Starting phenix.real_space_refine on Tue Apr 7 22:50:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ww5_21928/04_2026/6ww5_21928_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ww5_21928/04_2026/6ww5_21928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ww5_21928/04_2026/6ww5_21928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ww5_21928/04_2026/6ww5_21928.map" model { file = "/net/cci-nas-00/data/ceres_data/6ww5_21928/04_2026/6ww5_21928_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ww5_21928/04_2026/6ww5_21928_trim.cif" } resolution = 3.15 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5984 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 74 5.16 5 C 8686 2.51 5 N 2166 2.21 5 O 2454 1.98 5 H 13425 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26807 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 6814 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 15, 'TRANS': 429} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 6814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 6814 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 15, 'TRANS': 429} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3385 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 215} Chain: "E" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3384 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 215} Chain: "F" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3164 Classifications: {'peptide': 209} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 198} Chain: "D" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3164 Classifications: {'peptide': 209} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 198} Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'6PE': 1, 'HEX': 1, 'OCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'6PE': 1, 'HEX': 1, 'OCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.83, per 1000 atoms: 0.18 Number of scatterers: 26807 At special positions: 0 Unit cell: (113.058, 122.194, 138.182, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 74 16.00 P 2 15.00 O 2454 8.00 N 2166 7.00 C 8686 6.00 H 13425 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 210 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 210 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 826.4 milliseconds 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3268 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 22 sheets defined 45.1% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 19 through 39 Processing helix chain 'A' and resid 42 through 61 Processing helix chain 'A' and resid 65 through 79 Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 113 removed outlier: 3.738A pdb=" N PHE A 98 " --> pdb=" O ASN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 127 removed outlier: 3.666A pdb=" N VAL A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 127 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 146 removed outlier: 4.728A pdb=" N PHE A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 166 removed outlier: 3.518A pdb=" N ALA A 155 " --> pdb=" O ASN A 151 " (cutoff:3.500A) Proline residue: A 160 - end of helix Processing helix chain 'A' and resid 175 through 193 Processing helix chain 'A' and resid 200 through 211 removed outlier: 3.983A pdb=" N ALA A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 240 removed outlier: 3.811A pdb=" N LYS A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N PHE A 220 " --> pdb=" O ASP A 216 " (cutoff:3.500A) Proline residue: A 223 - end of helix Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 260 through 277 removed outlier: 3.553A pdb=" N THR A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 284 Processing helix chain 'A' and resid 290 through 307 Processing helix chain 'A' and resid 310 through 318 removed outlier: 3.598A pdb=" N ILE A 314 " --> pdb=" O HIS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 339 removed outlier: 3.519A pdb=" N LEU A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 349 through 356 Processing helix chain 'A' and resid 358 through 373 Processing helix chain 'A' and resid 377 through 397 Proline residue: A 387 - end of helix Processing helix chain 'A' and resid 399 through 411 removed outlier: 3.740A pdb=" N LEU A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 431 removed outlier: 3.835A pdb=" N ALA A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER A 430 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY A 431 " --> pdb=" O VAL A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 462 removed outlier: 3.871A pdb=" N GLN A 462 " --> pdb=" O MET A 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 39 Processing helix chain 'B' and resid 42 through 61 Processing helix chain 'B' and resid 65 through 79 Proline residue: B 74 - end of helix Processing helix chain 'B' and resid 84 through 90 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 94 through 113 removed outlier: 3.738A pdb=" N PHE B 98 " --> pdb=" O ASN B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 127 removed outlier: 3.667A pdb=" N VAL B 118 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B 127 " --> pdb=" O VAL B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 146 removed outlier: 4.729A pdb=" N PHE B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 166 removed outlier: 3.518A pdb=" N ALA B 155 " --> pdb=" O ASN B 151 " (cutoff:3.500A) Proline residue: B 160 - end of helix Processing helix chain 'B' and resid 175 through 193 Processing helix chain 'B' and resid 200 through 211 removed outlier: 3.983A pdb=" N ALA B 204 " --> pdb=" O SER B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 240 removed outlier: 3.810A pdb=" N LYS B 219 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N PHE B 220 " --> pdb=" O ASP B 216 " (cutoff:3.500A) Proline residue: B 223 - end of helix Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 260 through 277 removed outlier: 3.552A pdb=" N THR B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 284 Processing helix chain 'B' and resid 290 through 307 Processing helix chain 'B' and resid 310 through 318 removed outlier: 3.598A pdb=" N ILE B 314 " --> pdb=" O HIS B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 339 removed outlier: 3.520A pdb=" N LEU B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY B 327 " --> pdb=" O LEU B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 349 Processing helix chain 'B' and resid 349 through 356 Processing helix chain 'B' and resid 358 through 373 Processing helix chain 'B' and resid 377 through 397 Proline residue: B 387 - end of helix Processing helix chain 'B' and resid 399 through 411 removed outlier: 3.741A pdb=" N LEU B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 431 removed outlier: 3.835A pdb=" N ALA B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER B 430 " --> pdb=" O ILE B 426 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY B 431 " --> pdb=" O VAL B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 462 removed outlier: 3.870A pdb=" N GLN B 462 " --> pdb=" O MET B 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.955A pdb=" N THR C 91 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.955A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.001A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 128 removed outlier: 4.282A pdb=" N SER F 127 " --> pdb=" O SER F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 188 Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.001A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 removed outlier: 4.283A pdb=" N SER D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.515A pdb=" N VAL C 12 " --> pdb=" O THR C 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 134 through 137 removed outlier: 6.222A pdb=" N TYR C 190 " --> pdb=" O ASP C 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 134 through 137 removed outlier: 6.222A pdb=" N TYR C 190 " --> pdb=" O ASP C 158 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL C 183 " --> pdb=" O SER C 191 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 165 through 168 removed outlier: 3.554A pdb=" N SER C 167 " --> pdb=" O ASN C 211 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TYR C 208 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N CYS C 210 " --> pdb=" O LYS C 223 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS C 223 " --> pdb=" O CYS C 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.514A pdb=" N VAL E 12 " --> pdb=" O THR E 124 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 134 through 137 removed outlier: 6.221A pdb=" N TYR E 190 " --> pdb=" O ASP E 158 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 134 through 137 removed outlier: 6.221A pdb=" N TYR E 190 " --> pdb=" O ASP E 158 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL E 183 " --> pdb=" O SER E 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 165 through 168 removed outlier: 3.555A pdb=" N SER E 167 " --> pdb=" O ASN E 211 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TYR E 208 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N CYS E 210 " --> pdb=" O LYS E 223 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS E 223 " --> pdb=" O CYS E 210 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.591A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 114 through 117 removed outlier: 6.242A pdb=" N TYR F 173 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 129 through 132 Processing sheet with id=AB6, first strand: chain 'F' and resid 153 through 154 removed outlier: 6.475A pdb=" N HIS F 198 " --> pdb=" O SER F 203 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N SER F 203 " --> pdb=" O HIS F 198 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AB8, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.591A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 114 through 117 removed outlier: 6.242A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 129 through 132 Processing sheet with id=AC3, first strand: chain 'D' and resid 153 through 154 removed outlier: 6.475A pdb=" N HIS D 198 " --> pdb=" O SER D 203 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N SER D 203 " --> pdb=" O HIS D 198 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 153 through 154 742 hydrogen bonds defined for protein. 2064 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: 6.17 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 13419 1.01 - 1.21: 10 1.21 - 1.41: 5514 1.41 - 1.61: 8044 1.61 - 1.81: 130 Bond restraints: 27117 Sorted by residual: bond pdb=" CA ILE A 386 " pdb=" CB ILE A 386 " ideal model delta sigma weight residual 1.537 1.523 0.014 5.00e-03 4.00e+04 8.18e+00 bond pdb=" CA ILE B 386 " pdb=" CB ILE B 386 " ideal model delta sigma weight residual 1.537 1.523 0.014 5.00e-03 4.00e+04 8.09e+00 bond pdb=" CG LEU D 46 " pdb=" CD2 LEU D 46 " ideal model delta sigma weight residual 1.521 1.427 0.094 3.30e-02 9.18e+02 8.08e+00 bond pdb=" CG LEU F 46 " pdb=" CD2 LEU F 46 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 8.01e+00 bond pdb=" ND2 ASN B 44 " pdb="HD22 ASN B 44 " ideal model delta sigma weight residual 0.860 0.806 0.054 2.00e-02 2.50e+03 7.41e+00 ... (remaining 27112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.37: 48946 6.37 - 12.75: 41 12.75 - 19.12: 4 19.12 - 25.50: 2 25.50 - 31.87: 7 Bond angle restraints: 49000 Sorted by residual: angle pdb=" SD MET B 147 " pdb=" CE MET B 147 " pdb=" HE2 MET B 147 " ideal model delta sigma weight residual 109.00 77.13 31.87 3.00e+00 1.11e-01 1.13e+02 angle pdb=" SD MET B 147 " pdb=" CE MET B 147 " pdb=" HE3 MET B 147 " ideal model delta sigma weight residual 109.00 77.21 31.79 3.00e+00 1.11e-01 1.12e+02 angle pdb=" CB LEU A 58 " pdb=" CG LEU A 58 " pdb=" HG LEU A 58 " ideal model delta sigma weight residual 109.00 77.48 31.52 3.00e+00 1.11e-01 1.10e+02 angle pdb=" CD2 LEU A 58 " pdb=" CG LEU A 58 " pdb=" HG LEU A 58 " ideal model delta sigma weight residual 108.00 77.25 30.75 3.00e+00 1.11e-01 1.05e+02 angle pdb=" CD1 LEU A 58 " pdb=" CG LEU A 58 " pdb=" HG LEU A 58 " ideal model delta sigma weight residual 108.00 78.01 29.99 3.00e+00 1.11e-01 9.99e+01 ... (remaining 48995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.93: 12387 31.93 - 63.85: 523 63.85 - 95.78: 25 95.78 - 127.71: 0 127.71 - 159.64: 2 Dihedral angle restraints: 12937 sinusoidal: 6856 harmonic: 6081 Sorted by residual: dihedral pdb=" CA PHE C 160 " pdb=" C PHE C 160 " pdb=" N PRO C 161 " pdb=" CA PRO C 161 " ideal model delta harmonic sigma weight residual -180.00 -124.76 -55.24 0 5.00e+00 4.00e-02 1.22e+02 dihedral pdb=" CA PHE E 160 " pdb=" C PHE E 160 " pdb=" N PRO E 161 " pdb=" CA PRO E 161 " ideal model delta harmonic sigma weight residual -180.00 -124.77 -55.23 0 5.00e+00 4.00e-02 1.22e+02 dihedral pdb=" CA TYR F 140 " pdb=" C TYR F 140 " pdb=" N PRO F 141 " pdb=" CA PRO F 141 " ideal model delta harmonic sigma weight residual -180.00 -126.40 -53.60 0 5.00e+00 4.00e-02 1.15e+02 ... (remaining 12934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 2165 0.151 - 0.303: 29 0.303 - 0.454: 2 0.454 - 0.605: 0 0.605 - 0.756: 2 Chirality restraints: 2198 Sorted by residual: chirality pdb=" CG LEU A 58 " pdb=" CB LEU A 58 " pdb=" CD1 LEU A 58 " pdb=" CD2 LEU A 58 " both_signs ideal model delta sigma weight residual False -2.59 -1.83 -0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CG LEU B 58 " pdb=" CB LEU B 58 " pdb=" CD1 LEU B 58 " pdb=" CD2 LEU B 58 " both_signs ideal model delta sigma weight residual False -2.59 -1.83 -0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CB ILE E 129 " pdb=" CA ILE E 129 " pdb=" CG1 ILE E 129 " pdb=" CG2 ILE E 129 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.13e+00 ... (remaining 2195 not shown) Planarity restraints: 3988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 288 " -0.046 2.00e-02 2.50e+03 4.24e-02 5.40e+01 pdb=" CG PHE B 288 " 0.116 2.00e-02 2.50e+03 pdb=" CD1 PHE B 288 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 288 " -0.072 2.00e-02 2.50e+03 pdb=" CE1 PHE B 288 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 288 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE B 288 " -0.014 2.00e-02 2.50e+03 pdb=" HD1 PHE B 288 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 PHE B 288 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 PHE B 288 " -0.012 2.00e-02 2.50e+03 pdb=" HE2 PHE B 288 " 0.018 2.00e-02 2.50e+03 pdb=" HZ PHE B 288 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 288 " -0.045 2.00e-02 2.50e+03 4.20e-02 5.30e+01 pdb=" CG PHE A 288 " 0.120 2.00e-02 2.50e+03 pdb=" CD1 PHE A 288 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 288 " -0.060 2.00e-02 2.50e+03 pdb=" CE1 PHE A 288 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 288 " 0.024 2.00e-02 2.50e+03 pdb=" CZ PHE A 288 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 PHE A 288 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE A 288 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE A 288 " -0.020 2.00e-02 2.50e+03 pdb=" HE2 PHE A 288 " -0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 288 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 80 " -0.050 2.00e-02 2.50e+03 4.03e-02 4.87e+01 pdb=" CG PHE B 80 " 0.116 2.00e-02 2.50e+03 pdb=" CD1 PHE B 80 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 80 " -0.055 2.00e-02 2.50e+03 pdb=" CE1 PHE B 80 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 80 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 80 " -0.016 2.00e-02 2.50e+03 pdb=" HD1 PHE B 80 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE B 80 " 0.005 2.00e-02 2.50e+03 pdb=" HE1 PHE B 80 " -0.007 2.00e-02 2.50e+03 pdb=" HE2 PHE B 80 " 0.016 2.00e-02 2.50e+03 pdb=" HZ PHE B 80 " -0.002 2.00e-02 2.50e+03 ... (remaining 3985 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.07: 665 2.07 - 2.70: 45657 2.70 - 3.33: 78165 3.33 - 3.97: 102815 3.97 - 4.60: 162891 Nonbonded interactions: 390193 Sorted by model distance: nonbonded pdb=" O SER B 350 " pdb=" HH TYR D 92 " model vdw 1.434 2.450 nonbonded pdb=" O ILE A 191 " pdb=" H ILE A 194 " model vdw 1.521 2.450 nonbonded pdb=" O ILE B 191 " pdb=" H ILE B 194 " model vdw 1.522 2.450 nonbonded pdb=" O TRP B 461 " pdb="HH21 ARG D 66 " model vdw 1.543 2.450 nonbonded pdb=" HE ARG F 61 " pdb=" OD2 ASP F 82 " model vdw 1.559 2.450 ... (remaining 390188 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' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 1 through 101 or (resid 102 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 103 through 228)) selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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=0.33 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.150 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.120 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 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 : 0.013 0.094 13700 Z= 0.493 Angle : 0.980 13.492 18646 Z= 0.492 Chirality : 0.063 0.756 2198 Planarity : 0.008 0.138 2304 Dihedral : 16.537 159.637 4760 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.57 % Allowed : 10.56 % Favored : 88.87 % Rotamer: Outliers : 1.52 % Allowed : 1.38 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.36 % 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: -2.89 (0.18), residues: 1752 helix: -0.92 (0.18), residues: 730 sheet: -2.07 (0.24), residues: 376 loop : -2.85 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.002 ARG B 307 TYR 0.089 0.005 TYR D 55 PHE 0.118 0.007 PHE A 288 TRP 0.021 0.002 TRP C 106 HIS 0.031 0.003 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.01269 (13692) covalent geometry : angle 0.97972 (18630) SS BOND : bond 0.00692 ( 8) SS BOND : angle 1.15258 ( 16) hydrogen bonds : bond 0.12779 ( 704) hydrogen bonds : angle 7.52874 ( 2064) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 158 MET cc_start: 0.7693 (mmt) cc_final: 0.7489 (mmm) REVERT: B 94 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7705 (t0) REVERT: B 158 MET cc_start: 0.7981 (mmt) cc_final: 0.7551 (mmm) REVERT: E 223 LYS cc_start: 0.5895 (mmmt) cc_final: 0.5228 (mmtm) REVERT: D 167 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.7036 (m-30) REVERT: D 185 ASP cc_start: 0.6939 (m-30) cc_final: 0.6661 (m-30) outliers start: 22 outliers final: 4 residues processed: 173 average time/residue: 0.2551 time to fit residues: 65.4599 Evaluate side-chains 144 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 138 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 188 LYS Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 182 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.0030 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 6.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 203 ASN B 44 ASN B 94 ASN B 203 ASN F 90 GLN F 124 GLN F 199 GLN D 90 GLN D 199 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.184032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.142296 restraints weight = 39862.955| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.99 r_work: 0.3572 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13700 Z= 0.151 Angle : 0.698 12.737 18646 Z= 0.356 Chirality : 0.055 1.659 2198 Planarity : 0.008 0.140 2304 Dihedral : 9.325 141.620 1926 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.48 % Favored : 92.07 % Rotamer: Outliers : 1.45 % Allowed : 7.19 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.36 % 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: -2.11 (0.19), residues: 1752 helix: -0.07 (0.19), residues: 740 sheet: -1.87 (0.23), residues: 372 loop : -2.60 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 307 TYR 0.019 0.002 TYR F 36 PHE 0.019 0.002 PHE E 160 TRP 0.013 0.001 TRP C 106 HIS 0.005 0.001 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00348 (13692) covalent geometry : angle 0.69744 (18630) SS BOND : bond 0.00668 ( 8) SS BOND : angle 1.29008 ( 16) hydrogen bonds : bond 0.04004 ( 704) hydrogen bonds : angle 5.52106 ( 2064) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 169 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 158 MET cc_start: 0.8198 (mmt) cc_final: 0.7504 (mmm) REVERT: A 434 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7475 (mttm) REVERT: B 158 MET cc_start: 0.8272 (mmt) cc_final: 0.8062 (mmm) REVERT: B 226 MET cc_start: 0.8021 (mtm) cc_final: 0.7794 (mtm) REVERT: E 89 GLU cc_start: 0.7485 (mp0) cc_final: 0.7200 (mp0) REVERT: E 90 ASP cc_start: 0.7400 (m-30) cc_final: 0.7164 (m-30) REVERT: F 81 GLU cc_start: 0.7890 (pm20) cc_final: 0.7658 (pm20) REVERT: F 118 PHE cc_start: 0.6458 (m-10) cc_final: 0.5806 (m-10) REVERT: F 158 ASN cc_start: 0.6811 (p0) cc_final: 0.6445 (p0) REVERT: F 185 ASP cc_start: 0.6978 (m-30) cc_final: 0.6686 (m-30) REVERT: D 118 PHE cc_start: 0.6473 (m-10) cc_final: 0.5785 (m-10) REVERT: D 185 ASP cc_start: 0.6816 (m-30) cc_final: 0.6401 (m-30) outliers start: 21 outliers final: 12 residues processed: 164 average time/residue: 0.2409 time to fit residues: 60.0931 Evaluate side-chains 152 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 188 LYS Chi-restraints excluded: chain F residue 199 GLN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 182 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 67 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN D 199 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.178641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.134109 restraints weight = 40167.359| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.76 r_work: 0.3494 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13700 Z= 0.152 Angle : 0.633 11.499 18646 Z= 0.323 Chirality : 0.054 1.680 2198 Planarity : 0.008 0.137 2304 Dihedral : 8.807 138.087 1924 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.79 % Favored : 92.81 % Rotamer: Outliers : 1.31 % Allowed : 8.71 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.24 % 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: -1.72 (0.20), residues: 1752 helix: 0.30 (0.20), residues: 742 sheet: -1.81 (0.23), residues: 416 loop : -2.36 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 61 TYR 0.016 0.001 TYR F 36 PHE 0.021 0.001 PHE C 160 TRP 0.013 0.001 TRP E 106 HIS 0.004 0.001 HIS B 112 Details of bonding type rmsd covalent geometry : bond 0.00353 (13692) covalent geometry : angle 0.63320 (18630) SS BOND : bond 0.00411 ( 8) SS BOND : angle 0.70537 ( 16) hydrogen bonds : bond 0.03723 ( 704) hydrogen bonds : angle 5.15116 ( 2064) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 157 MET cc_start: 0.7709 (ptm) cc_final: 0.7240 (ptm) REVERT: B 158 MET cc_start: 0.8372 (mmt) cc_final: 0.8132 (mmm) REVERT: B 427 VAL cc_start: 0.7087 (t) cc_final: 0.6884 (t) REVERT: E 89 GLU cc_start: 0.7520 (mp0) cc_final: 0.7316 (mp0) REVERT: E 90 ASP cc_start: 0.7533 (m-30) cc_final: 0.7304 (m-30) REVERT: F 81 GLU cc_start: 0.7823 (pm20) cc_final: 0.7610 (pm20) REVERT: F 82 ASP cc_start: 0.7973 (m-30) cc_final: 0.7763 (m-30) REVERT: F 118 PHE cc_start: 0.6421 (m-10) cc_final: 0.5666 (m-10) REVERT: F 158 ASN cc_start: 0.6802 (p0) cc_final: 0.6489 (p0) REVERT: F 185 ASP cc_start: 0.6861 (m-30) cc_final: 0.6542 (m-30) REVERT: D 185 ASP cc_start: 0.6680 (m-30) cc_final: 0.6348 (m-30) outliers start: 19 outliers final: 14 residues processed: 155 average time/residue: 0.2341 time to fit residues: 54.8420 Evaluate side-chains 153 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 438 MET Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain F residue 188 LYS Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 203 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 91 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.173160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.127038 restraints weight = 41081.543| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.79 r_work: 0.3400 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13700 Z= 0.174 Angle : 0.628 10.782 18646 Z= 0.325 Chirality : 0.055 1.689 2198 Planarity : 0.008 0.135 2304 Dihedral : 8.675 138.724 1924 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.91 % Favored : 92.75 % Rotamer: Outliers : 1.66 % Allowed : 10.79 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.24 % 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: -1.53 (0.20), residues: 1752 helix: 0.43 (0.20), residues: 744 sheet: -1.71 (0.24), residues: 412 loop : -2.24 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 98 TYR 0.014 0.002 TYR F 36 PHE 0.021 0.002 PHE E 160 TRP 0.016 0.001 TRP C 106 HIS 0.004 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00406 (13692) covalent geometry : angle 0.62783 (18630) SS BOND : bond 0.00368 ( 8) SS BOND : angle 0.79895 ( 16) hydrogen bonds : bond 0.03577 ( 704) hydrogen bonds : angle 4.87394 ( 2064) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 169 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.506 Fit side-chains REVERT: A 157 MET cc_start: 0.8013 (ptm) cc_final: 0.7428 (ptm) REVERT: B 157 MET cc_start: 0.8031 (ptm) cc_final: 0.7424 (ptm) REVERT: B 158 MET cc_start: 0.8531 (mmt) cc_final: 0.8098 (mmm) REVERT: B 226 MET cc_start: 0.8135 (mtm) cc_final: 0.7801 (mtm) REVERT: B 427 VAL cc_start: 0.7537 (t) cc_final: 0.7294 (t) REVERT: C 89 GLU cc_start: 0.7668 (mp0) cc_final: 0.7249 (mp0) REVERT: E 89 GLU cc_start: 0.7528 (mp0) cc_final: 0.7032 (mp0) REVERT: E 90 ASP cc_start: 0.7868 (m-30) cc_final: 0.7574 (m-30) REVERT: E 223 LYS cc_start: 0.5560 (mmmt) cc_final: 0.4709 (mmtm) REVERT: F 81 GLU cc_start: 0.7835 (pm20) cc_final: 0.7584 (pm20) REVERT: F 82 ASP cc_start: 0.8019 (m-30) cc_final: 0.7795 (m-30) REVERT: F 118 PHE cc_start: 0.6432 (m-10) cc_final: 0.5600 (m-10) REVERT: F 133 VAL cc_start: 0.5707 (t) cc_final: 0.5406 (t) outliers start: 24 outliers final: 14 residues processed: 166 average time/residue: 0.2542 time to fit residues: 63.4520 Evaluate side-chains 154 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 182 SER Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 203 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 74 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 147 optimal weight: 20.0000 chunk 133 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.173972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.126342 restraints weight = 41070.892| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.85 r_work: 0.3404 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13700 Z= 0.151 Angle : 0.592 10.685 18646 Z= 0.303 Chirality : 0.054 1.684 2198 Planarity : 0.007 0.132 2304 Dihedral : 8.482 140.018 1920 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.74 % Favored : 92.92 % Rotamer: Outliers : 1.80 % Allowed : 11.20 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.24 % 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: -1.29 (0.21), residues: 1752 helix: 0.58 (0.20), residues: 748 sheet: -1.59 (0.24), residues: 412 loop : -2.06 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 61 TYR 0.010 0.001 TYR D 36 PHE 0.017 0.001 PHE C 160 TRP 0.014 0.001 TRP C 106 HIS 0.004 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00349 (13692) covalent geometry : angle 0.59228 (18630) SS BOND : bond 0.00341 ( 8) SS BOND : angle 0.65694 ( 16) hydrogen bonds : bond 0.03407 ( 704) hydrogen bonds : angle 4.67742 ( 2064) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 168 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.8034 (ptm) cc_final: 0.7398 (ptm) REVERT: A 427 VAL cc_start: 0.7205 (t) cc_final: 0.7004 (t) REVERT: B 157 MET cc_start: 0.8061 (ptm) cc_final: 0.7504 (ptm) REVERT: B 158 MET cc_start: 0.8573 (mmt) cc_final: 0.8105 (mmm) REVERT: B 226 MET cc_start: 0.8163 (mtm) cc_final: 0.7822 (mtm) REVERT: C 89 GLU cc_start: 0.7622 (mp0) cc_final: 0.7133 (pp20) REVERT: E 89 GLU cc_start: 0.7550 (mp0) cc_final: 0.6954 (pp20) REVERT: E 90 ASP cc_start: 0.7844 (m-30) cc_final: 0.7439 (m-30) REVERT: E 223 LYS cc_start: 0.5595 (mmmt) cc_final: 0.4781 (mmtm) REVERT: F 81 GLU cc_start: 0.7842 (pm20) cc_final: 0.7582 (pm20) REVERT: F 82 ASP cc_start: 0.8020 (m-30) cc_final: 0.7796 (m-30) REVERT: F 118 PHE cc_start: 0.6502 (m-10) cc_final: 0.5697 (m-10) REVERT: F 133 VAL cc_start: 0.5727 (t) cc_final: 0.5433 (t) outliers start: 26 outliers final: 20 residues processed: 160 average time/residue: 0.2529 time to fit residues: 61.3542 Evaluate side-chains 158 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 338 GLN Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 199 GLN Chi-restraints excluded: chain D residue 203 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.172747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.126604 restraints weight = 41449.674| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.78 r_work: 0.3396 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13700 Z= 0.151 Angle : 0.587 10.736 18646 Z= 0.301 Chirality : 0.054 1.692 2198 Planarity : 0.007 0.132 2304 Dihedral : 8.374 139.738 1918 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.56 % Favored : 93.09 % Rotamer: Outliers : 1.73 % Allowed : 11.34 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.24 % 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: -1.15 (0.21), residues: 1752 helix: 0.73 (0.20), residues: 742 sheet: -1.54 (0.24), residues: 412 loop : -2.00 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 98 TYR 0.011 0.001 TYR D 36 PHE 0.017 0.001 PHE C 160 TRP 0.014 0.001 TRP C 106 HIS 0.004 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00349 (13692) covalent geometry : angle 0.58659 (18630) SS BOND : bond 0.00342 ( 8) SS BOND : angle 0.72329 ( 16) hydrogen bonds : bond 0.03387 ( 704) hydrogen bonds : angle 4.59079 ( 2064) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8320 (OUTLIER) cc_final: 0.7870 (t0) REVERT: A 157 MET cc_start: 0.7998 (ptm) cc_final: 0.7677 (ptm) REVERT: A 459 LEU cc_start: 0.7204 (mp) cc_final: 0.6672 (tt) REVERT: B 94 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8022 (t0) REVERT: B 157 MET cc_start: 0.8064 (ptm) cc_final: 0.7770 (ptm) REVERT: B 158 MET cc_start: 0.8614 (mmt) cc_final: 0.8048 (mmm) REVERT: B 226 MET cc_start: 0.8183 (mtm) cc_final: 0.7620 (mtm) REVERT: B 307 ARG cc_start: 0.7481 (mtp85) cc_final: 0.7273 (mtp85) REVERT: B 459 LEU cc_start: 0.7196 (mp) cc_final: 0.6627 (tt) REVERT: C 89 GLU cc_start: 0.7699 (mp0) cc_final: 0.7153 (pp20) REVERT: E 89 GLU cc_start: 0.7634 (mp0) cc_final: 0.7038 (pp20) REVERT: E 90 ASP cc_start: 0.7987 (m-30) cc_final: 0.7586 (m-30) REVERT: E 223 LYS cc_start: 0.5487 (mmmt) cc_final: 0.4712 (mmtm) REVERT: F 81 GLU cc_start: 0.7839 (pm20) cc_final: 0.7579 (pm20) REVERT: F 82 ASP cc_start: 0.8033 (m-30) cc_final: 0.7810 (m-30) REVERT: F 118 PHE cc_start: 0.6492 (m-10) cc_final: 0.5681 (m-10) REVERT: F 133 VAL cc_start: 0.5727 (t) cc_final: 0.5421 (t) REVERT: D 185 ASP cc_start: 0.6832 (m-30) cc_final: 0.6504 (m-30) outliers start: 25 outliers final: 20 residues processed: 158 average time/residue: 0.2554 time to fit residues: 60.6172 Evaluate side-chains 158 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 203 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 132 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 40 optimal weight: 0.0670 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.174843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.128862 restraints weight = 41033.927| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.11 r_work: 0.3409 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13700 Z= 0.122 Angle : 0.566 10.760 18646 Z= 0.288 Chirality : 0.053 1.671 2198 Planarity : 0.007 0.130 2304 Dihedral : 8.229 139.916 1918 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.34 % Favored : 93.32 % Rotamer: Outliers : 1.52 % Allowed : 12.17 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.12 % 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: -0.94 (0.21), residues: 1752 helix: 0.92 (0.20), residues: 742 sheet: -1.44 (0.24), residues: 412 loop : -1.89 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 307 TYR 0.012 0.001 TYR D 36 PHE 0.020 0.001 PHE E 160 TRP 0.013 0.001 TRP C 106 HIS 0.004 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00281 (13692) covalent geometry : angle 0.56543 (18630) SS BOND : bond 0.00311 ( 8) SS BOND : angle 0.66669 ( 16) hydrogen bonds : bond 0.03248 ( 704) hydrogen bonds : angle 4.42982 ( 2064) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8407 (OUTLIER) cc_final: 0.8030 (t0) REVERT: A 157 MET cc_start: 0.7978 (ptm) cc_final: 0.7695 (ptm) REVERT: A 459 LEU cc_start: 0.7226 (mp) cc_final: 0.6722 (tt) REVERT: B 94 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.8079 (t0) REVERT: B 157 MET cc_start: 0.8036 (ptm) cc_final: 0.7787 (ptm) REVERT: B 158 MET cc_start: 0.8636 (mmt) cc_final: 0.8039 (mmm) REVERT: B 226 MET cc_start: 0.8146 (mtm) cc_final: 0.7590 (mtm) REVERT: B 459 LEU cc_start: 0.7232 (mp) cc_final: 0.6755 (tt) REVERT: C 78 THR cc_start: 0.7024 (OUTLIER) cc_final: 0.6626 (p) REVERT: C 89 GLU cc_start: 0.7653 (mp0) cc_final: 0.7125 (pp20) REVERT: E 89 GLU cc_start: 0.7612 (mp0) cc_final: 0.7056 (pp20) REVERT: E 90 ASP cc_start: 0.7938 (m-30) cc_final: 0.7524 (m-30) REVERT: E 223 LYS cc_start: 0.5460 (mmmt) cc_final: 0.4751 (mmtm) REVERT: F 81 GLU cc_start: 0.7843 (pm20) cc_final: 0.7583 (pm20) REVERT: F 82 ASP cc_start: 0.7957 (m-30) cc_final: 0.7725 (m-30) REVERT: F 118 PHE cc_start: 0.6476 (m-10) cc_final: 0.5684 (m-10) REVERT: F 133 VAL cc_start: 0.5663 (t) cc_final: 0.5368 (t) outliers start: 22 outliers final: 13 residues processed: 159 average time/residue: 0.2414 time to fit residues: 58.7052 Evaluate side-chains 150 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 203 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 134 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.174217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.126340 restraints weight = 41388.034| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.85 r_work: 0.3407 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3303 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13700 Z= 0.129 Angle : 0.568 10.744 18646 Z= 0.291 Chirality : 0.054 1.683 2198 Planarity : 0.007 0.130 2304 Dihedral : 8.185 139.062 1918 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.28 % Favored : 93.44 % Rotamer: Outliers : 1.52 % Allowed : 12.31 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.12 % 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: -0.82 (0.21), residues: 1752 helix: 1.01 (0.20), residues: 742 sheet: -1.36 (0.25), residues: 412 loop : -1.85 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 307 TYR 0.010 0.001 TYR D 36 PHE 0.020 0.001 PHE B 305 TRP 0.013 0.001 TRP C 106 HIS 0.003 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00299 (13692) covalent geometry : angle 0.56825 (18630) SS BOND : bond 0.00336 ( 8) SS BOND : angle 0.69171 ( 16) hydrogen bonds : bond 0.03256 ( 704) hydrogen bonds : angle 4.36647 ( 2064) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.8072 (t0) REVERT: A 157 MET cc_start: 0.7983 (ptm) cc_final: 0.7721 (ptm) REVERT: A 459 LEU cc_start: 0.7258 (mp) cc_final: 0.6760 (tt) REVERT: B 94 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8072 (t0) REVERT: B 157 MET cc_start: 0.8041 (ptm) cc_final: 0.7800 (ptm) REVERT: B 158 MET cc_start: 0.8644 (mmt) cc_final: 0.8027 (mmm) REVERT: B 226 MET cc_start: 0.8163 (mtm) cc_final: 0.7644 (mtm) REVERT: B 459 LEU cc_start: 0.7236 (mp) cc_final: 0.6750 (tt) REVERT: C 89 GLU cc_start: 0.7684 (mp0) cc_final: 0.7174 (pp20) REVERT: E 78 THR cc_start: 0.6984 (OUTLIER) cc_final: 0.6601 (p) REVERT: E 89 GLU cc_start: 0.7610 (mp0) cc_final: 0.7078 (pp20) REVERT: E 90 ASP cc_start: 0.7962 (m-30) cc_final: 0.7554 (m-30) REVERT: E 223 LYS cc_start: 0.5593 (mmmt) cc_final: 0.4817 (mmtm) REVERT: F 66 ARG cc_start: 0.7692 (ttp80) cc_final: 0.7279 (ttp80) REVERT: F 81 GLU cc_start: 0.7843 (pm20) cc_final: 0.7589 (pm20) REVERT: F 82 ASP cc_start: 0.7966 (m-30) cc_final: 0.7748 (m-30) REVERT: F 118 PHE cc_start: 0.6515 (m-10) cc_final: 0.5731 (m-10) REVERT: F 133 VAL cc_start: 0.5778 (t) cc_final: 0.5496 (t) outliers start: 22 outliers final: 15 residues processed: 156 average time/residue: 0.2555 time to fit residues: 60.1185 Evaluate side-chains 154 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 203 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 43 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 155 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 160 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.174325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.129224 restraints weight = 41372.222| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.13 r_work: 0.3418 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3315 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13700 Z= 0.127 Angle : 0.562 10.756 18646 Z= 0.287 Chirality : 0.053 1.678 2198 Planarity : 0.007 0.129 2304 Dihedral : 8.134 139.189 1918 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.22 % Favored : 93.49 % Rotamer: Outliers : 1.38 % Allowed : 12.31 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.12 % 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: -0.75 (0.21), residues: 1752 helix: 1.05 (0.20), residues: 742 sheet: -1.32 (0.25), residues: 412 loop : -1.78 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 307 TYR 0.009 0.001 TYR D 36 PHE 0.015 0.001 PHE E 160 TRP 0.013 0.001 TRP C 106 HIS 0.003 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00295 (13692) covalent geometry : angle 0.56200 (18630) SS BOND : bond 0.00353 ( 8) SS BOND : angle 0.69304 ( 16) hydrogen bonds : bond 0.03222 ( 704) hydrogen bonds : angle 4.31807 ( 2064) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7967 (ptm) cc_final: 0.7716 (ptm) REVERT: A 459 LEU cc_start: 0.7270 (mp) cc_final: 0.6792 (tt) REVERT: B 157 MET cc_start: 0.8040 (ptm) cc_final: 0.7811 (ptm) REVERT: B 158 MET cc_start: 0.8651 (mmt) cc_final: 0.8014 (mmm) REVERT: B 226 MET cc_start: 0.8139 (mtm) cc_final: 0.7666 (mtm) REVERT: B 459 LEU cc_start: 0.7224 (mp) cc_final: 0.6764 (tt) REVERT: C 78 THR cc_start: 0.6931 (OUTLIER) cc_final: 0.6545 (p) REVERT: C 89 GLU cc_start: 0.7655 (mp0) cc_final: 0.7134 (pp20) REVERT: E 78 THR cc_start: 0.6997 (OUTLIER) cc_final: 0.6620 (p) REVERT: E 89 GLU cc_start: 0.7615 (mp0) cc_final: 0.7078 (pp20) REVERT: E 90 ASP cc_start: 0.7944 (m-30) cc_final: 0.7534 (m-30) REVERT: E 223 LYS cc_start: 0.5478 (mmmt) cc_final: 0.4790 (mmtm) REVERT: F 66 ARG cc_start: 0.7786 (ttp80) cc_final: 0.7334 (ttp80) REVERT: F 81 GLU cc_start: 0.7847 (pm20) cc_final: 0.7598 (pm20) REVERT: F 82 ASP cc_start: 0.7973 (m-30) cc_final: 0.7760 (m-30) REVERT: F 118 PHE cc_start: 0.6514 (m-10) cc_final: 0.5736 (m-10) REVERT: F 133 VAL cc_start: 0.5873 (t) cc_final: 0.5648 (t) REVERT: D 81 GLU cc_start: 0.7586 (pm20) cc_final: 0.7232 (pm20) REVERT: D 158 ASN cc_start: 0.6886 (p0) cc_final: 0.6571 (p0) outliers start: 20 outliers final: 16 residues processed: 154 average time/residue: 0.2601 time to fit residues: 60.2151 Evaluate side-chains 155 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 203 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 89 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 160 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.173665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.128481 restraints weight = 41524.476| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.13 r_work: 0.3406 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13700 Z= 0.135 Angle : 0.561 10.731 18646 Z= 0.287 Chirality : 0.053 1.679 2198 Planarity : 0.007 0.129 2304 Dihedral : 8.066 139.084 1914 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.34 % Favored : 93.44 % Rotamer: Outliers : 1.52 % Allowed : 12.38 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.12 % 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: -0.70 (0.21), residues: 1752 helix: 1.04 (0.20), residues: 744 sheet: -1.28 (0.25), residues: 398 loop : -1.70 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 307 TYR 0.009 0.001 TYR D 49 PHE 0.013 0.001 PHE E 160 TRP 0.014 0.001 TRP C 106 HIS 0.003 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00314 (13692) covalent geometry : angle 0.56127 (18630) SS BOND : bond 0.00360 ( 8) SS BOND : angle 0.70123 ( 16) hydrogen bonds : bond 0.03237 ( 704) hydrogen bonds : angle 4.30410 ( 2064) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7981 (ptm) cc_final: 0.7744 (ptm) REVERT: A 459 LEU cc_start: 0.7220 (mp) cc_final: 0.6776 (tt) REVERT: B 157 MET cc_start: 0.8067 (ptm) cc_final: 0.7819 (ptm) REVERT: B 158 MET cc_start: 0.8667 (mmt) cc_final: 0.8012 (mmm) REVERT: B 226 MET cc_start: 0.8187 (mtm) cc_final: 0.7723 (mtm) REVERT: B 356 MET cc_start: 0.8203 (mtp) cc_final: 0.7979 (mtp) REVERT: B 459 LEU cc_start: 0.7220 (mp) cc_final: 0.6770 (tt) REVERT: C 78 THR cc_start: 0.7037 (OUTLIER) cc_final: 0.6662 (p) REVERT: C 89 GLU cc_start: 0.7671 (mp0) cc_final: 0.7161 (pp20) REVERT: C 223 LYS cc_start: 0.5659 (mmmt) cc_final: 0.4840 (mmtm) REVERT: E 78 THR cc_start: 0.6983 (OUTLIER) cc_final: 0.6600 (p) REVERT: E 89 GLU cc_start: 0.7704 (mp0) cc_final: 0.7128 (pp20) REVERT: E 90 ASP cc_start: 0.7977 (m-30) cc_final: 0.7573 (m-30) REVERT: F 66 ARG cc_start: 0.7929 (ttp80) cc_final: 0.7722 (ttp80) REVERT: F 81 GLU cc_start: 0.7881 (pm20) cc_final: 0.7610 (pm20) REVERT: F 82 ASP cc_start: 0.7992 (m-30) cc_final: 0.7768 (m-30) REVERT: F 118 PHE cc_start: 0.6549 (m-10) cc_final: 0.5778 (m-10) REVERT: F 133 VAL cc_start: 0.5771 (t) cc_final: 0.5571 (t) REVERT: D 66 ARG cc_start: 0.7859 (ttp80) cc_final: 0.7632 (ttp80) REVERT: D 81 GLU cc_start: 0.7645 (pm20) cc_final: 0.7401 (pm20) REVERT: D 158 ASN cc_start: 0.6931 (p0) cc_final: 0.6389 (p0) outliers start: 22 outliers final: 18 residues processed: 163 average time/residue: 0.2664 time to fit residues: 64.5799 Evaluate side-chains 161 residues out of total 1450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 213 ASN Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 203 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 51 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 169 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.172150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.126157 restraints weight = 41399.922| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.77 r_work: 0.3406 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13700 Z= 0.134 Angle : 0.561 10.754 18646 Z= 0.287 Chirality : 0.053 1.677 2198 Planarity : 0.007 0.129 2304 Dihedral : 8.064 139.519 1914 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.39 % Favored : 93.38 % Rotamer: Outliers : 1.59 % Allowed : 12.52 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 5.41 % Twisted General : 0.12 % 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: -0.62 (0.21), residues: 1752 helix: 1.06 (0.20), residues: 744 sheet: -1.18 (0.26), residues: 386 loop : -1.64 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 307 TYR 0.009 0.001 TYR D 36 PHE 0.013 0.001 PHE E 160 TRP 0.013 0.001 TRP C 106 HIS 0.003 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00310 (13692) covalent geometry : angle 0.56098 (18630) SS BOND : bond 0.00351 ( 8) SS BOND : angle 0.69518 ( 16) hydrogen bonds : bond 0.03231 ( 704) hydrogen bonds : angle 4.28207 ( 2064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6909.44 seconds wall clock time: 117 minutes 49.73 seconds (7069.73 seconds total)