Starting phenix.real_space_refine on Thu Jul 31 11:20:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vtb_43522/07_2025/8vtb_43522_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vtb_43522/07_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_43522/07_2025/8vtb_43522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vtb_43522/07_2025/8vtb_43522.map" model { file = "/net/cci-nas-00/data/ceres_data/8vtb_43522/07_2025/8vtb_43522_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vtb_43522/07_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-5711/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: 8.85, per 1000 atoms: 0.66 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: 3.47 Conformation dependent library (CDL) restraints added in 1.6 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: 1.42 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: 3.91 Time building geometry restraints manager: 4.05 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 32.580 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.690 ------------------------------------------------------------------------------- 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= 0.389 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 Details of bonding type rmsd hydrogen bonds : bond 0.11778 ( 836) hydrogen bonds : angle 5.71106 ( 2388) covalent geometry : bond 0.00699 (13672) covalent geometry : angle 0.92430 (18508) *********************** 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 : 1.478 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: 1.2778 time to fit residues: 184.8989 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 : 1.375 ------------------------------------------------------------------------------- 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 = 49)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.073649 restraints weight = 22292.334| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.55 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= 0.190 Angle : 0.699 8.577 18508 Z= 0.334 Chirality : 0.042 0.138 2144 Planarity : 0.005 0.060 2248 Dihedral : 15.884 131.871 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 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 836) hydrogen bonds : angle 4.32177 ( 2388) covalent geometry : bond 0.00451 (13672) covalent geometry : angle 0.69878 (18508) *********************** 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 : 2.048 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: 0.8520 (OUTLIER) cc_final: 0.8192 (mp0) REVERT: A 290 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8538 (tt0) REVERT: B 237 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: B 290 GLU cc_start: 0.8905 (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: 0.8862 (OUTLIER) cc_final: 0.8597 (tt0) REVERT: D 290 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8651 (tt0) outliers start: 33 outliers final: 8 residues processed: 146 average time/residue: 1.5746 time to fit residues: 255.1219 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 : 2.029 ------------------------------------------------------------------------------- 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: 4.9990 chunk 112 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 110 optimal weight: 0.4980 chunk 82 optimal weight: 0.0570 chunk 122 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- 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 = 0.119369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.075125 restraints weight = 22401.232| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.53 r_work: 0.2778 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13672 Z= 0.132 Angle : 0.620 8.897 18508 Z= 0.297 Chirality : 0.040 0.128 2144 Planarity : 0.005 0.055 2248 Dihedral : 14.809 132.611 2310 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.54 % Allowed : 11.80 % Favored : 86.66 % 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: 2.43 (0.21), residues: 1584 helix: 1.94 (0.16), residues: 976 sheet: 1.16 (0.54), residues: 92 loop : 1.26 (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 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 836) hydrogen bonds : angle 4.02248 ( 2388) covalent geometry : bond 0.00294 (13672) covalent geometry : angle 0.61962 (18508) *********************** 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 139 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 1.665 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: 0.8526 (OUTLIER) cc_final: 0.8133 (mp0) REVERT: B 237 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8162 (mp0) REVERT: C 47 ASP cc_start: 0.8883 (t0) cc_final: 0.8527 (t0) REVERT: C 237 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8157 (mp0) REVERT: D 47 ASP cc_start: 0.8915 (t0) cc_final: 0.8577 (t0) REVERT: D 237 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8167 (mp0) outliers start: 21 outliers final: 7 residues processed: 134 average time/residue: 1.5957 time to fit residues: 235.0152 Evaluate side-chains 112 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 1.578 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 136 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 152 optimal weight: 5.9990 chunk 146 optimal weight: 0.0040 chunk 95 optimal weight: 0.9980 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.119566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.077466 restraints weight = 22191.385| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.70 r_work: 0.2768 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13672 Z= 0.129 Angle : 0.630 9.329 18508 Z= 0.293 Chirality : 0.039 0.147 2144 Planarity : 0.005 0.045 2248 Dihedral : 14.153 133.141 2308 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.30 % Allowed : 10.48 % Favored : 86.22 % 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: 2.60 (0.21), residues: 1584 helix: 2.15 (0.16), residues: 980 sheet: 1.07 (0.55), residues: 92 loop : 1.20 (0.29), residues: 512 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 C 242 TYR 0.010 0.001 TYR D 170 ARG 0.009 0.000 ARG A 129 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 836) hydrogen bonds : angle 3.89254 ( 2388) covalent geometry : bond 0.00289 (13672) covalent geometry : angle 0.62953 (18508) *********************** 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 159 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 114 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8850 (t0) cc_final: 0.8537 (t0) REVERT: A 237 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: A 290 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8540 (tt0) REVERT: A 368 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8398 (pm20) REVERT: A 374 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.8066 (mmm160) REVERT: B 237 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7926 (mp0) REVERT: B 290 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8525 (tt0) REVERT: B 368 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8175 (pm20) REVERT: B 374 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8153 (mmm160) REVERT: C 47 ASP cc_start: 0.8770 (t0) cc_final: 0.8419 (t0) REVERT: C 237 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7922 (mp0) REVERT: C 290 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8483 (tt0) REVERT: C 368 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8250 (pm20) REVERT: C 374 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.8036 (mmm160) REVERT: D 47 ASP cc_start: 0.8832 (t0) cc_final: 0.8507 (t0) REVERT: D 237 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: D 290 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8607 (tt0) REVERT: D 334 MET cc_start: 0.8950 (tpp) cc_final: 0.8677 (mmm) REVERT: D 368 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8269 (pm20) REVERT: D 374 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8153 (mmm160) outliers start: 45 outliers final: 6 residues processed: 156 average time/residue: 1.5208 time to fit residues: 257.5905 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 : 1.373 ------------------------------------------------------------------------------- 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 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 19 ILE 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: 1.9990 chunk 50 optimal weight: 1.9990 chunk 106 optimal weight: 0.0040 chunk 151 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 0.0980 chunk 63 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 156 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.119754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.075170 restraints weight = 22213.318| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.57 r_work: 0.2784 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13672 Z= 0.125 Angle : 0.630 10.339 18508 Z= 0.296 Chirality : 0.040 0.159 2144 Planarity : 0.004 0.051 2248 Dihedral : 13.830 133.223 2304 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.30 % Allowed : 11.00 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.21), residues: 1584 helix: 2.19 (0.16), residues: 984 sheet: 1.13 (0.55), residues: 92 loop : 1.08 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 176 HIS 0.003 0.001 HIS C 99 PHE 0.008 0.001 PHE C 242 TYR 0.031 0.001 TYR B 25 ARG 0.010 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 836) hydrogen bonds : angle 3.88304 ( 2388) covalent geometry : bond 0.00278 (13672) covalent geometry : angle 0.63008 (18508) *********************** 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 160 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 115 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 TYR cc_start: 0.7995 (p90) cc_final: 0.7757 (p90) REVERT: A 237 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7876 (mp0) REVERT: A 290 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8531 (tt0) REVERT: A 368 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8165 (pm20) REVERT: A 369 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8010 (mpp) REVERT: A 374 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8041 (mmm160) REVERT: B 237 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: B 290 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8568 (tt0) REVERT: B 368 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.7907 (pm20) REVERT: B 369 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.7875 (mpp) REVERT: B 374 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8155 (mmm160) REVERT: C 47 ASP cc_start: 0.8772 (t0) cc_final: 0.8414 (t0) REVERT: C 237 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: C 289 MET cc_start: 0.8474 (mmm) cc_final: 0.8216 (mmm) REVERT: C 290 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8457 (tt0) REVERT: C 368 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.7995 (pm20) REVERT: C 369 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.7912 (mpp) REVERT: C 374 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.8075 (mmm160) REVERT: C 394 LYS cc_start: 0.8569 (tttt) cc_final: 0.8002 (tptt) REVERT: D 47 ASP cc_start: 0.8831 (t0) cc_final: 0.7896 (m-30) REVERT: D 237 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: D 290 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8559 (tt0) REVERT: D 334 MET cc_start: 0.8956 (tpp) cc_final: 0.8633 (mmm) REVERT: D 368 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8229 (pm20) REVERT: D 374 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8158 (mmm160) outliers start: 45 outliers final: 3 residues processed: 155 average time/residue: 1.4146 time to fit residues: 239.5615 Evaluate side-chains 128 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 1.447 ------------------------------------------------------------------------------- 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 369 MET Chi-restraints excluded: chain A residue 374 ARG 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 369 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 70 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 106 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.118821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.073808 restraints weight = 22520.490| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.59 r_work: 0.2755 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13672 Z= 0.150 Angle : 0.656 12.528 18508 Z= 0.305 Chirality : 0.040 0.167 2144 Planarity : 0.004 0.046 2248 Dihedral : 13.781 132.701 2304 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.74 % Allowed : 11.73 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.21), residues: 1584 helix: 2.29 (0.16), residues: 972 sheet: 1.13 (0.55), residues: 92 loop : 1.05 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 176 HIS 0.003 0.001 HIS B 281 PHE 0.009 0.001 PHE C 242 TYR 0.022 0.002 TYR B 26 ARG 0.003 0.000 ARG D 111 Details of bonding type rmsd hydrogen bonds : bond 0.03455 ( 836) hydrogen bonds : angle 3.87812 ( 2388) covalent geometry : bond 0.00352 (13672) covalent geometry : angle 0.65647 (18508) *********************** 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 165 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 114 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8842 (t0) cc_final: 0.8047 (m-30) REVERT: A 100 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8903 (pp) REVERT: A 237 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7860 (mp0) REVERT: A 290 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8518 (tt0) REVERT: A 359 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8724 (mt) REVERT: A 368 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8157 (pm20) REVERT: A 369 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8009 (mpp) REVERT: A 374 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8097 (mmm160) REVERT: B 100 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8908 (pp) REVERT: B 237 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7855 (mp0) REVERT: B 290 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8552 (tt0) REVERT: B 368 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8041 (pm20) REVERT: B 369 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.7933 (mpp) REVERT: B 374 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8184 (mmm160) REVERT: C 47 ASP cc_start: 0.8784 (t0) cc_final: 0.8461 (t0) REVERT: C 100 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8905 (pp) REVERT: C 237 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: C 289 MET cc_start: 0.8539 (mmm) cc_final: 0.8291 (mmm) REVERT: C 290 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8484 (tt0) REVERT: C 359 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8757 (mt) REVERT: C 368 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8142 (pm20) REVERT: C 369 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.7994 (mpp) REVERT: C 374 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.8030 (mmm160) REVERT: D 47 ASP cc_start: 0.8849 (t0) cc_final: 0.7923 (m-30) REVERT: D 100 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8877 (pp) REVERT: D 237 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7846 (mp0) REVERT: D 290 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8541 (tt0) REVERT: D 334 MET cc_start: 0.8966 (tpp) cc_final: 0.8617 (mmm) REVERT: D 368 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8187 (pm20) REVERT: D 374 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8189 (mmm160) outliers start: 51 outliers final: 5 residues processed: 159 average time/residue: 1.3932 time to fit residues: 241.1678 Evaluate side-chains 140 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 1.342 ------------------------------------------------------------------------------- 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 290 GLU Chi-restraints excluded: chain A residue 359 ILE 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 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 100 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 359 ILE 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 94 LEU Chi-restraints excluded: chain D residue 100 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 152 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 63 optimal weight: 0.0170 chunk 68 optimal weight: 0.8980 chunk 125 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 overall best weight: 1.7822 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.117652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.072575 restraints weight = 22398.548| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.57 r_work: 0.2726 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13672 Z= 0.205 Angle : 0.682 12.062 18508 Z= 0.321 Chirality : 0.042 0.186 2144 Planarity : 0.004 0.041 2248 Dihedral : 14.049 131.966 2304 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.03 % Allowed : 11.29 % Favored : 84.68 % 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: 2.48 (0.21), residues: 1584 helix: 2.14 (0.16), residues: 996 sheet: 1.05 (0.55), residues: 92 loop : 0.89 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 264 HIS 0.004 0.001 HIS C 281 PHE 0.012 0.001 PHE D 242 TYR 0.023 0.002 TYR B 26 ARG 0.006 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 836) hydrogen bonds : angle 3.92337 ( 2388) covalent geometry : bond 0.00492 (13672) covalent geometry : angle 0.68174 (18508) *********************** 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 175 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 120 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8805 (pp) REVERT: A 128 TYR cc_start: 0.7973 (p90) cc_final: 0.7587 (p90) REVERT: A 237 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8085 (mp0) REVERT: A 334 MET cc_start: 0.9015 (tpp) cc_final: 0.8671 (mmp) REVERT: A 359 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8705 (mt) REVERT: A 368 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8344 (pm20) REVERT: A 374 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8073 (mmm160) REVERT: B 16 LYS cc_start: 0.8406 (mmmm) cc_final: 0.8182 (mmpt) REVERT: B 100 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8797 (pp) REVERT: B 128 TYR cc_start: 0.8025 (p90) cc_final: 0.7642 (p90) REVERT: B 237 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: B 334 MET cc_start: 0.9010 (tpp) cc_final: 0.8756 (mmp) REVERT: B 368 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8333 (pm20) REVERT: B 374 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8230 (mmm160) REVERT: C 47 ASP cc_start: 0.8868 (t0) cc_final: 0.8581 (t0) REVERT: C 100 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8823 (pp) REVERT: C 128 TYR cc_start: 0.8003 (p90) cc_final: 0.7728 (p90) REVERT: C 237 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8111 (mp0) REVERT: C 289 MET cc_start: 0.8782 (mmm) cc_final: 0.8565 (mmm) REVERT: C 334 MET cc_start: 0.9020 (tpp) cc_final: 0.8776 (mmp) REVERT: C 359 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8683 (mt) REVERT: C 368 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8380 (pm20) REVERT: C 374 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8092 (mmm160) REVERT: D 100 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8781 (pp) REVERT: D 128 TYR cc_start: 0.7981 (p90) cc_final: 0.7621 (p90) REVERT: D 237 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: D 334 MET cc_start: 0.9007 (tpp) cc_final: 0.8624 (mmm) REVERT: D 368 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8394 (pm20) REVERT: D 374 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8231 (mmm160) outliers start: 55 outliers final: 10 residues processed: 169 average time/residue: 1.3111 time to fit residues: 241.3749 Evaluate side-chains 139 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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 125 ILE Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 359 ILE 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 100 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 374 ARG 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: 0.0470 chunk 118 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 17 optimal weight: 0.0470 chunk 32 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 125 optimal weight: 9.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.119323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.074500 restraints weight = 22476.549| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.57 r_work: 0.2768 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13672 Z= 0.126 Angle : 0.673 11.563 18508 Z= 0.312 Chirality : 0.040 0.191 2144 Planarity : 0.004 0.039 2248 Dihedral : 13.785 132.945 2304 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.49 % Allowed : 13.42 % 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: 2.69 (0.21), residues: 1584 helix: 2.34 (0.16), residues: 972 sheet: 1.06 (0.55), residues: 92 loop : 0.98 (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 C 281 PHE 0.008 0.001 PHE C 242 TYR 0.018 0.001 TYR B 26 ARG 0.007 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.03283 ( 836) hydrogen bonds : angle 3.85727 ( 2388) covalent geometry : bond 0.00283 (13672) covalent geometry : angle 0.67343 (18508) *********************** 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 147 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 2.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8908 (t0) cc_final: 0.8093 (m-30) REVERT: A 100 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8814 (pp) REVERT: A 237 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: A 359 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8743 (mt) REVERT: A 368 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8394 (pm20) REVERT: A 374 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8129 (mmm160) REVERT: A 412 GLN cc_start: 0.9631 (tp40) cc_final: 0.9417 (mp10) REVERT: B 16 LYS cc_start: 0.8380 (mmmm) cc_final: 0.8137 (mmpt) REVERT: B 100 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8791 (pp) REVERT: B 128 TYR cc_start: 0.8023 (p90) cc_final: 0.7615 (p90) REVERT: B 237 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8075 (mp0) REVERT: B 334 MET cc_start: 0.9054 (tpp) cc_final: 0.8816 (mmp) REVERT: B 368 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8328 (pm20) REVERT: B 374 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8209 (mmm160) REVERT: C 47 ASP cc_start: 0.8824 (t0) cc_final: 0.8531 (t0) REVERT: C 100 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8823 (pp) REVERT: C 128 TYR cc_start: 0.8046 (p90) cc_final: 0.7719 (p90) REVERT: C 237 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8092 (mp0) REVERT: C 289 MET cc_start: 0.8687 (mmm) cc_final: 0.8461 (mmm) REVERT: C 359 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8766 (mt) REVERT: C 368 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8410 (pm20) REVERT: C 374 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8064 (mmm160) REVERT: D 16 LYS cc_start: 0.8370 (mmmm) cc_final: 0.8115 (mmpt) REVERT: D 100 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8780 (pp) REVERT: D 128 TYR cc_start: 0.8038 (p90) cc_final: 0.7646 (p90) REVERT: D 237 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8015 (mp0) REVERT: D 334 MET cc_start: 0.9010 (tpp) cc_final: 0.8630 (mmm) REVERT: D 368 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8375 (pm20) REVERT: D 374 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8190 (mmm160) outliers start: 34 outliers final: 11 residues processed: 145 average time/residue: 1.7373 time to fit residues: 276.6912 Evaluate side-chains 137 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 3.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 116 ILE Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain A residue 359 ILE 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 181 LEU Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain C residue 359 ILE 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 110 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 181 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 76 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 69 optimal weight: 0.3980 chunk 59 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3821 r_free = 0.3821 target = 0.119085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.074205 restraints weight = 22246.526| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.57 r_work: 0.2763 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2307 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= 0.137 Angle : 0.683 13.748 18508 Z= 0.316 Chirality : 0.040 0.241 2144 Planarity : 0.004 0.047 2248 Dihedral : 13.715 132.830 2304 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.13 % Allowed : 13.86 % 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: 2.70 (0.21), residues: 1584 helix: 2.34 (0.16), residues: 976 sheet: 1.03 (0.55), residues: 92 loop : 0.99 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 176 HIS 0.002 0.001 HIS C 281 PHE 0.008 0.001 PHE C 242 TYR 0.012 0.001 TYR A 128 ARG 0.007 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 836) hydrogen bonds : angle 3.89004 ( 2388) covalent geometry : bond 0.00319 (13672) covalent geometry : angle 0.68308 (18508) *********************** 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: 29 poor density : 111 time to evaluate : 2.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8893 (t0) cc_final: 0.8081 (m-30) REVERT: A 100 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8817 (pp) REVERT: A 237 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8039 (mp0) REVERT: A 334 MET cc_start: 0.8999 (tpp) cc_final: 0.8736 (mmp) REVERT: A 359 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8730 (mt) REVERT: A 368 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8392 (pm20) REVERT: A 374 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8137 (mmm160) REVERT: B 16 LYS cc_start: 0.8371 (mmmm) cc_final: 0.8112 (mmpt) REVERT: B 100 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8784 (pp) REVERT: B 128 TYR cc_start: 0.8036 (p90) cc_final: 0.7664 (p90) REVERT: B 237 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: B 334 MET cc_start: 0.9049 (tpp) cc_final: 0.8729 (mmm) REVERT: B 368 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8321 (pm20) REVERT: B 374 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8233 (mmm160) REVERT: B 394 LYS cc_start: 0.8391 (tttt) cc_final: 0.7698 (tptt) REVERT: C 47 ASP cc_start: 0.8827 (t0) cc_final: 0.8534 (t0) REVERT: C 100 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8814 (pp) REVERT: C 128 TYR cc_start: 0.8045 (p90) cc_final: 0.7720 (p90) REVERT: C 237 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8084 (mp0) REVERT: C 289 MET cc_start: 0.8699 (mmm) cc_final: 0.8476 (mmm) REVERT: C 334 MET cc_start: 0.8990 (tpp) cc_final: 0.8690 (mmp) REVERT: C 359 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8757 (mt) REVERT: C 368 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8417 (pm20) REVERT: C 374 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8053 (mmm160) REVERT: D 16 LYS cc_start: 0.8350 (mmmm) cc_final: 0.8084 (mmpt) REVERT: D 47 ASP cc_start: 0.8891 (t0) cc_final: 0.7964 (m-30) REVERT: D 100 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8773 (pp) REVERT: D 237 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7993 (mp0) REVERT: D 334 MET cc_start: 0.8995 (tpp) cc_final: 0.8618 (mmm) REVERT: D 368 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8386 (pm20) REVERT: D 374 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8191 (mmm160) outliers start: 29 outliers final: 7 residues processed: 139 average time/residue: 2.1703 time to fit residues: 327.6794 Evaluate side-chains 131 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR 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 359 ILE 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 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 359 ILE 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 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 116 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 130 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3826 r_free = 0.3826 target = 0.119379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.074609 restraints weight = 22246.291| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.57 r_work: 0.2771 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: 0.7960 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13672 Z= 0.134 Angle : 0.692 12.901 18508 Z= 0.319 Chirality : 0.041 0.234 2144 Planarity : 0.004 0.047 2248 Dihedral : 13.602 132.884 2304 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.83 % Allowed : 14.37 % Favored : 83.80 % 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: 2.71 (0.21), residues: 1584 helix: 2.36 (0.16), residues: 976 sheet: 1.03 (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 C 281 PHE 0.011 0.001 PHE B 302 TYR 0.011 0.001 TYR A 128 ARG 0.006 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.03295 ( 836) hydrogen bonds : angle 3.88269 ( 2388) covalent geometry : bond 0.00311 (13672) covalent geometry : angle 0.69155 (18508) ********************** 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: 25 poor density : 106 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8889 (t0) cc_final: 0.8033 (m-30) REVERT: A 100 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8831 (pp) REVERT: A 237 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: A 334 MET cc_start: 0.9025 (tpp) cc_final: 0.8744 (mmp) REVERT: A 359 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8737 (mt) REVERT: A 368 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8414 (pm20) REVERT: A 374 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8144 (mmm160) REVERT: B 16 LYS cc_start: 0.8374 (mmmm) cc_final: 0.8101 (mmpt) REVERT: B 100 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8774 (pp) REVERT: B 237 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8037 (mp0) REVERT: B 334 MET cc_start: 0.9053 (tpp) cc_final: 0.8801 (tpp) REVERT: B 368 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8351 (pm20) REVERT: B 374 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8189 (mmm160) REVERT: C 47 ASP cc_start: 0.8814 (t0) cc_final: 0.8511 (t0) REVERT: C 100 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8813 (pp) REVERT: C 128 TYR cc_start: 0.8046 (p90) cc_final: 0.7724 (p90) REVERT: C 237 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8085 (mp0) REVERT: C 289 MET cc_start: 0.8674 (mmm) cc_final: 0.8451 (mmm) REVERT: C 334 MET cc_start: 0.9019 (tpp) cc_final: 0.8708 (mmp) REVERT: C 359 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8762 (mt) REVERT: C 368 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8400 (pm20) REVERT: C 374 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8080 (mmm160) REVERT: D 16 LYS cc_start: 0.8358 (mmmm) cc_final: 0.8067 (mmpt) REVERT: D 47 ASP cc_start: 0.8892 (t0) cc_final: 0.7957 (m-30) REVERT: D 100 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8772 (pp) REVERT: D 237 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7990 (mp0) REVERT: D 334 MET cc_start: 0.9013 (tpp) cc_final: 0.8616 (mmm) REVERT: D 368 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8383 (pm20) REVERT: D 374 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8185 (mmm160) REVERT: D 394 LYS cc_start: 0.8396 (tttt) cc_final: 0.7709 (tptt) outliers start: 25 outliers final: 8 residues processed: 131 average time/residue: 1.6584 time to fit residues: 235.9926 Evaluate side-chains 129 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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 359 ILE 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 94 LEU 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 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 359 ILE 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: 4.9990 chunk 137 optimal weight: 0.0010 chunk 77 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 36 optimal weight: 0.0010 chunk 61 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 overall best weight: 0.9996 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.118926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.073972 restraints weight = 22383.548| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.58 r_work: 0.2753 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13672 Z= 0.151 Angle : 0.691 12.289 18508 Z= 0.319 Chirality : 0.041 0.231 2144 Planarity : 0.004 0.048 2248 Dihedral : 13.637 132.559 2304 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.20 % Allowed : 14.15 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.21), residues: 1584 helix: 2.25 (0.16), residues: 1000 sheet: 1.01 (0.55), residues: 92 loop : 0.97 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 176 HIS 0.002 0.001 HIS B 281 PHE 0.009 0.001 PHE D 242 TYR 0.013 0.001 TYR B 26 ARG 0.004 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 836) hydrogen bonds : angle 3.89075 ( 2388) covalent geometry : bond 0.00356 (13672) covalent geometry : angle 0.69058 (18508) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13448.16 seconds wall clock time: 243 minutes 16.30 seconds (14596.30 seconds total)