Starting phenix.real_space_refine on Sun Jan 19 07:02:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vtb_43522/01_2025/8vtb_43522_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vtb_43522/01_2025/8vtb_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/cci-nas-00/data/ceres_data/8vtb_43522/01_2025/8vtb_43522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vtb_43522/01_2025/8vtb_43522.map" model { file = "/net/cci-nas-00/data/ceres_data/8vtb_43522/01_2025/8vtb_43522_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vtb_43522/01_2025/8vtb_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-5571/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: 8.59, per 1000 atoms: 0.64 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: 3.48 Conformation dependent library (CDL) restraints added in 1.7 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: 1.37 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: 4.39 Time building geometry restraints manager: 3.97 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.270 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.060 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:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.300 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 1.437 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: 1.3213 time to fit residues: 191.1497 Evaluate side-chains 98 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 1.519 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.118482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.073636 restraints weight = 22292.347| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.56 r_work: 0.2747 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 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 to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 1.447 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: 0.8521 (OUTLIER) cc_final: 0.8194 (mp0) REVERT: A 290 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8537 (tt0) REVERT: B 237 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8188 (mp0) REVERT: B 290 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8691 (tt0) REVERT: B 394 LYS cc_start: 0.8453 (tttt) cc_final: 0.7775 (ttmt) REVERT: C 47 ASP cc_start: 0.8943 (t0) cc_final: 0.8582 (t0) REVERT: C 237 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8294 (mp0) REVERT: C 290 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8595 (tt0) REVERT: D 290 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8650 (tt0) outliers start: 33 outliers final: 8 residues processed: 146 average time/residue: 1.2244 time to fit residues: 197.0901 Evaluate side-chains 120 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 1.618 ------------------------------------------------------------------------------- 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 B residue 290 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 C residue 290 GLU Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 290 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 chunk 82 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.119539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.074687 restraints weight = 22483.624| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.58 r_work: 0.2771 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13672 Z= 0.196 Angle : 0.622 8.984 18508 Z= 0.298 Chirality : 0.040 0.132 2144 Planarity : 0.005 0.052 2248 Dihedral : 14.880 132.887 2310 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.61 % Allowed : 11.88 % 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: 2.41 (0.21), residues: 1584 helix: 1.94 (0.16), residues: 976 sheet: 1.13 (0.53), residues: 92 loop : 1.25 (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 399 *********************** 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 140 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 1.479 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: 0.8332 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: B 237 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7939 (mp0) REVERT: C 47 ASP cc_start: 0.8806 (t0) cc_final: 0.8435 (t0) REVERT: C 237 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: D 47 ASP cc_start: 0.8852 (t0) cc_final: 0.8491 (t0) REVERT: D 237 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7968 (mp0) outliers start: 22 outliers final: 8 residues processed: 134 average time/residue: 1.2500 time to fit residues: 184.6333 Evaluate side-chains 113 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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 114 optimal weight: 0.9980 chunk 136 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 146 optimal weight: 0.0060 chunk 95 optimal weight: 0.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.119528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.074767 restraints weight = 22198.864| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.57 r_work: 0.2770 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1649 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= 0.188 Angle : 0.626 9.498 18508 Z= 0.292 Chirality : 0.039 0.152 2144 Planarity : 0.005 0.044 2248 Dihedral : 14.236 133.113 2308 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.45 % Allowed : 10.19 % Favored : 86.36 % 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: 2.53 (0.21), residues: 1584 helix: 2.10 (0.16), residues: 984 sheet: 1.06 (0.54), residues: 92 loop : 1.14 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 176 HIS 0.003 0.001 HIS A 99 PHE 0.009 0.001 PHE D 242 TYR 0.012 0.001 TYR A 128 ARG 0.009 0.000 ARG A 129 *********************** 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 162 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 115 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: A 290 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8654 (tt0) REVERT: A 368 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8443 (pm20) REVERT: A 374 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8096 (mmm160) REVERT: B 237 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8141 (mp0) REVERT: B 290 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8689 (tt0) REVERT: B 368 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.7983 (pm20) REVERT: B 369 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.7954 (mpp) REVERT: B 374 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8186 (mmm160) REVERT: C 47 ASP cc_start: 0.8846 (t0) cc_final: 0.8488 (t0) REVERT: C 237 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8156 (mp0) REVERT: C 290 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8583 (tt0) REVERT: C 368 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8291 (pm20) REVERT: C 374 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8065 (mmm160) REVERT: D 47 ASP cc_start: 0.8906 (t0) cc_final: 0.8600 (t0) REVERT: D 237 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: D 290 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8677 (tt0) REVERT: D 334 MET cc_start: 0.9026 (tpp) cc_final: 0.8720 (mmm) REVERT: D 368 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8277 (pm20) REVERT: D 374 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8183 (mmm160) outliers start: 47 outliers final: 5 residues processed: 157 average time/residue: 1.4015 time to fit residues: 239.4541 Evaluate side-chains 130 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 374 ARG 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 290 GLU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 290 GLU Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain D residue 374 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 106 optimal weight: 0.0070 chunk 151 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 51 optimal weight: 0.0870 chunk 63 optimal weight: 0.0470 chunk 116 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 156 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 overall best weight: 0.3474 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.120121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.075703 restraints weight = 22183.416| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.57 r_work: 0.2795 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13672 Z= 0.162 Angle : 0.627 10.194 18508 Z= 0.294 Chirality : 0.039 0.154 2144 Planarity : 0.005 0.048 2248 Dihedral : 13.793 133.378 2304 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.49 % Allowed : 12.10 % Favored : 85.41 % 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: 2.59 (0.21), residues: 1584 helix: 2.19 (0.16), residues: 984 sheet: 1.11 (0.55), residues: 92 loop : 1.07 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 176 HIS 0.003 0.001 HIS C 99 PHE 0.007 0.001 PHE C 242 TYR 0.035 0.001 TYR B 25 ARG 0.014 0.000 ARG B 111 *********************** 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 149 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 1.481 Fit side-chains revert: symmetry clash REVERT: A 237 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7861 (mp0) REVERT: A 368 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.7998 (pm20) REVERT: A 369 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.7896 (mpp) REVERT: A 374 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.8043 (mmm160) REVERT: A 394 LYS cc_start: 0.8527 (tttt) cc_final: 0.7899 (tptt) REVERT: B 237 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: B 368 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.7939 (pm20) REVERT: B 369 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7880 (mpp) REVERT: B 374 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8140 (mmm160) REVERT: C 47 ASP cc_start: 0.8772 (t0) cc_final: 0.8407 (t0) REVERT: C 237 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: C 290 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8514 (tt0) REVERT: C 368 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8005 (pm20) REVERT: C 369 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.7914 (mpp) REVERT: C 374 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.8062 (mmm160) REVERT: C 394 LYS cc_start: 0.8572 (tttt) cc_final: 0.8011 (tptt) REVERT: D 47 ASP cc_start: 0.8832 (t0) cc_final: 0.8007 (m-30) REVERT: D 237 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7857 (mp0) REVERT: D 334 MET cc_start: 0.8960 (tpp) cc_final: 0.8620 (mmm) REVERT: D 368 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8227 (pm20) REVERT: D 374 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8157 (mmm160) REVERT: D 394 LYS cc_start: 0.8451 (tttt) cc_final: 0.7783 (tptt) outliers start: 34 outliers final: 3 residues processed: 145 average time/residue: 1.4964 time to fit residues: 235.4262 Evaluate side-chains 123 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR 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 A residue 369 MET Chi-restraints excluded: chain A residue 374 ARG 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 B residue 374 ARG Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain D residue 374 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 70 optimal weight: 0.1980 chunk 41 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 106 optimal weight: 0.0980 chunk 79 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.120044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.075494 restraints weight = 22449.892| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.58 r_work: 0.2791 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13672 Z= 0.178 Angle : 0.642 12.939 18508 Z= 0.298 Chirality : 0.040 0.190 2144 Planarity : 0.004 0.043 2248 Dihedral : 13.634 133.270 2304 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % 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: 2.66 (0.21), residues: 1584 helix: 2.25 (0.16), residues: 984 sheet: 1.11 (0.55), residues: 92 loop : 1.09 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 176 HIS 0.002 0.001 HIS C 99 PHE 0.008 0.001 PHE C 242 TYR 0.034 0.002 TYR D 26 ARG 0.002 0.000 ARG A 111 *********************** 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 155 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8890 (pp) REVERT: A 128 TYR cc_start: 0.7828 (p90) cc_final: 0.7499 (p90) REVERT: A 237 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7838 (mp0) REVERT: A 368 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8138 (pm20) REVERT: A 369 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.7947 (mpp) REVERT: A 374 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.8074 (mmm160) REVERT: A 394 LYS cc_start: 0.8474 (tttt) cc_final: 0.7801 (tptt) REVERT: B 100 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8890 (pp) REVERT: B 237 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7867 (mp0) REVERT: B 368 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.7900 (pm20) REVERT: B 369 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.7841 (mpp) REVERT: B 374 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8178 (mmm160) REVERT: C 47 ASP cc_start: 0.8776 (t0) cc_final: 0.8431 (t0) REVERT: C 100 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8889 (pp) REVERT: C 237 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7861 (mp0) REVERT: C 290 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8492 (tt0) REVERT: C 368 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.7969 (pm20) REVERT: C 369 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.7891 (mpp) REVERT: C 374 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.8060 (mmm160) REVERT: C 394 LYS cc_start: 0.8506 (tttt) cc_final: 0.7835 (tptt) REVERT: D 47 ASP cc_start: 0.8769 (t0) cc_final: 0.7969 (m-30) REVERT: D 100 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8887 (pp) REVERT: D 237 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: D 334 MET cc_start: 0.8964 (tpp) cc_final: 0.8634 (mmm) REVERT: D 368 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8218 (pm20) REVERT: D 374 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8108 (mmm160) outliers start: 41 outliers final: 5 residues processed: 150 average time/residue: 1.4042 time to fit residues: 229.0989 Evaluate side-chains 132 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 1.447 ------------------------------------------------------------------------------- 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 A residue 369 MET Chi-restraints excluded: chain A residue 374 ARG 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 B residue 374 ARG Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain D residue 26 TYR 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 Chi-restraints excluded: chain D residue 374 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 152 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.117230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.072025 restraints weight = 22391.591| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.57 r_work: 0.2716 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13672 Z= 0.363 Angle : 0.700 11.445 18508 Z= 0.331 Chirality : 0.043 0.206 2144 Planarity : 0.005 0.043 2248 Dihedral : 14.110 131.837 2304 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.96 % Allowed : 11.44 % Favored : 84.60 % 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: 2.36 (0.21), residues: 1584 helix: 2.05 (0.16), residues: 996 sheet: 0.71 (0.55), residues: 88 loop : 0.90 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 264 HIS 0.004 0.002 HIS D 281 PHE 0.013 0.001 PHE D 242 TYR 0.031 0.002 TYR B 26 ARG 0.004 0.000 ARG B 111 *********************** 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 173 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 119 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8887 (t0) cc_final: 0.8075 (m-30) REVERT: A 100 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8834 (pp) REVERT: A 128 TYR cc_start: 0.8012 (p90) cc_final: 0.7628 (p90) REVERT: A 237 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8091 (mp0) REVERT: A 334 MET cc_start: 0.9017 (tpp) cc_final: 0.8687 (mmp) REVERT: A 368 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8373 (pm20) REVERT: A 374 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8090 (mmm160) REVERT: B 100 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8797 (pp) REVERT: B 128 TYR cc_start: 0.8028 (p90) cc_final: 0.7665 (p90) REVERT: B 237 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: B 368 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8342 (pm20) REVERT: B 374 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8243 (mmm160) REVERT: B 394 LYS cc_start: 0.8362 (tttt) cc_final: 0.7674 (tttt) REVERT: C 47 ASP cc_start: 0.8865 (t0) cc_final: 0.8576 (t0) REVERT: C 100 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8838 (pp) REVERT: C 128 TYR cc_start: 0.8094 (p90) cc_final: 0.7798 (p90) REVERT: C 237 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8125 (mp0) REVERT: C 334 MET cc_start: 0.9037 (tpp) cc_final: 0.8396 (mmp) REVERT: C 368 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8391 (pm20) REVERT: C 374 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8248 (tpt170) REVERT: D 100 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8792 (pp) REVERT: D 128 TYR cc_start: 0.8073 (p90) cc_final: 0.7736 (p90) REVERT: D 237 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8075 (mp0) REVERT: D 334 MET cc_start: 0.9002 (tpp) cc_final: 0.8605 (mmm) REVERT: D 368 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8374 (pm20) REVERT: D 374 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8227 (mmm160) outliers start: 54 outliers final: 9 residues processed: 167 average time/residue: 1.3589 time to fit residues: 249.5849 Evaluate side-chains 136 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 1.581 ------------------------------------------------------------------------------- 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 125 ILE Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 374 ARG 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 374 ARG Chi-restraints excluded: chain C residue 89 LEU 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 374 ARG Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain D residue 374 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 126 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 17 optimal weight: 0.0980 chunk 32 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 84 optimal weight: 0.9990 chunk 145 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.118565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.073491 restraints weight = 22485.374| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.58 r_work: 0.2742 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13672 Z= 0.230 Angle : 0.697 12.033 18508 Z= 0.320 Chirality : 0.041 0.225 2144 Planarity : 0.004 0.049 2248 Dihedral : 14.005 132.412 2304 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.42 % Allowed : 13.42 % Favored : 84.16 % 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: 2.44 (0.21), residues: 1584 helix: 2.13 (0.16), residues: 996 sheet: 0.75 (0.56), residues: 88 loop : 0.89 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 264 HIS 0.003 0.001 HIS A 281 PHE 0.010 0.001 PHE C 242 TYR 0.017 0.001 TYR B 26 ARG 0.006 0.000 ARG B 111 *********************** REFINEMENT MACRO_CYCLE 8 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 145 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8880 (pp) REVERT: A 237 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: A 368 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8305 (pm20) REVERT: A 374 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8077 (mmm160) REVERT: B 16 LYS cc_start: 0.8332 (mmmm) cc_final: 0.8052 (mmpt) REVERT: B 100 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8870 (pp) REVERT: B 128 TYR cc_start: 0.7982 (p90) cc_final: 0.7636 (p90) REVERT: B 237 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: B 334 MET cc_start: 0.8949 (tpp) cc_final: 0.8570 (mmp) REVERT: B 368 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8206 (pm20) REVERT: B 374 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8119 (mmm160) REVERT: C 47 ASP cc_start: 0.8773 (t0) cc_final: 0.8469 (t0) REVERT: C 100 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8889 (pp) REVERT: C 128 TYR cc_start: 0.7982 (p90) cc_final: 0.7728 (p90) REVERT: C 237 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7873 (mp0) REVERT: C 368 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8323 (pm20) REVERT: C 374 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8061 (mmm160) REVERT: D 100 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8862 (pp) REVERT: D 128 TYR cc_start: 0.8016 (p90) cc_final: 0.7696 (p90) REVERT: D 237 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: D 334 MET cc_start: 0.8992 (tpp) cc_final: 0.8597 (mmm) REVERT: D 368 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8317 (pm20) REVERT: D 374 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8179 (mmm160) outliers start: 33 outliers final: 8 residues processed: 143 average time/residue: 1.3690 time to fit residues: 213.7332 Evaluate side-chains 134 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU 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 374 ARG 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 B residue 374 ARG 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 237 GLU Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain D residue 85 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 Chi-restraints excluded: chain D residue 374 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 76 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 118 optimal weight: 0.0980 chunk 72 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 69 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.118926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.073973 restraints weight = 22233.617| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.57 r_work: 0.2757 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13672 Z= 0.208 Angle : 0.694 14.018 18508 Z= 0.320 Chirality : 0.041 0.228 2144 Planarity : 0.004 0.049 2248 Dihedral : 13.868 132.724 2304 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.05 % Allowed : 13.86 % Favored : 84.09 % 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: 2.59 (0.21), residues: 1584 helix: 2.25 (0.16), residues: 972 sheet: 1.04 (0.55), residues: 92 loop : 0.96 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 176 HIS 0.002 0.001 HIS A 281 PHE 0.009 0.001 PHE C 242 TYR 0.012 0.001 TYR A 128 ARG 0.006 0.000 ARG B 111 *********************** REFINEMENT MACRO_CYCLE 9 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 140 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8870 (t0) cc_final: 0.8075 (m-30) REVERT: A 100 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8813 (pp) REVERT: A 237 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: A 334 MET cc_start: 0.9008 (tpp) cc_final: 0.8749 (mmp) REVERT: A 368 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8380 (pm20) REVERT: A 374 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8121 (mmm160) REVERT: B 16 LYS cc_start: 0.8358 (mmmm) cc_final: 0.8043 (mmpt) REVERT: B 100 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8783 (pp) REVERT: B 128 TYR cc_start: 0.8052 (p90) cc_final: 0.7701 (p90) REVERT: B 237 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: B 334 MET cc_start: 0.9047 (tpp) cc_final: 0.8811 (mmp) REVERT: B 368 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8268 (pm20) REVERT: B 374 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8187 (mmm160) REVERT: C 47 ASP cc_start: 0.8815 (t0) cc_final: 0.8524 (t0) REVERT: C 100 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8814 (pp) REVERT: C 128 TYR cc_start: 0.8081 (p90) cc_final: 0.7768 (p90) REVERT: C 237 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: C 334 MET cc_start: 0.8992 (tpp) cc_final: 0.8735 (mmp) REVERT: C 368 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8394 (pm20) REVERT: C 374 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8094 (mmm160) REVERT: D 47 ASP cc_start: 0.8943 (t0) cc_final: 0.8108 (m-30) REVERT: D 100 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8767 (pp) REVERT: D 128 TYR cc_start: 0.8089 (p90) cc_final: 0.7731 (p90) REVERT: D 237 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: D 334 MET cc_start: 0.9046 (tpp) cc_final: 0.8634 (mmm) REVERT: D 368 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8374 (pm20) REVERT: D 374 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8187 (mmm160) outliers start: 28 outliers final: 8 residues processed: 138 average time/residue: 1.4196 time to fit residues: 212.8824 Evaluate side-chains 132 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 85 LEU 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 374 ARG 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 B residue 374 ARG 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 237 GLU Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 368 GLU Chi-restraints excluded: chain D residue 374 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 116 optimal weight: 0.0980 chunk 131 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.119019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.074093 restraints weight = 22248.768| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.56 r_work: 0.2761 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13672 Z= 0.214 Angle : 0.692 12.638 18508 Z= 0.320 Chirality : 0.041 0.227 2144 Planarity : 0.004 0.047 2248 Dihedral : 13.781 132.710 2304 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.91 % Allowed : 14.00 % Favored : 84.09 % 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: 2.59 (0.21), residues: 1584 helix: 2.23 (0.16), residues: 976 sheet: 1.04 (0.55), residues: 92 loop : 0.98 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 176 HIS 0.002 0.001 HIS D 281 PHE 0.009 0.001 PHE C 242 TYR 0.011 0.001 TYR A 128 ARG 0.004 0.000 ARG B 111 ********************** REFINEMENT MACRO_CYCLE 10 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 131 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8826 (pp) REVERT: A 237 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: A 334 MET cc_start: 0.9040 (tpp) cc_final: 0.8768 (mmp) REVERT: A 368 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8382 (pm20) REVERT: A 374 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8115 (mmm160) REVERT: B 100 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8772 (pp) REVERT: B 128 TYR cc_start: 0.8039 (p90) cc_final: 0.7681 (p90) REVERT: B 237 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: B 334 MET cc_start: 0.9047 (tpp) cc_final: 0.8786 (mmp) REVERT: B 368 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8329 (pm20) REVERT: B 374 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8180 (mmm160) REVERT: C 47 ASP cc_start: 0.8819 (t0) cc_final: 0.8513 (t0) REVERT: C 100 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8805 (pp) REVERT: C 128 TYR cc_start: 0.8103 (p90) cc_final: 0.7788 (p90) REVERT: C 237 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: C 334 MET cc_start: 0.9015 (tpp) cc_final: 0.8712 (mmp) REVERT: C 368 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8391 (pm20) REVERT: C 374 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8108 (mmm160) REVERT: D 47 ASP cc_start: 0.8943 (t0) cc_final: 0.8005 (m-30) REVERT: D 100 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8759 (pp) REVERT: D 237 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: D 334 MET cc_start: 0.9035 (tpp) cc_final: 0.8610 (mmm) REVERT: D 368 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8377 (pm20) REVERT: D 374 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8187 (mmm160) REVERT: D 394 LYS cc_start: 0.8403 (tttt) cc_final: 0.7701 (tptt) outliers start: 26 outliers final: 8 residues processed: 129 average time/residue: 1.4808 time to fit residues: 207.3632 Evaluate side-chains 127 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 94 LEU 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 A residue 374 ARG 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 B residue 374 ARG 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 237 GLU Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 374 ARG 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 Chi-restraints excluded: chain D residue 374 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 87 optimal weight: 6.9990 chunk 137 optimal weight: 0.0270 chunk 77 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 overall best weight: 1.0840 ------------------------------------------------------------------------------- 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 = 0.3816 r_free = 0.3816 target = 0.118704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.073744 restraints weight = 22341.131| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.57 r_work: 0.2751 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13672 Z= 0.239 Angle : 0.693 12.330 18508 Z= 0.321 Chirality : 0.041 0.228 2144 Planarity : 0.004 0.046 2248 Dihedral : 13.808 132.455 2304 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.76 % Allowed : 14.22 % Favored : 84.02 % 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: 2.53 (0.21), residues: 1584 helix: 2.16 (0.16), residues: 1000 sheet: 1.02 (0.55), residues: 92 loop : 0.96 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 176 HIS 0.003 0.001 HIS B 281 PHE 0.009 0.001 PHE C 242 TYR 0.011 0.001 TYR A 128 ARG 0.004 0.000 ARG B 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11135.92 seconds wall clock time: 196 minutes 40.84 seconds (11800.84 seconds total)