Starting phenix.real_space_refine on Thu Aug 6 04:07:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vtb_43522/08_2026/8vtb_43522_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vtb_43522/08_2026/8vtb_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_43522/08_2026/8vtb_43522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vtb_43522/08_2026/8vtb_43522.map" model { file = "/net/cci-nas-00/data/ceres_data/8vtb_43522/08_2026/8vtb_43522_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vtb_43522/08_2026/8vtb_43522_neut.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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: {'RNAv2': 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-4': 5, 'PCW:plan-3': 3, 'PCW:plan-2': 2, 'PCW:plan-1': 1} 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: {'RNAv2': 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-4': 5, 'PCW:plan-3': 3, 'PCW:plan-2': 1, 'PCW:plan-1': 1} 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: {'RNAv2': 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-4': 5, 'PCW:plan-3': 3, 'PCW:plan-2': 1, 'PCW:plan-1': 1} 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: {'RNAv2': 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-3': 3, 'PCW:plan-4': 5, 'PCW:plan-1': 1} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 2.63, per 1000 atoms: 0.20 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: 0.95 Conformation dependent library (CDL) restraints added in 546.0 milliseconds 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: 0.38 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: 2.03 Time building geometry restraints manager: 1.19 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 - 2.28: 17844 2.28 - 4.57: 511 4.57 - 6.85: 105 6.85 - 9.14: 32 9.14 - 11.42: 16 Bond angle restraints: 18508 Sorted by residual: angle pdb=" C1' CMP D 504 " pdb=" C2' CMP D 504 " pdb=" C3' CMP D 504 " ideal model delta sigma weight residual 111.00 99.58 11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" C1' CMP A 501 " pdb=" C2' CMP A 501 " pdb=" C3' CMP A 501 " ideal model delta sigma weight residual 111.00 99.58 11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" C1' CMP C 501 " pdb=" C2' CMP C 501 " pdb=" C3' CMP C 501 " ideal model delta sigma weight residual 111.00 99.58 11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" C1' CMP B 501 " pdb=" C2' CMP B 501 " pdb=" C3' CMP B 501 " ideal model delta sigma weight residual 111.00 99.59 11.41 3.00e+00 1.11e-01 1.45e+01 angle pdb=" C2' CMP D 504 " pdb=" C3' CMP D 504 " pdb=" C4' CMP D 504 " ideal model delta sigma weight residual 111.00 100.51 10.49 3.00e+00 1.11e-01 1.22e+01 ... (remaining 18503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.88: 7876 25.88 - 51.77: 308 51.77 - 77.65: 128 77.65 - 103.54: 12 103.54 - 129.42: 12 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 - 0.070: 1865 0.070 - 0.140: 259 0.140 - 0.211: 16 0.211 - 0.281: 0 0.281 - 0.351: 4 Chirality restraints: 2144 Sorted by residual: chirality pdb=" C2' CMP A 501 " pdb=" C1' CMP A 501 " pdb=" C3' CMP A 501 " pdb=" O2' CMP A 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.86 0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" C2' CMP C 501 " pdb=" C1' CMP C 501 " pdb=" C3' CMP C 501 " pdb=" O2' CMP C 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.86 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" C2' CMP B 501 " pdb=" C1' CMP B 501 " pdb=" C3' CMP B 501 " pdb=" O2' CMP B 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.86 0.35 2.00e-01 2.50e+01 3.05e+00 ... (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: 2.210 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.450 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.020 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 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= 0.381 Angle : 0.966 11.422 18508 Z= 0.474 Chirality : 0.049 0.351 2144 Planarity : 0.008 0.117 2248 Dihedral : 16.923 129.419 5296 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.82 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.010 0.001 ARG B 81 TYR 0.015 0.002 TYR B 186 PHE 0.013 0.001 PHE C 397 TRP 0.023 0.002 TRP C 264 HIS 0.003 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00694 / 0.38 (13672) covalent geometry : angle 0.96616 / 0.47 (18508) hydrogen bonds : bond 0.11778 / 7.61 ( 836) hydrogen bonds : angle 5.71106 / 4.12 ( 2388) *********************** 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 : 0.456 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: 0.5663 time to fit residues: 81.6757 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 : 0.504 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.119195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.075017 restraints weight = 22228.775| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.57 r_work: 0.2775 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13672 Z= 0.152 Angle : 0.718 10.555 18508 Z= 0.327 Chirality : 0.042 0.178 2144 Planarity : 0.005 0.052 2248 Dihedral : 14.742 125.885 2310 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.98 % Allowed : 11.29 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.21), residues: 1584 helix: 1.66 (0.16), residues: 996 sheet: 1.10 (0.53), residues: 88 loop : 1.21 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 111 TYR 0.012 0.001 TYR D 170 PHE 0.010 0.001 PHE D 242 TRP 0.011 0.001 TRP C 176 HIS 0.004 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (13672) covalent geometry : angle 0.71804 / 0.33 (18508) hydrogen bonds : bond 0.04046 / 2.65 ( 836) hydrogen bonds : angle 4.31748 / 3.11 ( 2388) *********************** 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 147 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.400 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: 0.8276 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: B 237 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: B 394 LYS cc_start: 0.8432 (tttt) cc_final: 0.7732 (ttmt) REVERT: C 47 ASP cc_start: 0.8795 (t0) cc_final: 0.8393 (t0) REVERT: C 237 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8039 (mp0) REVERT: D 237 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8010 (mp0) outliers start: 27 outliers final: 8 residues processed: 139 average time/residue: 0.4865 time to fit residues: 74.4081 Evaluate side-chains 114 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 B residue 110 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 237 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 141 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.119280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.074379 restraints weight = 22354.927| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.57 r_work: 0.2767 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1409 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= 0.140 Angle : 0.660 9.027 18508 Z= 0.301 Chirality : 0.041 0.171 2144 Planarity : 0.005 0.055 2248 Dihedral : 13.642 125.634 2310 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.91 % Allowed : 11.73 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.21), residues: 1584 helix: 1.93 (0.16), residues: 976 sheet: 1.13 (0.54), residues: 92 loop : 1.27 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 111 TYR 0.011 0.001 TYR D 170 PHE 0.010 0.001 PHE C 242 TRP 0.009 0.001 TRP B 176 HIS 0.003 0.001 HIS D 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (13672) covalent geometry : angle 0.65966 / 0.30 (18508) hydrogen bonds : bond 0.03684 / 2.43 ( 836) hydrogen bonds : angle 4.03871 / 2.91 ( 2388) *********************** 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 145 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7912 (mp0) REVERT: A 290 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8540 (tt0) REVERT: B 237 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: B 290 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8591 (tt0) REVERT: C 47 ASP cc_start: 0.8795 (t0) cc_final: 0.8420 (t0) REVERT: C 237 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: C 290 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8463 (tt0) REVERT: D 290 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8573 (tt0) outliers start: 26 outliers final: 8 residues processed: 138 average time/residue: 0.5401 time to fit residues: 81.8047 Evaluate side-chains 115 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 148 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 147 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 110 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.118136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.073106 restraints weight = 22354.682| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.56 r_work: 0.2742 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13672 Z= 0.177 Angle : 0.688 9.175 18508 Z= 0.310 Chirality : 0.041 0.170 2144 Planarity : 0.005 0.046 2248 Dihedral : 13.315 126.252 2308 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.52 % Allowed : 10.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.21), residues: 1584 helix: 1.99 (0.16), residues: 1000 sheet: 0.99 (0.54), residues: 92 loop : 0.97 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 129 TYR 0.012 0.002 TYR C 390 PHE 0.011 0.001 PHE C 242 TRP 0.008 0.001 TRP A 176 HIS 0.003 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (13672) covalent geometry : angle 0.68808 / 0.31 (18508) hydrogen bonds : bond 0.03730 / 2.46 ( 836) hydrogen bonds : angle 3.96151 / 2.85 ( 2388) *********************** 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: 48 poor density : 111 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8913 (t0) cc_final: 0.8065 (m-30) REVERT: A 237 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8149 (mp0) REVERT: A 289 MET cc_start: 0.8832 (mmm) cc_final: 0.8595 (mmm) REVERT: A 290 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8635 (tt0) REVERT: A 368 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8460 (pm20) REVERT: A 374 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8100 (mmm160) REVERT: B 237 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8177 (mp0) REVERT: B 290 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8669 (tt0) REVERT: B 368 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8036 (pm20) REVERT: B 369 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.7964 (mpp) REVERT: B 374 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8178 (mmm160) REVERT: C 47 ASP cc_start: 0.8860 (t0) cc_final: 0.8521 (t0) REVERT: C 237 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8181 (mp0) REVERT: C 290 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8606 (tt0) REVERT: C 334 MET cc_start: 0.9017 (tpp) cc_final: 0.8797 (tpp) REVERT: C 374 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8084 (mmm160) REVERT: D 237 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8153 (mp0) REVERT: D 290 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8641 (tt0) REVERT: D 334 MET cc_start: 0.8982 (tpp) cc_final: 0.8673 (mmm) REVERT: D 374 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8192 (mmm160) outliers start: 48 outliers final: 11 residues processed: 155 average time/residue: 0.5850 time to fit residues: 98.5519 Evaluate side-chains 135 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 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 19 ILE 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 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 19 ILE Chi-restraints excluded: chain C residue 52 LEU 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 374 ARG Chi-restraints excluded: chain D residue 19 ILE 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 290 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 152 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.118486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.073566 restraints weight = 22619.547| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.58 r_work: 0.2747 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13672 Z= 0.148 Angle : 0.667 10.113 18508 Z= 0.301 Chirality : 0.041 0.163 2144 Planarity : 0.004 0.043 2248 Dihedral : 12.972 124.819 2306 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.89 % Allowed : 10.92 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.21), residues: 1584 helix: 2.11 (0.17), residues: 980 sheet: 1.03 (0.55), residues: 92 loop : 1.07 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 129 TYR 0.012 0.001 TYR D 128 PHE 0.010 0.001 PHE C 242 TRP 0.008 0.001 TRP D 176 HIS 0.003 0.001 HIS B 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (13672) covalent geometry : angle 0.66675 / 0.30 (18508) hydrogen bonds : bond 0.03540 / 2.34 ( 836) hydrogen bonds : angle 3.95110 / 2.85 ( 2388) *********************** 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 167 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 114 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8892 (t0) cc_final: 0.8097 (m-30) REVERT: A 237 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8110 (mp0) REVERT: A 289 MET cc_start: 0.8821 (mmm) cc_final: 0.8594 (mmm) REVERT: A 290 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8639 (tt0) REVERT: A 368 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8248 (pm20) REVERT: A 369 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8068 (mpp) REVERT: A 374 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8082 (mmm160) REVERT: B 237 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8130 (mp0) REVERT: B 290 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8633 (tt0) REVERT: B 334 MET cc_start: 0.8998 (tpp) cc_final: 0.8679 (mmm) REVERT: B 368 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8038 (pm20) REVERT: B 369 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.7933 (mpp) REVERT: B 374 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8208 (mmm160) REVERT: C 47 ASP cc_start: 0.8854 (t0) cc_final: 0.8546 (t0) REVERT: C 100 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8828 (pp) REVERT: C 237 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8130 (mp0) REVERT: C 290 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8580 (tt0) REVERT: C 334 MET cc_start: 0.9029 (tpp) cc_final: 0.8791 (tpp) REVERT: C 359 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8796 (mt) REVERT: C 368 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8305 (pm20) REVERT: C 374 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8126 (mmm160) REVERT: D 47 ASP cc_start: 0.8913 (t0) cc_final: 0.8069 (m-30) REVERT: D 237 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8101 (mp0) REVERT: D 290 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8656 (tt0) REVERT: D 334 MET cc_start: 0.9016 (tpp) cc_final: 0.8675 (mmm) REVERT: D 368 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8289 (pm20) REVERT: D 374 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8207 (mmm160) outliers start: 53 outliers final: 8 residues processed: 162 average time/residue: 0.5918 time to fit residues: 104.5173 Evaluate side-chains 134 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 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 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 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 19 ILE 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 290 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 110 VAL Chi-restraints excluded: chain D residue 116 ILE 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 146 optimal weight: 0.0770 chunk 59 optimal weight: 2.9990 chunk 42 optimal weight: 0.0870 chunk 6 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 150 optimal weight: 0.6980 chunk 85 optimal weight: 30.0000 chunk 39 optimal weight: 10.0000 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 ASN B 217 ASN C 217 ASN ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.119268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.074585 restraints weight = 22343.003| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.58 r_work: 0.2770 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13672 Z= 0.121 Angle : 0.675 13.544 18508 Z= 0.301 Chirality : 0.040 0.167 2144 Planarity : 0.004 0.051 2248 Dihedral : 12.586 121.403 2306 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.81 % Allowed : 11.80 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.21), residues: 1584 helix: 2.22 (0.16), residues: 980 sheet: 1.07 (0.55), residues: 92 loop : 1.09 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 129 TYR 0.022 0.001 TYR A 128 PHE 0.008 0.001 PHE C 242 TRP 0.007 0.001 TRP C 176 HIS 0.003 0.001 HIS D 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (13672) covalent geometry : angle 0.67538 / 0.30 (18508) hydrogen bonds : bond 0.03312 / 2.19 ( 836) hydrogen bonds : angle 3.89589 / 2.82 ( 2388) *********************** 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 166 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 114 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8897 (pp) REVERT: A 128 TYR cc_start: 0.7821 (p90) cc_final: 0.7479 (p90) REVERT: A 237 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7854 (mp0) REVERT: A 289 MET cc_start: 0.8577 (mmm) cc_final: 0.8333 (mmm) REVERT: A 290 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8537 (tt0) REVERT: A 368 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8194 (pm20) REVERT: A 369 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8003 (mpp) REVERT: A 374 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8072 (mmm160) REVERT: B 100 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8892 (pp) REVERT: B 128 TYR cc_start: 0.7912 (p90) cc_final: 0.7588 (p90) REVERT: B 237 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: B 290 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8539 (tt0) REVERT: B 334 MET cc_start: 0.8956 (tpp) cc_final: 0.8635 (mmm) REVERT: B 368 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.7952 (pm20) REVERT: B 369 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.7853 (mpp) REVERT: B 374 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8200 (mmm160) REVERT: C 47 ASP cc_start: 0.8793 (t0) cc_final: 0.8458 (t0) REVERT: C 100 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8873 (pp) REVERT: C 237 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7867 (mp0) REVERT: C 290 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8490 (tt0) REVERT: C 334 MET cc_start: 0.8959 (tpp) cc_final: 0.8541 (mmm) REVERT: C 368 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8245 (pm20) REVERT: C 371 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8894 (mt) REVERT: C 394 LYS cc_start: 0.8514 (tttt) cc_final: 0.7814 (tptt) REVERT: D 100 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8869 (pp) REVERT: D 237 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: D 290 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8583 (tt0) REVERT: D 334 MET cc_start: 0.8939 (tpp) cc_final: 0.8584 (mmm) REVERT: D 368 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8235 (pm20) REVERT: D 374 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8171 (mmm160) outliers start: 52 outliers final: 7 residues processed: 161 average time/residue: 0.6017 time to fit residues: 105.4278 Evaluate side-chains 133 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 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 100 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 374 ARG Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 127 SER 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 371 LEU 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 150 optimal weight: 0.9990 chunk 159 optimal weight: 8.9990 chunk 109 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 56 optimal weight: 0.0570 chunk 121 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 137 optimal weight: 0.0870 chunk 67 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.119333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.074672 restraints weight = 22389.581| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.57 r_work: 0.2775 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13672 Z= 0.125 Angle : 0.688 12.051 18508 Z= 0.309 Chirality : 0.041 0.202 2144 Planarity : 0.004 0.048 2248 Dihedral : 12.416 119.186 2304 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.93 % Allowed : 12.76 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.21), residues: 1584 helix: 2.28 (0.16), residues: 980 sheet: 0.80 (0.56), residues: 88 loop : 1.06 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 111 TYR 0.038 0.001 TYR A 26 PHE 0.008 0.001 PHE C 242 TRP 0.007 0.001 TRP C 176 HIS 0.002 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (13672) covalent geometry : angle 0.68803 / 0.31 (18508) hydrogen bonds : bond 0.03293 / 2.17 ( 836) hydrogen bonds : angle 3.89653 / 2.82 ( 2388) *********************** 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 151 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8754 (t0) cc_final: 0.8073 (m-30) REVERT: A 100 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8823 (pp) REVERT: A 128 TYR cc_start: 0.7949 (p90) cc_final: 0.7562 (p90) REVERT: A 237 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: A 289 MET cc_start: 0.8712 (mmm) cc_final: 0.8481 (mmm) REVERT: A 290 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8662 (tt0) REVERT: A 334 MET cc_start: 0.8996 (tpp) cc_final: 0.8732 (mmp) REVERT: A 368 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8258 (pm20) REVERT: A 369 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8081 (mpp) REVERT: A 374 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8118 (mmm160) REVERT: B 100 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8798 (pp) REVERT: B 128 TYR cc_start: 0.8046 (p90) cc_final: 0.7669 (p90) REVERT: B 237 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: B 290 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8704 (tt0) REVERT: B 334 MET cc_start: 0.9041 (tpp) cc_final: 0.8665 (mmm) REVERT: B 368 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8267 (pm20) REVERT: B 374 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8227 (mmm160) REVERT: C 47 ASP cc_start: 0.8867 (t0) cc_final: 0.8560 (t0) REVERT: C 100 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8793 (pp) REVERT: C 237 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: C 290 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8609 (tt0) REVERT: C 334 MET cc_start: 0.8931 (tpp) cc_final: 0.8729 (tpp) REVERT: C 359 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8773 (mt) REVERT: C 368 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8305 (pm20) REVERT: C 371 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8879 (mt) REVERT: C 394 LYS cc_start: 0.8485 (tttt) cc_final: 0.7783 (tptt) REVERT: D 100 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8783 (pp) REVERT: D 128 TYR cc_start: 0.8001 (p90) cc_final: 0.7703 (p90) REVERT: D 237 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8035 (mp0) REVERT: D 290 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8707 (tt0) REVERT: D 334 MET cc_start: 0.9028 (tpp) cc_final: 0.8657 (mmm) REVERT: D 368 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8285 (pm20) REVERT: D 374 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8185 (mmm160) outliers start: 40 outliers final: 3 residues processed: 148 average time/residue: 0.5729 time to fit residues: 92.2328 Evaluate side-chains 133 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU 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 100 LEU 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 100 LEU 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 359 ILE Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 371 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 57 optimal weight: 0.2980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.119156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.074274 restraints weight = 22269.237| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.56 r_work: 0.2766 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13672 Z= 0.135 Angle : 0.706 11.813 18508 Z= 0.315 Chirality : 0.041 0.214 2144 Planarity : 0.004 0.044 2248 Dihedral : 12.372 116.909 2304 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.08 % Allowed : 12.68 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.21), residues: 1584 helix: 2.31 (0.16), residues: 976 sheet: 0.80 (0.56), residues: 88 loop : 1.06 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 111 TYR 0.013 0.001 TYR A 128 PHE 0.008 0.001 PHE C 242 TRP 0.007 0.001 TRP C 176 HIS 0.002 0.001 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (13672) covalent geometry : angle 0.70624 / 0.32 (18508) hydrogen bonds : bond 0.03322 / 2.19 ( 836) hydrogen bonds : angle 3.88494 / 2.81 ( 2388) *********************** 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 154 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 112 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8901 (t0) cc_final: 0.8117 (m-30) REVERT: A 100 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8816 (pp) REVERT: A 237 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8078 (mp0) REVERT: A 289 MET cc_start: 0.8708 (mmm) cc_final: 0.8480 (mmm) REVERT: A 290 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8661 (tt0) REVERT: A 368 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8462 (pm20) REVERT: A 374 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8149 (mmm160) REVERT: B 16 LYS cc_start: 0.8331 (mmmm) cc_final: 0.8108 (mmpt) REVERT: B 100 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8790 (pp) REVERT: B 237 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: B 290 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8637 (tt0) REVERT: B 334 MET cc_start: 0.9024 (tpp) cc_final: 0.8631 (mmm) REVERT: B 368 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8263 (pm20) REVERT: B 374 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8235 (mmm160) REVERT: B 394 LYS cc_start: 0.8403 (tttt) cc_final: 0.7705 (tptt) REVERT: C 47 ASP cc_start: 0.8843 (t0) cc_final: 0.8552 (t0) REVERT: C 100 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8781 (pp) REVERT: C 128 TYR cc_start: 0.8022 (p90) cc_final: 0.7777 (p90) REVERT: C 237 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: C 290 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8623 (tt0) REVERT: C 334 MET cc_start: 0.8956 (tpp) cc_final: 0.8736 (tpp) REVERT: C 359 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8761 (mt) REVERT: C 368 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8299 (pm20) REVERT: C 371 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8865 (mt) REVERT: C 394 LYS cc_start: 0.8478 (tttt) cc_final: 0.7758 (tptt) REVERT: D 100 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8782 (pp) REVERT: D 128 TYR cc_start: 0.8065 (p90) cc_final: 0.7736 (p90) REVERT: D 237 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8004 (mp0) REVERT: D 290 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8696 (tt0) REVERT: D 334 MET cc_start: 0.9017 (tpp) cc_final: 0.8632 (mmm) REVERT: D 368 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8275 (pm20) REVERT: D 374 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8183 (mmm160) REVERT: D 394 LYS cc_start: 0.8379 (tttt) cc_final: 0.7695 (tptt) outliers start: 42 outliers final: 7 residues processed: 152 average time/residue: 0.6365 time to fit residues: 104.9626 Evaluate side-chains 131 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 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 94 LEU Chi-restraints excluded: chain B residue 100 LEU 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 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 290 GLU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain D residue 26 TYR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 141 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 137 optimal weight: 0.0970 chunk 87 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.119424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.077115 restraints weight = 22469.950| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.72 r_work: 0.2773 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2293 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= 0.130 Angle : 0.703 11.704 18508 Z= 0.317 Chirality : 0.041 0.228 2144 Planarity : 0.004 0.046 2248 Dihedral : 12.303 114.752 2304 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.20 % Allowed : 13.56 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.67 (0.21), residues: 1584 helix: 2.33 (0.16), residues: 976 sheet: 0.80 (0.56), residues: 88 loop : 1.01 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 111 TYR 0.013 0.001 TYR A 128 PHE 0.009 0.001 PHE B 302 TRP 0.007 0.001 TRP A 176 HIS 0.002 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (13672) covalent geometry : angle 0.70280 / 0.32 (18508) hydrogen bonds : bond 0.03290 / 2.17 ( 836) hydrogen bonds : angle 3.87186 / 2.80 ( 2388) *********************** 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 136 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8944 (t0) cc_final: 0.8050 (m-30) REVERT: A 100 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8792 (pp) REVERT: A 237 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: A 289 MET cc_start: 0.8644 (mmm) cc_final: 0.8411 (mmm) REVERT: A 290 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8665 (tt0) REVERT: A 334 MET cc_start: 0.9005 (tpp) cc_final: 0.8711 (mmp) REVERT: A 368 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8400 (pm20) REVERT: A 374 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8137 (mmm160) REVERT: B 16 LYS cc_start: 0.8352 (mmmm) cc_final: 0.8151 (mmpt) REVERT: B 100 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8756 (pp) REVERT: B 237 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8029 (mp0) REVERT: B 290 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8590 (tt0) REVERT: B 334 MET cc_start: 0.9041 (tpp) cc_final: 0.8642 (mmm) REVERT: B 368 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8241 (pm20) REVERT: B 374 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8244 (mmm160) REVERT: B 394 LYS cc_start: 0.8364 (tttt) cc_final: 0.7670 (tptt) REVERT: C 47 ASP cc_start: 0.8829 (t0) cc_final: 0.8530 (t0) REVERT: C 100 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8757 (pp) REVERT: C 128 TYR cc_start: 0.8051 (p90) cc_final: 0.7732 (p90) REVERT: C 237 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: C 290 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8618 (tt0) REVERT: C 334 MET cc_start: 0.8974 (tpp) cc_final: 0.8688 (mmm) REVERT: C 359 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8737 (mt) REVERT: C 368 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8279 (pm20) REVERT: D 100 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8741 (pp) REVERT: D 128 TYR cc_start: 0.8064 (p90) cc_final: 0.7736 (p90) REVERT: D 237 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7960 (mp0) REVERT: D 290 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8660 (tt0) REVERT: D 334 MET cc_start: 0.9008 (tpp) cc_final: 0.8621 (mmm) REVERT: D 368 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8245 (pm20) REVERT: D 374 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8198 (mmm160) REVERT: D 394 LYS cc_start: 0.8349 (tttt) cc_final: 0.7681 (tptt) outliers start: 30 outliers final: 8 residues processed: 136 average time/residue: 0.5816 time to fit residues: 85.7843 Evaluate side-chains 135 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 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 54 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 100 LEU 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 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 290 GLU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 368 GLU 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 290 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 58 optimal weight: 1.9990 chunk 57 optimal weight: 0.0970 chunk 62 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 83 optimal weight: 0.0770 chunk 116 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.118961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.074024 restraints weight = 22320.653| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.57 r_work: 0.2757 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2354 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= 0.146 Angle : 0.722 11.589 18508 Z= 0.323 Chirality : 0.042 0.230 2144 Planarity : 0.004 0.045 2248 Dihedral : 12.349 112.979 2304 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.27 % Allowed : 13.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.21), residues: 1584 helix: 2.30 (0.16), residues: 976 sheet: 0.79 (0.56), residues: 88 loop : 1.02 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 111 TYR 0.011 0.001 TYR A 128 PHE 0.009 0.001 PHE C 302 TRP 0.007 0.001 TRP A 176 HIS 0.002 0.001 HIS B 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (13672) covalent geometry : angle 0.72187 / 0.32 (18508) hydrogen bonds : bond 0.03373 / 2.23 ( 836) hydrogen bonds : angle 3.89071 / 2.82 ( 2388) ********************** 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 137 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8881 (t0) cc_final: 0.8041 (m-30) REVERT: A 100 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8894 (pp) REVERT: A 237 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7803 (mp0) REVERT: A 289 MET cc_start: 0.8531 (mmm) cc_final: 0.8294 (mmm) REVERT: A 290 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8519 (tt0) REVERT: A 334 MET cc_start: 0.8957 (tpp) cc_final: 0.8651 (mmp) REVERT: A 368 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8388 (pm20) REVERT: A 374 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8087 (mmm160) REVERT: B 16 LYS cc_start: 0.8355 (mmmm) cc_final: 0.8153 (mmpt) REVERT: B 100 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8857 (pp) REVERT: B 237 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: B 290 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8460 (tt0) REVERT: B 334 MET cc_start: 0.8965 (tpp) cc_final: 0.8587 (mmm) REVERT: B 368 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8368 (pm20) REVERT: B 374 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8181 (mmm160) REVERT: B 394 LYS cc_start: 0.8426 (tttt) cc_final: 0.7704 (tptt) REVERT: C 47 ASP cc_start: 0.8741 (t0) cc_final: 0.8426 (t0) REVERT: C 100 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8855 (pp) REVERT: C 128 TYR cc_start: 0.7978 (p90) cc_final: 0.7660 (p90) REVERT: C 237 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: C 290 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8468 (tt0) REVERT: C 334 MET cc_start: 0.8929 (tpp) cc_final: 0.8654 (mmm) REVERT: C 359 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8735 (mt) REVERT: C 368 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8399 (pm20) REVERT: D 16 LYS cc_start: 0.8367 (mmmm) cc_final: 0.8148 (mmpt) REVERT: D 100 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8831 (pp) REVERT: D 128 TYR cc_start: 0.7964 (p90) cc_final: 0.7633 (p90) REVERT: D 237 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: D 290 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8494 (tt0) REVERT: D 303 LYS cc_start: 0.8757 (tppp) cc_final: 0.8439 (tppt) REVERT: D 334 MET cc_start: 0.8942 (tpp) cc_final: 0.8572 (mmm) REVERT: D 368 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8219 (pm20) REVERT: D 374 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8171 (mmm160) REVERT: D 394 LYS cc_start: 0.8412 (tttt) cc_final: 0.7723 (tptt) outliers start: 31 outliers final: 9 residues processed: 137 average time/residue: 0.6257 time to fit residues: 92.6951 Evaluate side-chains 131 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 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 54 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 100 LEU 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 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 290 GLU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 368 GLU 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 290 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 107 optimal weight: 0.0980 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 0.0010 chunk 118 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 116 optimal weight: 0.0670 chunk 123 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 95 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 overall best weight: 0.2324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.120599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.076042 restraints weight = 22370.447| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.58 r_work: 0.2802 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2420 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= 0.117 Angle : 0.698 10.346 18508 Z= 0.312 Chirality : 0.041 0.231 2144 Planarity : 0.004 0.047 2248 Dihedral : 11.997 107.956 2304 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.35 % Allowed : 13.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.21), residues: 1584 helix: 2.44 (0.16), residues: 976 sheet: 0.78 (0.56), residues: 88 loop : 1.01 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 111 TYR 0.011 0.001 TYR A 128 PHE 0.007 0.001 PHE A 302 TRP 0.006 0.001 TRP B 264 HIS 0.002 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (13672) covalent geometry : angle 0.69815 / 0.31 (18508) hydrogen bonds : bond 0.03101 / 2.05 ( 836) hydrogen bonds : angle 3.84685 / 2.79 ( 2388) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5069.23 seconds wall clock time: 86 minutes 47.18 seconds (5207.18 seconds total)