 nonbonded pdb=" OG SER A 294 " pdb=" OD1 ASP A 295 " model vdw 2.315 3.040 nonbonded pdb=" OG SER B 294 " pdb=" OD1 ASP B 295 " model vdw 2.338 3.040 nonbonded pdb=" NH1 ARG B 720 " pdb=" O ASP B 786 " model vdw 2.341 3.120 nonbonded pdb=" N GLY A 35 " pdb=" O GLY A 138 " model vdw 2.349 3.120 ... (remaining 78160 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 24 through 62 or (resid 63 through 64 and (name N or name \ CA or name C or name O or name CB )) or resid 65 through 88 or (resid 89 and (na \ me N or name CA or name C or name O or name CB )) or resid 90 through 109 or (re \ sid 110 through 112 and (name N or name CA or name C or name O or name CB )) or \ resid 113 through 254 or (resid 255 through 256 and (name N or name CA or name C \ or name O or name CB )) or resid 257 through 300 or (resid 301 and (name N or n \ ame CA or name C or name O or name CB )) or resid 302 through 317 or (resid 318 \ and (name N or name CA or name C or name O or name CB )) or resid 319 through 34 \ 5 or (resid 346 through 347 and (name N or name CA or name C or name O or name C \ B )) or resid 348 through 532 or (resid 533 and (name N or name CA or name C or \ name O or name CB )) or resid 534 through 538 or (resid 539 and (name N or name \ CA or name C or name O or name CB )) or resid 540 through 604 or (resid 605 and \ (name N or name CA or name C or name O or name CB )) or resid 606 through 644 or \ (resid 645 and (name N or name CA or name C or name O or name CB )) or resid 64 \ 6 through 685 or (resid 686 through 688 and (name N or name CA or name C or name \ O or name CB )) or resid 689 through 820)) selection = (chain 'B' and (resid 24 through 28 or (resid 29 and (name N or name CA or name \ C or name O or name CB )) or resid 30 through 41 or (resid 42 and (name N or nam \ e CA or name C or name O or name CB )) or resid 43 through 93 or (resid 94 and ( \ name N or name CA or name C or name O or name CB )) or resid 95 through 196 or ( \ resid 197 and (name N or name CA or name C or name O or name CB )) or resid 198 \ through 199 or (resid 200 and (name N or name CA or name C or name O or name CB \ )) or resid 201 through 272 or (resid 273 and (name N or name CA or name C or na \ me O or name CB )) or resid 274 through 285 or (resid 286 through 287 and (name \ N or name CA or name C or name O or name CB )) or resid 288 through 432 or (resi \ d 433 and (name N or name CA or name C or name O or name CB )) or resid 434 thro \ ugh 469 or (resid 470 and (name N or name CA or name C or name O or name CB )) o \ r resid 471 through 505 or (resid 506 through 507 and (name N or name CA or name \ C or name O or name CB )) or resid 508 through 525 or (resid 526 and (name N or \ name CA or name C or name O or name CB )) or resid 527 through 607 or (resid 60 \ 8 through 610 and (name N or name CA or name C or name O or name CB )) or resid \ 611 through 719 or (resid 720 and (name N or name CA or name C or name O or name \ CB )) or resid 721 through 820)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.670 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 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 : 0.002 0.036 10866 Z= 0.099 Angle : 0.482 6.408 14877 Z= 0.273 Chirality : 0.038 0.122 1730 Planarity : 0.003 0.041 1976 Dihedral : 11.031 80.407 3495 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % 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: -1.51 (0.19), residues: 1556 helix: 0.45 (0.18), residues: 718 sheet: -0.80 (0.40), residues: 166 loop : -2.76 (0.20), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 487 HIS 0.002 0.000 HIS B 41 PHE 0.008 0.000 PHE B 189 TYR 0.005 0.001 TYR B 386 ARG 0.001 0.000 ARG B 714 Details of bonding type rmsd hydrogen bonds : bond 0.10722 ( 571) hydrogen bonds : angle 3.98156 ( 1671) SS BOND : bond 0.00140 ( 19) SS BOND : angle 0.46837 ( 38) covalent geometry : bond 0.00187 (10847) covalent geometry : angle 0.48206 (14839) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 1.238 Fit side-chains revert: symmetry clash REVERT: A 63 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8369 (mm-30) REVERT: A 70 ASP cc_start: 0.7933 (t0) cc_final: 0.7656 (t0) REVERT: A 137 THR cc_start: 0.9223 (m) cc_final: 0.9016 (p) REVERT: A 159 GLN cc_start: 0.8368 (mm-40) cc_final: 0.7298 (mm-40) REVERT: A 180 TYR cc_start: 0.7840 (m-10) cc_final: 0.6820 (m-10) REVERT: B 70 ASP cc_start: 0.8290 (t0) cc_final: 0.8082 (t0) REVERT: B 162 GLN cc_start: 0.7825 (tt0) cc_final: 0.7623 (tm-30) REVERT: B 269 PHE cc_start: 0.8476 (m-80) cc_final: 0.7720 (m-80) REVERT: B 399 LEU cc_start: 0.8935 (tp) cc_final: 0.8659 (tp) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.2630 time to fit residues: 88.4068 Evaluate side-chains 189 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 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 351 GLN ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.128699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.107944 restraints weight = 30227.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.111026 restraints weight = 15870.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.113057 restraints weight = 9563.029| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10866 Z= 0.164 Angle : 0.580 8.544 14877 Z= 0.293 Chirality : 0.040 0.141 1730 Planarity : 0.005 0.058 1976 Dihedral : 3.431 22.975 1677 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.21 % Allowed : 17.60 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.21), residues: 1556 helix: 1.67 (0.19), residues: 722 sheet: -0.25 (0.45), residues: 144 loop : -2.16 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 291 HIS 0.002 0.001 HIS B 87 PHE 0.015 0.001 PHE B 158 TYR 0.017 0.001 TYR A 180 ARG 0.007 0.001 ARG B 360 Details of bonding type rmsd hydrogen bonds : bond 0.02778 ( 571) hydrogen bonds : angle 3.18511 ( 1671) SS BOND : bond 0.00993 ( 19) SS BOND : angle 0.65139 ( 38) covalent geometry : bond 0.00351 (10847) covalent geometry : angle 0.57961 (14839) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 200 time to evaluate : 1.132 Fit side-chains REVERT: A 56 HIS cc_start: 0.8592 (OUTLIER) cc_final: 0.8360 (t-90) REVERT: A 63 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8375 (mm-30) REVERT: A 70 ASP cc_start: 0.8007 (t0) cc_final: 0.7675 (t0) REVERT: A 165 TYR cc_start: 0.8757 (p90) cc_final: 0.8498 (p90) REVERT: A 173 SER cc_start: 0.8878 (m) cc_final: 0.8499 (p) REVERT: B 70 ASP cc_start: 0.8169 (t0) cc_final: 0.7904 (t0) REVERT: B 165 TYR cc_start: 0.8619 (p90) cc_final: 0.8255 (p90) REVERT: B 206 TYR cc_start: 0.6539 (t80) cc_final: 0.6333 (t80) REVERT: B 399 LEU cc_start: 0.9014 (tp) cc_final: 0.8691 (tp) REVERT: B 499 ARG cc_start: 0.7245 (mmm160) cc_final: 0.6944 (mmm160) outliers start: 19 outliers final: 9 residues processed: 204 average time/residue: 0.2310 time to fit residues: 65.3540 Evaluate side-chains 185 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 291 TRP Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 372 PHE Chi-restraints excluded: chain B residue 410 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 28 optimal weight: 3.9990 chunk 130 optimal weight: 0.0270 chunk 133 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 overall best weight: 2.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN B 101 GLN ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 526 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.115460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.095037 restraints weight = 30836.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.097997 restraints weight = 15381.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.099914 restraints weight = 9012.779| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10866 Z= 0.248 Angle : 0.676 8.153 14877 Z= 0.355 Chirality : 0.043 0.212 1730 Planarity : 0.005 0.077 1976 Dihedral : 4.631 23.653 1677 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.43 % Allowed : 20.86 % Favored : 74.71 % 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: -0.10 (0.22), residues: 1556 helix: 1.77 (0.19), residues: 708 sheet: -0.54 (0.43), residues: 150 loop : -2.01 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 291 HIS 0.004 0.001 HIS B 390 PHE 0.023 0.002 PHE A 158 TYR 0.027 0.002 TYR B 386 ARG 0.006 0.001 ARG A 499 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 571) hydrogen bonds : angle 4.03162 ( 1671) SS BOND : bond 0.00391 ( 19) SS BOND : angle 0.94638 ( 38) covalent geometry : bond 0.00515 (10847) covalent geometry : angle 0.67525 (14839) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 1.258 Fit side-chains revert: symmetry clash REVERT: A 56 HIS cc_start: 0.8873 (OUTLIER) cc_final: 0.8337 (t-90) REVERT: A 63 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8215 (mm-30) REVERT: A 70 ASP cc_start: 0.8258 (t0) cc_final: 0.7911 (t0) REVERT: A 148 SER cc_start: 0.9061 (OUTLIER) cc_final: 0.8717 (t) REVERT: A 173 SER cc_start: 0.9048 (m) cc_final: 0.8751 (p) REVERT: A 483 SER cc_start: 0.8683 (m) cc_final: 0.8448 (p) REVERT: B 56 HIS cc_start: 0.8908 (OUTLIER) cc_final: 0.8474 (t-90) REVERT: B 70 ASP cc_start: 0.8327 (t0) cc_final: 0.8078 (t0) REVERT: B 206 TYR cc_start: 0.7173 (t80) cc_final: 0.6846 (t80) REVERT: B 433 ARG cc_start: 0.7581 (ttt180) cc_final: 0.7368 (ttt180) outliers start: 38 outliers final: 20 residues processed: 195 average time/residue: 0.2584 time to fit residues: 68.2606 Evaluate side-chains 169 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 372 PHE Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 458 TYR Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 84 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 chunk 81 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 396 HIS B 414 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.113606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.093507 restraints weight = 30508.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.096439 restraints weight = 15217.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.098315 restraints weight = 8898.236| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10866 Z= 0.224 Angle : 0.648 7.261 14877 Z= 0.333 Chirality : 0.042 0.191 1730 Planarity : 0.005 0.058 1976 Dihedral : 4.486 24.539 1677 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 5.36 % Allowed : 24.24 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.22), residues: 1556 helix: 1.97 (0.19), residues: 706 sheet: -0.77 (0.41), residues: 152 loop : -2.01 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 291 HIS 0.003 0.001 HIS A 390 PHE 0.020 0.002 PHE B 158 TYR 0.018 0.001 TYR B 386 ARG 0.010 0.001 ARG A 368 Details of bonding type rmsd hydrogen bonds : bond 0.03565 ( 571) hydrogen bonds : angle 3.97287 ( 1671) SS BOND : bond 0.00496 ( 19) SS BOND : angle 0.81662 ( 38) covalent geometry : bond 0.00467 (10847) covalent geometry : angle 0.64730 (14839) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 161 time to evaluate : 1.222 Fit side-chains REVERT: A 56 HIS cc_start: 0.8822 (OUTLIER) cc_final: 0.8302 (t-90) REVERT: A 63 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8195 (mm-30) REVERT: A 66 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8471 (mm) REVERT: A 70 ASP cc_start: 0.8232 (t0) cc_final: 0.7845 (t0) REVERT: A 173 SER cc_start: 0.9134 (m) cc_final: 0.8776 (p) REVERT: A 379 MET cc_start: 0.8076 (tmm) cc_final: 0.7872 (tmm) REVERT: A 483 SER cc_start: 0.8677 (m) cc_final: 0.8472 (p) REVERT: A 499 ARG cc_start: 0.7396 (mmm160) cc_final: 0.7029 (mmm160) REVERT: B 56 HIS cc_start: 0.8832 (OUTLIER) cc_final: 0.8343 (t-90) REVERT: B 70 ASP cc_start: 0.8256 (t0) cc_final: 0.7976 (t0) REVERT: B 206 TYR cc_start: 0.7234 (t80) cc_final: 0.6893 (t80) REVERT: B 291 TRP cc_start: 0.7666 (OUTLIER) cc_final: 0.7363 (m-10) REVERT: B 351 GLN cc_start: 0.8914 (tp-100) cc_final: 0.8649 (tp-100) REVERT: B 414 ASN cc_start: 0.8329 (t0) cc_final: 0.7910 (t0) REVERT: B 499 ARG cc_start: 0.7294 (mmm160) cc_final: 0.6924 (mmm160) outliers start: 46 outliers final: 27 residues processed: 188 average time/residue: 0.2334 time to fit residues: 62.3466 Evaluate side-chains 188 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 291 TRP Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 458 TYR Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 639 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 5 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 145 optimal weight: 0.0020 chunk 150 optimal weight: 2.9990 chunk 130 optimal weight: 0.0000 chunk 64 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 116 optimal weight: 0.0010 overall best weight: 0.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.120056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.099728 restraints weight = 30102.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.102814 restraints weight = 15036.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.104773 restraints weight = 8767.644| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10866 Z= 0.103 Angle : 0.583 9.057 14877 Z= 0.281 Chirality : 0.040 0.155 1730 Planarity : 0.004 0.035 1976 Dihedral : 3.829 22.404 1677 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.61 % Allowed : 26.34 % Favored : 70.05 % 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: 0.45 (0.22), residues: 1556 helix: 2.43 (0.19), residues: 708 sheet: -0.52 (0.42), residues: 148 loop : -1.91 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 291 HIS 0.003 0.000 HIS B 390 PHE 0.012 0.001 PHE B 158 TYR 0.018 0.001 TYR B 386 ARG 0.006 0.001 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.02851 ( 571) hydrogen bonds : angle 3.48138 ( 1671) SS BOND : bond 0.00182 ( 19) SS BOND : angle 0.54592 ( 38) covalent geometry : bond 0.00235 (10847) covalent geometry : angle 0.58286 (14839) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 HIS cc_start: 0.8538 (OUTLIER) cc_final: 0.8331 (t-90) REVERT: A 63 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8223 (mm-30) REVERT: A 66 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8356 (mm) REVERT: A 70 ASP cc_start: 0.7958 (t0) cc_final: 0.7539 (t0) REVERT: A 99 LEU cc_start: 0.8316 (mt) cc_final: 0.8081 (mt) REVERT: A 140 ILE cc_start: 0.8777 (mp) cc_final: 0.8279 (pt) REVERT: A 173 SER cc_start: 0.9045 (m) cc_final: 0.8751 (p) REVERT: A 195 MET cc_start: 0.8067 (ttm) cc_final: 0.7624 (mtt) REVERT: A 245 MET cc_start: 0.7364 (ptp) cc_final: 0.7125 (ptp) REVERT: A 639 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8116 (pp) REVERT: A 766 MET cc_start: 0.5471 (ppp) cc_final: 0.5204 (ppp) REVERT: B 56 HIS cc_start: 0.8569 (OUTLIER) cc_final: 0.8346 (t-90) REVERT: B 70 ASP cc_start: 0.8081 (t0) cc_final: 0.7789 (t0) REVERT: B 154 LEU cc_start: 0.9195 (tp) cc_final: 0.8944 (tt) REVERT: B 165 TYR cc_start: 0.8515 (p90) cc_final: 0.8089 (p90) REVERT: B 206 TYR cc_start: 0.6931 (t80) cc_final: 0.6730 (t80) outliers start: 31 outliers final: 12 residues processed: 200 average time/residue: 0.2215 time to fit residues: 62.7850 Evaluate side-chains 179 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 55 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 124 optimal weight: 0.0970 chunk 111 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 11 optimal weight: 0.0770 chunk 153 optimal weight: 20.0000 overall best weight: 2.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.113839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.093669 restraints weight = 30347.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.096674 restraints weight = 15058.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.098601 restraints weight = 8756.760| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10866 Z= 0.204 Angle : 0.648 9.845 14877 Z= 0.325 Chirality : 0.042 0.177 1730 Planarity : 0.005 0.056 1976 Dihedral : 4.272 23.819 1677 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.73 % Allowed : 28.09 % Favored : 68.18 % 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: 0.34 (0.22), residues: 1556 helix: 2.30 (0.20), residues: 708 sheet: -0.75 (0.41), residues: 152 loop : -1.88 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 291 HIS 0.003 0.001 HIS B 393 PHE 0.019 0.002 PHE B 158 TYR 0.014 0.001 TYR A 206 ARG 0.011 0.001 ARG B 368 Details of bonding type rmsd hydrogen bonds : bond 0.03457 ( 571) hydrogen bonds : angle 3.79424 ( 1671) SS BOND : bond 0.00324 ( 19) SS BOND : angle 0.74980 ( 38) covalent geometry : bond 0.00431 (10847) covalent geometry : angle 0.64784 (14839) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: A 56 HIS cc_start: 0.8795 (OUTLIER) cc_final: 0.8478 (t-90) REVERT: A 63 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8233 (mm-30) REVERT: A 66 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8389 (mm) REVERT: A 70 ASP cc_start: 0.8148 (t0) cc_final: 0.7731 (t0) REVERT: A 173 SER cc_start: 0.9115 (m) cc_final: 0.8875 (p) REVERT: B 56 HIS cc_start: 0.8907 (OUTLIER) cc_final: 0.8540 (t-90) REVERT: B 70 ASP cc_start: 0.8213 (t0) cc_final: 0.7907 (t0) REVERT: B 154 LEU cc_start: 0.9189 (tp) cc_final: 0.8932 (tt) REVERT: B 206 TYR cc_start: 0.7259 (t80) cc_final: 0.6915 (t80) REVERT: B 351 GLN cc_start: 0.8886 (tp-100) cc_final: 0.8541 (tp-100) outliers start: 32 outliers final: 20 residues processed: 182 average time/residue: 0.2211 time to fit residues: 57.0550 Evaluate side-chains 182 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 56 HIS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 365 HIS Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 463 SER Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: 72.6014 > 50: distance: 61 - 131: 35.183 distance: 64 - 128: 35.860 distance: 75 - 115: 34.543 distance: 78 - 112: 36.550 distance: 95 - 100: 33.511 distance: 100 - 101: 36.479 distance: 100 - 259: 30.821 distance: 101 - 102: 40.599 distance: 101 - 104: 40.522 distance: 102 - 103: 38.776 distance: 102 - 112: 40.481 distance: 103 - 256: 33.097 distance: 105 - 106: 60.491 distance: 105 - 107: 57.579 distance: 106 - 108: 58.045 distance: 107 - 109: 57.686 distance: 108 - 110: 56.794 distance: 109 - 110: 40.945 distance: 110 - 111: 68.364 distance: 112 - 113: 38.882 distance: 113 - 114: 58.066 distance: 113 - 116: 53.357 distance: 114 - 115: 38.871 distance: 114 - 120: 56.735 distance: 117 - 118: 52.254 distance: 117 - 119: 55.909 distance: 120 - 121: 41.288 distance: 120 - 249: 32.106 distance: 121 - 122: 39.167 distance: 121 - 124: 40.359 distance: 122 - 123: 39.071 distance: 122 - 128: 57.087 distance: 125 - 127: 70.120 distance: 128 - 129: 48.390 distance: 129 - 130: 62.200 distance: 129 - 132: 10.693 distance: 130 - 131: 34.172 distance: 130 - 139: 35.029 distance: 132 - 133: 40.422 distance: 133 - 134: 22.295 distance: 134 - 136: 28.958 distance: 135 - 137: 67.985 distance: 136 - 138: 59.954 distance: 137 - 138: 39.945 distance: 139 - 140: 48.206 distance: 140 - 141: 27.530 distance: 140 - 143: 13.205 distance: 141 - 142: 57.135 distance: 143 - 144: 68.549 distance: 143 - 145: 56.439 distance: 146 - 147: 38.941 distance: 147 - 150: 28.430 distance: 150 - 151: 40.735 distance: 151 - 152: 19.555 distance: 152 - 154: 15.783 distance: 153 - 155: 55.860 distance: 154 - 156: 58.267 distance: 155 - 156: 39.665 distance: 156 - 157: 41.361 distance: 158 - 159: 55.715 distance: 159 - 160: 18.376 distance: 159 - 162: 55.947 distance: 160 - 161: 46.397 distance: 160 - 166: 46.626 distance: 162 - 163: 42.758 distance: 163 - 164: 26.582 distance: 163 - 165: 26.551 distance: 166 - 167: 38.952 distance: 167 - 168: 62.937 distance: 167 - 170: 56.327 distance: 168 - 169: 46.073 distance: 168 - 171: 57.368 distance: 171 - 172: 57.184 distance: 172 - 173: 55.141 distance: 172 - 175: 39.344 distance: 173 - 176: 70.105 distance: 176 - 177: 56.478 distance: 177 - 178: 40.178 distance: 178 - 179: 38.777 distance: 178 - 180: 34.202