Starting phenix.real_space_refine on Sat Oct 12 21:51:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vtb_43522/10_2024/8vtb_43522_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vtb_43522/10_2024/8vtb_43522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vtb_43522/10_2024/8vtb_43522.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vtb_43522/10_2024/8vtb_43522.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vtb_43522/10_2024/8vtb_43522_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vtb_43522/10_2024/8vtb_43522_neut.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 28 5.16 5 C 8860 2.51 5 N 2112 2.21 5 O 2376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 13392 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3168 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 25, 'TRANS': 374} Chain breaks: 1 Chain: "B" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3168 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 25, 'TRANS': 374} Chain breaks: 1 Chain: "C" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3168 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 25, 'TRANS': 374} Chain breaks: 1 Chain: "D" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3168 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 25, 'TRANS': 374} Chain breaks: 1 Chain: "A" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 216 Unusual residues: {'PCW': 7} Classifications: {'RNA': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 2, 'PCW:plan-3': 3, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 180 Unusual residues: {'PCW': 6} Classifications: {'RNA': 1, 'undetermined': 6} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-3': 3, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 180 Unusual residues: {'PCW': 6} Classifications: {'RNA': 1, 'undetermined': 6} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-3': 3, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 29 Chain: "D" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 144 Unusual residues: {'PCW': 5} Classifications: {'RNA': 1, 'undetermined': 5} Modifications used: {'rna3p': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 3, 'PCW:plan-4': 5} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 8.34, per 1000 atoms: 0.62 Number of scatterers: 13392 At special positions: 0 Unit cell: (99.9, 99.9, 118.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 16 15.00 O 2376 8.00 N 2112 7.00 C 8860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.62 Conformation dependent library (CDL) restraints added in 1.8 seconds 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3040 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 8 sheets defined 70.3% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 10 through 36 removed outlier: 3.708A pdb=" N VAL A 14 " --> pdb=" O THR A 10 " (cutoff:3.500A) Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 37 through 42 removed outlier: 4.229A pdb=" N SER A 41 " --> pdb=" O SER A 38 " (cutoff:3.500A) Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 43 through 58 removed outlier: 3.692A pdb=" N ILE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 81 through 87 Processing helix chain 'A' and resid 90 through 99 Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 107 through 112 removed outlier: 3.647A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 removed outlier: 4.143A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 159 Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 193 through 224 removed outlier: 3.659A pdb=" N LYS A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 246 Processing helix chain 'A' and resid 249 through 268 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 299 through 303 removed outlier: 3.922A pdb=" N LYS A 303 " --> pdb=" O PRO A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 316 removed outlier: 3.711A pdb=" N HIS A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.903A pdb=" N ILE A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 404 through 415 Processing helix chain 'B' and resid 11 through 36 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 37 through 42 removed outlier: 4.230A pdb=" N SER B 41 " --> pdb=" O SER B 38 " (cutoff:3.500A) Proline residue: B 42 - end of helix Processing helix chain 'B' and resid 43 through 58 removed outlier: 3.692A pdb=" N ILE B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 64 Processing helix chain 'B' and resid 81 through 87 Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 107 through 112 removed outlier: 3.647A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 126 removed outlier: 4.143A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 159 Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 193 through 224 removed outlier: 3.659A pdb=" N LYS B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 246 Processing helix chain 'B' and resid 249 through 268 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 277 through 279 No H-bonds generated for 'chain 'B' and resid 277 through 279' Processing helix chain 'B' and resid 280 through 292 Processing helix chain 'B' and resid 299 through 303 removed outlier: 3.923A pdb=" N LYS B 303 " --> pdb=" O PRO B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 316 removed outlier: 3.711A pdb=" N HIS B 316 " --> pdb=" O ASP B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.903A pdb=" N ILE B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 404 through 415 Processing helix chain 'C' and resid 11 through 36 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 37 through 42 removed outlier: 4.229A pdb=" N SER C 41 " --> pdb=" O SER C 38 " (cutoff:3.500A) Proline residue: C 42 - end of helix Processing helix chain 'C' and resid 43 through 58 removed outlier: 3.692A pdb=" N ILE C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 64 Processing helix chain 'C' and resid 81 through 87 Processing helix chain 'C' and resid 90 through 99 Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.647A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 removed outlier: 4.143A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 159 Processing helix chain 'C' and resid 165 through 182 Processing helix chain 'C' and resid 193 through 224 removed outlier: 3.659A pdb=" N LYS C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 246 Processing helix chain 'C' and resid 249 through 268 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 277 through 279 No H-bonds generated for 'chain 'C' and resid 277 through 279' Processing helix chain 'C' and resid 280 through 292 Processing helix chain 'C' and resid 299 through 303 removed outlier: 3.922A pdb=" N LYS C 303 " --> pdb=" O PRO C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 316 removed outlier: 3.712A pdb=" N HIS C 316 " --> pdb=" O ASP C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.904A pdb=" N ILE C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 402 Processing helix chain 'C' and resid 404 through 415 Processing helix chain 'D' and resid 11 through 36 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 37 through 42 removed outlier: 4.229A pdb=" N SER D 41 " --> pdb=" O SER D 38 " (cutoff:3.500A) Proline residue: D 42 - end of helix Processing helix chain 'D' and resid 43 through 58 removed outlier: 3.691A pdb=" N ILE D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 64 Processing helix chain 'D' and resid 81 through 87 Processing helix chain 'D' and resid 90 through 99 Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 107 through 112 removed outlier: 3.647A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 126 removed outlier: 4.143A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 159 Processing helix chain 'D' and resid 165 through 182 Processing helix chain 'D' and resid 193 through 224 removed outlier: 3.659A pdb=" N LYS D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 246 Processing helix chain 'D' and resid 249 through 268 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 277 through 279 No H-bonds generated for 'chain 'D' and resid 277 through 279' Processing helix chain 'D' and resid 280 through 292 Processing helix chain 'D' and resid 299 through 303 removed outlier: 3.922A pdb=" N LYS D 303 " --> pdb=" O PRO D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 316 removed outlier: 3.711A pdb=" N HIS D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.902A pdb=" N ILE D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 404 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 322 removed outlier: 6.405A pdb=" N ASP A 388 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 6.639A pdb=" N TYR A 327 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA A 383 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 318 through 322 removed outlier: 6.405A pdb=" N ASP B 388 " --> pdb=" O ASN B 342 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 329 removed outlier: 6.639A pdb=" N TYR B 327 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA B 383 " --> pdb=" O TYR B 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 318 through 322 removed outlier: 6.405A pdb=" N ASP C 388 " --> pdb=" O ASN C 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 329 removed outlier: 6.639A pdb=" N TYR C 327 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA C 383 " --> pdb=" O TYR C 327 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 318 through 322 removed outlier: 6.405A pdb=" N ASP D 388 " --> pdb=" O ASN D 342 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 329 removed outlier: 6.638A pdb=" N TYR D 327 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA D 383 " --> pdb=" O TYR D 327 " (cutoff:3.500A) 836 hydrogen bonds defined for protein. 2388 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.06 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2174 1.32 - 1.45: 3370 1.45 - 1.57: 8048 1.57 - 1.69: 32 1.69 - 1.82: 48 Bond restraints: 13672 Sorted by residual: bond pdb=" C4 CMP C 501 " pdb=" C5 CMP C 501 " ideal model delta sigma weight residual 1.490 1.348 0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" C4 CMP B 501 " pdb=" C5 CMP B 501 " ideal model delta sigma weight residual 1.490 1.348 0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" C4 CMP A 501 " pdb=" C5 CMP A 501 " ideal model delta sigma weight residual 1.490 1.348 0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C4 CMP D 504 " pdb=" C5 CMP D 504 " ideal model delta sigma weight residual 1.490 1.348 0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" C5 CMP A 501 " pdb=" C6 CMP A 501 " ideal model delta sigma weight residual 1.490 1.392 0.098 2.00e-02 2.50e+03 2.39e+01 ... (remaining 13667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 17658 1.95 - 3.89: 662 3.89 - 5.84: 112 5.84 - 7.79: 66 7.79 - 9.73: 10 Bond angle restraints: 18508 Sorted by residual: angle pdb=" C3' CMP C 501 " pdb=" C4' CMP C 501 " pdb=" O4' CMP C 501 " ideal model delta sigma weight residual 104.00 100.54 3.46 1.00e+00 1.00e+00 1.20e+01 angle pdb=" C4' CMP A 501 " pdb=" C5' CMP A 501 " pdb=" O5' CMP A 501 " ideal model delta sigma weight residual 111.50 106.31 5.19 1.50e+00 4.44e-01 1.20e+01 angle pdb=" C3' CMP D 504 " pdb=" C4' CMP D 504 " pdb=" O4' CMP D 504 " ideal model delta sigma weight residual 104.00 100.54 3.46 1.00e+00 1.00e+00 1.20e+01 angle pdb=" C4' CMP D 504 " pdb=" C5' CMP D 504 " pdb=" O5' CMP D 504 " ideal model delta sigma weight residual 111.50 106.31 5.19 1.50e+00 4.44e-01 1.20e+01 angle pdb=" C4' CMP C 501 " pdb=" C5' CMP C 501 " pdb=" O5' CMP C 501 " ideal model delta sigma weight residual 111.50 106.32 5.18 1.50e+00 4.44e-01 1.19e+01 ... (remaining 18503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.88: 7872 25.88 - 51.77: 308 51.77 - 77.65: 128 77.65 - 103.54: 12 103.54 - 129.42: 16 Dihedral angle restraints: 8336 sinusoidal: 3628 harmonic: 4708 Sorted by residual: dihedral pdb=" C33 PCW B 505 " pdb=" C31 PCW B 505 " pdb=" C32 PCW B 505 " pdb=" O2 PCW B 505 " ideal model delta sinusoidal sigma weight residual 191.83 62.41 129.42 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C33 PCW A 504 " pdb=" C31 PCW A 504 " pdb=" C32 PCW A 504 " pdb=" O2 PCW A 504 " ideal model delta sinusoidal sigma weight residual 191.83 62.43 129.40 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C33 PCW A 506 " pdb=" C31 PCW A 506 " pdb=" C32 PCW A 506 " pdb=" O2 PCW A 506 " ideal model delta sinusoidal sigma weight residual 191.83 62.44 129.39 1 3.00e+01 1.11e-03 1.74e+01 ... (remaining 8333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1402 0.036 - 0.072: 472 0.072 - 0.107: 179 0.107 - 0.143: 79 0.143 - 0.179: 12 Chirality restraints: 2144 Sorted by residual: chirality pdb=" CA VAL A 95 " pdb=" N VAL A 95 " pdb=" C VAL A 95 " pdb=" CB VAL A 95 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.00e-01 chirality pdb=" CA VAL D 95 " pdb=" N VAL D 95 " pdb=" C VAL D 95 " pdb=" CB VAL D 95 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CA VAL C 95 " pdb=" N VAL C 95 " pdb=" C VAL C 95 " pdb=" CB VAL C 95 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.87e-01 ... (remaining 2141 not shown) Planarity restraints: 2248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 PCW A 504 " -0.119 2.00e-02 2.50e+03 1.17e-01 1.37e+02 pdb=" C39 PCW A 504 " 0.127 2.00e-02 2.50e+03 pdb=" C40 PCW A 504 " 0.108 2.00e-02 2.50e+03 pdb=" C41 PCW A 504 " -0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 PCW A 506 " -0.119 2.00e-02 2.50e+03 1.17e-01 1.37e+02 pdb=" C39 PCW A 506 " 0.127 2.00e-02 2.50e+03 pdb=" C40 PCW A 506 " 0.107 2.00e-02 2.50e+03 pdb=" C41 PCW A 506 " -0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 PCW C 505 " 0.119 2.00e-02 2.50e+03 1.17e-01 1.37e+02 pdb=" C39 PCW C 505 " -0.126 2.00e-02 2.50e+03 pdb=" C40 PCW C 505 " -0.107 2.00e-02 2.50e+03 pdb=" C41 PCW C 505 " 0.115 2.00e-02 2.50e+03 ... (remaining 2245 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1804 2.76 - 3.29: 13730 3.29 - 3.83: 22776 3.83 - 4.36: 27262 4.36 - 4.90: 46341 Nonbonded interactions: 111913 Sorted by model distance: nonbonded pdb=" N GLU D 297 " pdb=" OE1 GLU D 297 " model vdw 2.221 3.120 nonbonded pdb=" N GLU A 297 " pdb=" OE1 GLU A 297 " model vdw 2.221 3.120 nonbonded pdb=" N GLU C 297 " pdb=" OE1 GLU C 297 " model vdw 2.222 3.120 nonbonded pdb=" N GLU B 297 " pdb=" OE1 GLU B 297 " model vdw 2.222 3.120 nonbonded pdb=" N GLU B 251 " pdb=" OE1 GLU B 251 " model vdw 2.261 3.120 ... (remaining 111908 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 10 through 415 or (resid 502 and (name C1 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C20 or name C21 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name O11 or name O1P or name O2 or name O2P or name O3 or n \ ame O31 or name O3P or name O4P or name P )) or (resid 503 and (name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or \ name C19 or name C20 or name C21)) or (resid 505 and (name C11 or name C12 or na \ me C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 o \ r name C20 or name O11 or name O3 )) or (resid 506 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C3 or name O11 or name O3 )))) selection = (chain 'B' and (resid 10 through 415 or (resid 502 and (name C1 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C20 or name C21 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name O11 or name O1P or name O2 or name O2P or name O3 or n \ ame O31 or name O3P or name O4P or name P )) or (resid 503 and (name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or \ name C19 or name C20 or name C21)) or (resid 505 and (name C11 or name C12 or na \ me C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 o \ r name C20 or name O11 or name O3 )) or (resid 506 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C3 or name O11 or name O3 )))) selection = (chain 'C' and (resid 10 through 415 or (resid 502 and (name C1 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C20 or name C21 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name O11 or name O1P or name O2 or name O2P or name O3 or n \ ame O31 or name O3P or name O4P or name P )) or (resid 503 and (name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or \ name C19 or name C20 or name C21)) or (resid 505 and (name C11 or name C12 or na \ me C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 o \ r name C20 or name O11 or name O3 )) or (resid 506 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C3 or name O11 or name O3 )))) selection = (chain 'D' and (resid 10 through 415 or (resid 502 and (name C1 or name C11 or n \ ame C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C20 or name C21 or name C3 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name O11 or name O1P or name O2 or name O2P or name O3 or n \ ame O31 or name O3P or name O4P or name P )) or (resid 503 and (name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or \ name C19 or name C20 or name C21)) or (resid 505 and (name C11 or name C12 or na \ me C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 o \ r name C20 or name O11 or name O3 )) or (resid 506 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C3 or name O11 or name O3 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 32.140 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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 : 0.007 0.142 13672 Z= 0.449 Angle : 0.924 9.732 18508 Z= 0.478 Chirality : 0.047 0.179 2144 Planarity : 0.008 0.117 2248 Dihedral : 17.212 129.419 5296 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.59 % Allowed : 12.61 % Favored : 86.80 % 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: 1.65 (0.22), residues: 1584 helix: 1.32 (0.17), residues: 968 sheet: 1.05 (0.58), residues: 88 loop : 0.92 (0.30), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 264 HIS 0.003 0.001 HIS D 281 PHE 0.013 0.001 PHE C 397 TYR 0.015 0.002 TYR B 186 ARG 0.010 0.001 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 394 LYS cc_start: 0.8543 (tttt) cc_final: 0.8325 (ttmt) outliers start: 8 outliers final: 3 residues processed: 132 average time/residue: 1.3626 time to fit residues: 196.9522 Evaluate side-chains 98 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain D residue 116 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13672 Z= 0.291 Angle : 0.699 8.577 18508 Z= 0.334 Chirality : 0.042 0.138 2144 Planarity : 0.005 0.060 2248 Dihedral : 15.884 131.872 2310 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.42 % Allowed : 11.29 % Favored : 86.29 % 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: 1.99 (0.21), residues: 1584 helix: 1.60 (0.16), residues: 996 sheet: 0.62 (0.55), residues: 88 loop : 1.13 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 176 HIS 0.003 0.001 HIS B 149 PHE 0.012 0.001 PHE D 242 TYR 0.013 0.002 TYR D 170 ARG 0.007 0.001 ARG D 111 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 120 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: A 290 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8544 (tt0) REVERT: B 237 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8032 (mp0) REVERT: B 394 LYS cc_start: 0.8668 (tttt) cc_final: 0.7939 (ttmt) REVERT: C 47 ASP cc_start: 0.8787 (t0) cc_final: 0.8444 (t0) REVERT: C 237 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8057 (mp0) outliers start: 33 outliers final: 8 residues processed: 146 average time/residue: 1.2068 time to fit residues: 194.3541 Evaluate side-chains 118 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 116 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 chunk 120 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 145 optimal weight: 0.7980 chunk 157 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13672 Z= 0.205 Angle : 0.625 8.874 18508 Z= 0.299 Chirality : 0.040 0.131 2144 Planarity : 0.005 0.053 2248 Dihedral : 14.899 132.732 2310 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.69 % Allowed : 11.80 % Favored : 86.51 % 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: 2.40 (0.21), residues: 1584 helix: 1.91 (0.16), residues: 976 sheet: 1.16 (0.53), residues: 92 loop : 1.28 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 176 HIS 0.003 0.001 HIS D 99 PHE 0.010 0.001 PHE C 242 TYR 0.011 0.001 TYR D 170 ARG 0.004 0.001 ARG D 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7973 (mp0) REVERT: B 237 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8001 (mp0) REVERT: C 47 ASP cc_start: 0.8758 (t0) cc_final: 0.8420 (t0) REVERT: C 237 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: D 47 ASP cc_start: 0.8789 (t0) cc_final: 0.8449 (t0) REVERT: D 237 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7978 (mp0) outliers start: 23 outliers final: 8 residues processed: 135 average time/residue: 1.2406 time to fit residues: 184.2329 Evaluate side-chains 115 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 237 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 69 optimal weight: 0.4980 chunk 97 optimal weight: 0.5980 chunk 146 optimal weight: 0.0670 chunk 154 optimal weight: 0.2980 chunk 76 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13672 Z= 0.157 Angle : 0.624 9.558 18508 Z= 0.290 Chirality : 0.039 0.127 2144 Planarity : 0.005 0.045 2248 Dihedral : 14.076 133.352 2308 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.86 % Allowed : 10.85 % Favored : 86.29 % 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: 2.61 (0.21), residues: 1584 helix: 2.14 (0.16), residues: 980 sheet: 1.11 (0.55), residues: 92 loop : 1.23 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 176 HIS 0.003 0.001 HIS D 99 PHE 0.008 0.001 PHE C 242 TYR 0.010 0.001 TYR C 259 ARG 0.004 0.000 ARG D 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 111 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8786 (t0) cc_final: 0.8509 (t0) REVERT: A 237 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: A 368 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8722 (pm20) REVERT: B 237 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7961 (mp0) REVERT: B 368 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8534 (pm20) REVERT: C 47 ASP cc_start: 0.8715 (t0) cc_final: 0.8397 (t0) REVERT: C 237 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: C 368 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8562 (pm20) REVERT: D 47 ASP cc_start: 0.8771 (t0) cc_final: 0.8471 (t0) REVERT: D 237 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: D 368 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8570 (pm20) outliers start: 39 outliers final: 7 residues processed: 147 average time/residue: 1.4507 time to fit residues: 232.6006 Evaluate side-chains 121 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 368 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 2 optimal weight: 0.0020 chunk 115 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 106 optimal weight: 0.0970 chunk 0 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13672 Z= 0.187 Angle : 0.638 9.980 18508 Z= 0.300 Chirality : 0.040 0.158 2144 Planarity : 0.005 0.052 2248 Dihedral : 13.774 133.254 2304 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.27 % Allowed : 11.44 % Favored : 86.29 % 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: 2.58 (0.21), residues: 1584 helix: 2.16 (0.16), residues: 984 sheet: 1.15 (0.55), residues: 92 loop : 1.09 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 176 HIS 0.003 0.001 HIS C 99 PHE 0.008 0.001 PHE D 242 TYR 0.031 0.002 TYR B 25 ARG 0.013 0.001 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7972 (mp0) REVERT: A 368 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8351 (pm20) REVERT: A 369 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8382 (mpp) REVERT: B 237 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: B 368 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8327 (pm20) REVERT: B 369 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8322 (mpp) REVERT: C 237 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: C 368 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8356 (pm20) REVERT: C 369 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8401 (mpp) REVERT: D 47 ASP cc_start: 0.8715 (t0) cc_final: 0.8135 (m-30) REVERT: D 237 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7906 (mp0) REVERT: D 368 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8557 (pm20) outliers start: 31 outliers final: 2 residues processed: 143 average time/residue: 1.3272 time to fit residues: 207.8359 Evaluate side-chains 116 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 368 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 154 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 ASN C 217 ASN D 217 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13672 Z= 0.262 Angle : 0.667 13.106 18508 Z= 0.312 Chirality : 0.041 0.160 2144 Planarity : 0.005 0.050 2248 Dihedral : 13.888 132.482 2304 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.01 % Allowed : 11.29 % Favored : 85.70 % 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: 2.51 (0.21), residues: 1584 helix: 2.13 (0.17), residues: 996 sheet: 1.11 (0.55), residues: 92 loop : 0.97 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 176 HIS 0.003 0.001 HIS D 281 PHE 0.011 0.001 PHE C 242 TYR 0.025 0.002 TYR B 26 ARG 0.009 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 117 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8786 (t0) cc_final: 0.8144 (m-30) REVERT: A 100 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9051 (pp) REVERT: A 128 TYR cc_start: 0.7615 (p90) cc_final: 0.7328 (p90) REVERT: A 237 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7949 (mp0) REVERT: A 368 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8680 (pm20) REVERT: B 100 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9064 (pp) REVERT: B 237 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7959 (mp0) REVERT: B 368 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8447 (pm20) REVERT: B 369 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8389 (mpp) REVERT: C 47 ASP cc_start: 0.8726 (t0) cc_final: 0.8434 (t0) REVERT: C 100 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9037 (pp) REVERT: C 237 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7984 (mp0) REVERT: C 368 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8539 (pm20) REVERT: C 369 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8459 (mpp) REVERT: D 47 ASP cc_start: 0.8807 (t0) cc_final: 0.8192 (m-30) REVERT: D 100 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9045 (pp) REVERT: D 237 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: D 368 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8520 (pm20) outliers start: 41 outliers final: 3 residues processed: 154 average time/residue: 1.2414 time to fit residues: 210.5061 Evaluate side-chains 126 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 368 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 4.9990 chunk 17 optimal weight: 0.0050 chunk 88 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 154 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13672 Z= 0.199 Angle : 0.657 11.759 18508 Z= 0.305 Chirality : 0.040 0.195 2144 Planarity : 0.004 0.041 2248 Dihedral : 13.728 132.828 2304 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.01 % Allowed : 12.17 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.21), residues: 1584 helix: 2.23 (0.16), residues: 980 sheet: 1.12 (0.55), residues: 92 loop : 1.05 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 176 HIS 0.002 0.001 HIS D 281 PHE 0.009 0.001 PHE B 302 TYR 0.018 0.001 TYR B 26 ARG 0.012 0.000 ARG B 374 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 116 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8789 (t0) cc_final: 0.8105 (m-30) REVERT: A 100 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9032 (pp) REVERT: A 128 TYR cc_start: 0.7665 (p90) cc_final: 0.7332 (p90) REVERT: A 237 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7926 (mp0) REVERT: A 368 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8537 (pm20) REVERT: A 369 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8446 (mpp) REVERT: B 100 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9038 (pp) REVERT: B 128 TYR cc_start: 0.7776 (p90) cc_final: 0.7517 (p90) REVERT: B 237 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: B 368 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8640 (pm20) REVERT: C 47 ASP cc_start: 0.8691 (t0) cc_final: 0.8403 (t0) REVERT: C 100 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9037 (pp) REVERT: C 128 TYR cc_start: 0.7752 (p90) cc_final: 0.7504 (p90) REVERT: C 237 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7974 (mp0) REVERT: C 368 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8535 (pm20) REVERT: C 369 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8434 (mpp) REVERT: C 371 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8860 (mt) REVERT: C 394 LYS cc_start: 0.8649 (tttt) cc_final: 0.7905 (tptt) REVERT: D 47 ASP cc_start: 0.8806 (t0) cc_final: 0.8219 (m-30) REVERT: D 100 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9036 (pp) REVERT: D 128 TYR cc_start: 0.7762 (p90) cc_final: 0.7498 (p90) REVERT: D 237 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: D 368 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8515 (pm20) outliers start: 41 outliers final: 9 residues processed: 151 average time/residue: 1.3423 time to fit residues: 222.2464 Evaluate side-chains 132 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 368 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-5477/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-5477/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-5477/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-5477/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-5477/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-5477/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-5477/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-5477/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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-5477/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-5477/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.924 > 50: distance: 19 - 24: 13.730 distance: 24 - 25: 13.482 distance: 25 - 26: 8.148 distance: 25 - 28: 21.336 distance: 26 - 27: 18.829 distance: 26 - 31: 34.400 distance: 28 - 29: 20.177 distance: 28 - 30: 22.021 distance: 31 - 32: 10.712 distance: 32 - 33: 12.189 distance: 32 - 35: 13.200 distance: 33 - 34: 15.858 distance: 33 - 39: 3.755 distance: 35 - 36: 11.642 distance: 36 - 37: 14.550 distance: 36 - 38: 8.859 distance: 39 - 40: 5.724 distance: 40 - 41: 3.810 distance: 40 - 43: 3.102 distance: 41 - 42: 4.095 distance: 41 - 47: 7.480 distance: 43 - 44: 5.207 distance: 44 - 45: 9.094 distance: 44 - 46: 4.087 distance: 48 - 49: 3.359 distance: 48 - 51: 7.307 distance: 49 - 50: 5.731 distance: 49 - 52: 15.966 distance: 52 - 53: 8.105 distance: 52 - 58: 5.318 distance: 53 - 54: 17.001 distance: 53 - 56: 7.899 distance: 54 - 55: 3.907 distance: 54 - 59: 10.779 distance: 56 - 57: 6.429 distance: 57 - 58: 7.508 distance: 59 - 60: 4.347 distance: 60 - 61: 4.859 distance: 60 - 63: 6.856 distance: 61 - 62: 21.001 distance: 61 - 65: 9.328 distance: 63 - 64: 13.207 distance: 65 - 66: 8.840 distance: 66 - 67: 9.212 distance: 66 - 69: 9.113 distance: 67 - 68: 13.932 distance: 67 - 76: 5.278 distance: 68 - 99: 9.333 distance: 69 - 70: 3.957 distance: 70 - 71: 4.387 distance: 71 - 72: 6.287 distance: 72 - 73: 3.900 distance: 76 - 77: 5.895 distance: 77 - 78: 19.017 distance: 77 - 80: 17.288 distance: 78 - 79: 7.927 distance: 78 - 84: 13.459 distance: 79 - 107: 8.565 distance: 80 - 81: 4.818 distance: 81 - 82: 9.936 distance: 81 - 83: 9.518 distance: 84 - 85: 6.579 distance: 84 - 90: 9.163 distance: 85 - 86: 13.689 distance: 85 - 88: 8.511 distance: 86 - 87: 17.371 distance: 86 - 91: 18.776 distance: 87 - 114: 25.812 distance: 88 - 89: 13.009 distance: 89 - 90: 5.491 distance: 91 - 92: 7.647 distance: 92 - 93: 9.895 distance: 92 - 95: 9.130 distance: 93 - 94: 10.346 distance: 93 - 99: 9.619 distance: 95 - 96: 12.728 distance: 96 - 97: 13.927 distance: 96 - 98: 15.070