Starting phenix.real_space_refine on Fri Jul 3 18:25:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8asj_15617/07_2026/8asj_15617.cif Found real_map, /net/cci-nas-00/data/ceres_data/8asj_15617/07_2026/8asj_15617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8asj_15617/07_2026/8asj_15617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8asj_15617/07_2026/8asj_15617.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8asj_15617/07_2026/8asj_15617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8asj_15617/07_2026/8asj_15617.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8asj_15617/07_2026/8asj_15617.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8asj_15617/07_2026/8asj_15617.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 10 7.16 5 P 12 5.49 5 S 74 5.16 5 C 9715 2.51 5 N 2338 2.21 5 O 2571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14720 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1342 Classifications: {'peptide': 179} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 168} Chain: "B" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3477 Classifications: {'peptide': 433} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 404} Chain: "C" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1944 Classifications: {'peptide': 254} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 233} Chain: "D" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 222 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "E" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1357 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 170} Chain: "F" Number of atoms: 3471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3471 Classifications: {'peptide': 432} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 403} Chain: "G" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1944 Classifications: {'peptide': 254} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 233} Chain: "H" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 203 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'FES': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 316 Unusual residues: {'HEM': 2, 'PEE': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 76 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'FES': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "F" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 265 Unusual residues: {'HEM': 2, 'PEE': 4, 'U10': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 84 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 913 SG CYS A 129 34.288 79.492 51.048 1.00 88.05 S ATOM 1053 SG CYS A 149 37.103 81.000 52.863 1.00 83.58 S ATOM 7913 SG CYS E 129 63.956 35.852 87.115 1.00178.24 S ATOM 8053 SG CYS E 149 59.607 34.141 86.774 1.00191.63 S Time building chain proxies: 3.21, per 1000 atoms: 0.22 Number of scatterers: 14720 At special positions: 0 Unit cell: (119.524, 114.836, 119.524, 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) Fe 10 26.01 S 74 16.00 P 12 15.00 O 2571 8.00 N 2338 7.00 C 9715 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 151 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 151 " 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 728.1 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 201 " pdb="FE2 FES A 201 " - pdb=" ND1 HIS A 152 " pdb="FE2 FES A 201 " - pdb=" ND1 HIS A 131 " pdb="FE1 FES A 201 " - pdb=" SG CYS A 149 " pdb="FE1 FES A 201 " - pdb=" SG CYS A 129 " pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" NE2 HIS E 131 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 149 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 129 " pdb="FE2 FES E 201 " - pdb=" ND1 HIS E 152 " Number of angles added : 6 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3254 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 12 sheets defined 57.9% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 10 through 37 Proline residue: A 33 - end of helix Processing helix chain 'A' and resid 41 through 47 Processing helix chain 'A' and resid 78 through 84 Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.747A pdb=" N LEU A 93 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'B' and resid 13 through 21 Processing helix chain 'B' and resid 24 through 34 Processing helix chain 'B' and resid 42 through 45 Processing helix chain 'B' and resid 46 through 66 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 89 through 119 removed outlier: 3.693A pdb=" N SER B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 149 Processing helix chain 'B' and resid 152 through 167 removed outlier: 4.139A pdb=" N PHE B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY B 167 " --> pdb=" O THR B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 182 removed outlier: 4.520A pdb=" N SER B 175 " --> pdb=" O GLY B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 220 Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 233 through 240 Processing helix chain 'B' and resid 244 through 270 removed outlier: 6.675A pdb=" N ILE B 249 " --> pdb=" O TRP B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 295 through 297 No H-bonds generated for 'chain 'B' and resid 295 through 297' Processing helix chain 'B' and resid 298 through 308 removed outlier: 3.895A pdb=" N PHE B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 322 Processing helix chain 'B' and resid 327 through 345 removed outlier: 4.015A pdb=" N ILE B 340 " --> pdb=" O MET B 336 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 356 through 360 Processing helix chain 'B' and resid 362 through 381 removed outlier: 3.532A pdb=" N TYR B 366 " --> pdb=" O MET B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 406 removed outlier: 3.686A pdb=" N PHE B 404 " --> pdb=" O TRP B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 415 removed outlier: 3.556A pdb=" N GLY B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B 413 " --> pdb=" O PRO B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 432 removed outlier: 3.554A pdb=" N HIS B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 57 Processing helix chain 'C' and resid 58 through 61 Processing helix chain 'C' and resid 68 through 74 Processing helix chain 'C' and resid 81 through 90 Processing helix chain 'C' and resid 139 through 146 Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 168 through 172 removed outlier: 4.307A pdb=" N GLU C 172 " --> pdb=" O GLU C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 242 Processing helix chain 'C' and resid 244 through 276 removed outlier: 3.705A pdb=" N GLY C 276 " --> pdb=" O ARG C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 278 No H-bonds generated for 'chain 'C' and resid 277 through 278' Processing helix chain 'D' and resid 78 through 78 No H-bonds generated for 'chain 'D' and resid 78 through 78' Processing helix chain 'D' and resid 79 through 102 removed outlier: 3.635A pdb=" N ARG D 83 " --> pdb=" O LYS D 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 37 removed outlier: 3.539A pdb=" N LEU E 15 " --> pdb=" O ARG E 11 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Proline residue: E 33 - end of helix Processing helix chain 'E' and resid 42 through 47 removed outlier: 3.687A pdb=" N GLN E 45 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU E 47 " --> pdb=" O VAL E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 62 removed outlier: 3.514A pdb=" N VAL E 61 " --> pdb=" O VAL E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 86 Processing helix chain 'F' and resid 13 through 21 Processing helix chain 'F' and resid 24 through 34 Processing helix chain 'F' and resid 42 through 45 Processing helix chain 'F' and resid 46 through 67 Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'F' and resid 89 through 118 removed outlier: 3.732A pdb=" N SER F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 149 Processing helix chain 'F' and resid 152 through 168 removed outlier: 3.777A pdb=" N PHE F 166 " --> pdb=" O ILE F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 182 Processing helix chain 'F' and resid 187 through 220 Proline residue: F 202 - end of helix Processing helix chain 'F' and resid 233 through 240 removed outlier: 3.505A pdb=" N LYS F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 270 removed outlier: 6.741A pdb=" N ILE F 249 " --> pdb=" O TRP F 245 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL F 262 " --> pdb=" O VAL F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 281 Processing helix chain 'F' and resid 295 through 297 No H-bonds generated for 'chain 'F' and resid 295 through 297' Processing helix chain 'F' and resid 298 through 308 removed outlier: 3.952A pdb=" N PHE F 308 " --> pdb=" O ILE F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 322 Processing helix chain 'F' and resid 327 through 345 removed outlier: 4.350A pdb=" N ILE F 340 " --> pdb=" O MET F 336 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET F 343 " --> pdb=" O ALA F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 350 Processing helix chain 'F' and resid 356 through 360 Processing helix chain 'F' and resid 362 through 382 removed outlier: 3.571A pdb=" N TYR F 366 " --> pdb=" O MET F 362 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA F 382 " --> pdb=" O THR F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 406 removed outlier: 3.777A pdb=" N PHE F 404 " --> pdb=" O TRP F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 415 removed outlier: 3.704A pdb=" N ALA F 413 " --> pdb=" O PRO F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 432 Processing helix chain 'G' and resid 43 through 57 Processing helix chain 'G' and resid 58 through 61 Processing helix chain 'G' and resid 68 through 74 Processing helix chain 'G' and resid 81 through 91 removed outlier: 3.738A pdb=" N GLN G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 146 Processing helix chain 'G' and resid 148 through 158 Processing helix chain 'G' and resid 225 through 242 Processing helix chain 'G' and resid 244 through 278 removed outlier: 4.142A pdb=" N GLY G 276 " --> pdb=" O ARG G 272 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL G 277 " --> pdb=" O LEU G 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 105 removed outlier: 3.572A pdb=" N LEU H 85 " --> pdb=" O TYR H 81 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY H 86 " --> pdb=" O ARG H 82 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE H 102 " --> pdb=" O LEU H 98 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER H 103 " --> pdb=" O ALA H 99 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 54 removed outlier: 6.063A pdb=" N VAL A 52 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 67 removed outlier: 3.678A pdb=" N VAL A 61 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 74 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 147 through 148 removed outlier: 6.553A pdb=" N HIS A 155 " --> pdb=" O ARG A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA5, first strand: chain 'C' and resid 93 through 95 Processing sheet with id=AA6, first strand: chain 'C' and resid 177 through 179 Processing sheet with id=AA7, first strand: chain 'C' and resid 192 through 193 Processing sheet with id=AA8, first strand: chain 'E' and resid 66 through 67 Processing sheet with id=AA9, first strand: chain 'E' and resid 145 through 148 removed outlier: 3.598A pdb=" N TRP E 147 " --> pdb=" O TYR E 156 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS E 164 " --> pdb=" O HIS E 155 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ASP E 157 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE E 162 " --> pdb=" O ASP E 157 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 36 through 38 Processing sheet with id=AB2, first strand: chain 'G' and resid 93 through 95 Processing sheet with id=AB3, first strand: chain 'G' and resid 177 through 179 739 hydrogen bonds defined for protein. 2109 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.39: 6218 1.39 - 1.60: 8804 1.60 - 1.80: 112 1.80 - 2.01: 34 2.01 - 2.21: 32 Bond restraints: 15200 Sorted by residual: bond pdb=" C18 PEE B 508 " pdb=" C19 PEE B 508 " ideal model delta sigma weight residual 1.523 1.328 0.195 2.00e-02 2.50e+03 9.48e+01 bond pdb=" C38 PEE B 503 " pdb=" C39 PEE B 503 " ideal model delta sigma weight residual 1.523 1.334 0.189 2.00e-02 2.50e+03 8.88e+01 bond pdb=" C38 PEE E 202 " pdb=" C39 PEE E 202 " ideal model delta sigma weight residual 1.523 1.335 0.188 2.00e-02 2.50e+03 8.82e+01 bond pdb=" C38 PEE B 507 " pdb=" C39 PEE B 507 " ideal model delta sigma weight residual 1.523 1.335 0.188 2.00e-02 2.50e+03 8.82e+01 bond pdb=" C38 PEE B 508 " pdb=" C39 PEE B 508 " ideal model delta sigma weight residual 1.523 1.338 0.185 2.00e-02 2.50e+03 8.52e+01 ... (remaining 15195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.11: 20630 6.11 - 12.22: 84 12.22 - 18.33: 16 18.33 - 24.44: 1 24.44 - 30.54: 3 Bond angle restraints: 20734 Sorted by residual: angle pdb=" C17 PEE B 508 " pdb=" C18 PEE B 508 " pdb=" C19 PEE B 508 " ideal model delta sigma weight residual 113.68 144.22 -30.54 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C38 PEE B 503 " pdb=" C39 PEE B 503 " pdb=" C40 PEE B 503 " ideal model delta sigma weight residual 112.47 85.91 26.56 3.00e+00 1.11e-01 7.84e+01 angle pdb=" C38 PEE B 507 " pdb=" C39 PEE B 507 " pdb=" C40 PEE B 507 " ideal model delta sigma weight residual 112.47 86.07 26.40 3.00e+00 1.11e-01 7.74e+01 angle pdb=" C38 PEE B 508 " pdb=" C39 PEE B 508 " pdb=" C40 PEE B 508 " ideal model delta sigma weight residual 112.47 91.41 21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" O3P PEE F 503 " pdb=" P PEE F 503 " pdb=" O4P PEE F 503 " ideal model delta sigma weight residual 92.91 110.59 -17.68 3.00e+00 1.11e-01 3.47e+01 ... (remaining 20729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.84: 8340 33.84 - 67.68: 174 67.68 - 101.52: 54 101.52 - 135.35: 13 135.35 - 169.19: 9 Dihedral angle restraints: 8590 sinusoidal: 3485 harmonic: 5105 Sorted by residual: dihedral pdb=" C6 U10 F 507 " pdb=" C7 U10 F 507 " pdb=" C8 U10 F 507 " pdb=" C9 U10 F 507 " ideal model delta sinusoidal sigma weight residual 101.51 -104.74 -153.75 1 2.00e+01 2.50e-03 4.55e+01 dihedral pdb=" C2B HEC G 301 " pdb=" C3B HEC G 301 " pdb=" CAB HEC G 301 " pdb=" CBB HEC G 301 " ideal model delta sinusoidal sigma weight residual 240.00 172.21 67.79 2 1.00e+01 1.00e-02 4.11e+01 dihedral pdb=" C2C HEC G 301 " pdb=" C3C HEC G 301 " pdb=" CAC HEC G 301 " pdb=" CBC HEC G 301 " ideal model delta sinusoidal sigma weight residual 240.00 179.16 60.84 2 1.00e+01 1.00e-02 3.66e+01 ... (remaining 8587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1542 0.043 - 0.087: 456 0.087 - 0.130: 127 0.130 - 0.173: 15 0.173 - 0.217: 7 Chirality restraints: 2147 Sorted by residual: chirality pdb=" C2 PEE A 202 " pdb=" C1 PEE A 202 " pdb=" C3 PEE A 202 " pdb=" O2 PEE A 202 " both_signs ideal model delta sigma weight residual False -2.33 -2.54 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB VAL F 242 " pdb=" CA VAL F 242 " pdb=" CG1 VAL F 242 " pdb=" CG2 VAL F 242 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C2 PEE F 504 " pdb=" C1 PEE F 504 " pdb=" C3 PEE F 504 " pdb=" O2 PEE F 504 " both_signs ideal model delta sigma weight residual False -2.33 -2.53 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 2144 not shown) Planarity restraints: 2582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC C 301 " 0.024 2.00e-02 2.50e+03 8.25e-02 1.53e+02 pdb=" C2C HEC C 301 " -0.225 2.00e-02 2.50e+03 pdb=" C3C HEC C 301 " 0.052 2.00e-02 2.50e+03 pdb=" C4C HEC C 301 " 0.012 2.00e-02 2.50e+03 pdb=" CAC HEC C 301 " 0.032 2.00e-02 2.50e+03 pdb=" CHC HEC C 301 " 0.037 2.00e-02 2.50e+03 pdb=" CHD HEC C 301 " -0.008 2.00e-02 2.50e+03 pdb=" CMC HEC C 301 " 0.069 2.00e-02 2.50e+03 pdb=" NC HEC C 301 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC G 301 " 0.025 2.00e-02 2.50e+03 8.20e-02 1.51e+02 pdb=" C2C HEC G 301 " -0.225 2.00e-02 2.50e+03 pdb=" C3C HEC G 301 " 0.044 2.00e-02 2.50e+03 pdb=" C4C HEC G 301 " 0.012 2.00e-02 2.50e+03 pdb=" CAC HEC G 301 " 0.038 2.00e-02 2.50e+03 pdb=" CHC HEC G 301 " 0.040 2.00e-02 2.50e+03 pdb=" CHD HEC G 301 " -0.008 2.00e-02 2.50e+03 pdb=" CMC HEC G 301 " 0.064 2.00e-02 2.50e+03 pdb=" NC HEC G 301 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 230 " -0.203 9.50e-02 1.11e+02 9.16e-02 6.68e+00 pdb=" NE ARG B 230 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG B 230 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG B 230 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 230 " -0.000 2.00e-02 2.50e+03 ... (remaining 2579 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 393 2.71 - 3.26: 15409 3.26 - 3.81: 25093 3.81 - 4.35: 31843 4.35 - 4.90: 52010 Nonbonded interactions: 124748 Sorted by model distance: nonbonded pdb=" NE2 HIS F 97 " pdb="FE HEM F 502 " model vdw 2.165 3.080 nonbonded pdb=" CE MET C 207 " pdb="FE HEC C 301 " model vdw 2.200 3.420 nonbonded pdb=" SD MET G 207 " pdb="FE HEC G 301 " model vdw 2.210 3.360 nonbonded pdb=" NE2 HIS B 97 " pdb="FE HEM B 502 " model vdw 2.217 3.080 nonbonded pdb=" OD1 ASN B 272 " pdb=" OH TYR B 280 " model vdw 2.247 3.040 ... (remaining 124743 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 201 or (resid 202 and (name N or name C1 or name \ C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or \ name C17 or name C18 or name C2 or name C3 or name C30 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C \ 39 or name C4 or name C5 or name O1P or name O2 or name O2P or name O3 or name O \ 3P or name O4 or name O4P or name O5 or name P )))) selection = (chain 'E' and resid 9 through 202) } ncs_group { reference = (chain 'B' and (resid 1 through 432 or resid 502 or resid 504 or (resid 505 and \ (name N or name C1 or name C10 or name C11 or name C12 or name C13 or name C14 o \ r name C15 or name C16 or name C2 or name C3 or name C30 or name C31 or name C32 \ or name C33 or name C34 or name C35 or name C4 or name C5 or name O1P or name O \ 2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P \ )) or resid 506 or (resid 507 and (name N or name C1 or name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C1 \ 8 or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name \ C24 or name C25 or name C26 or name C27 or name C3 or name C30 or name C31 or n \ ame C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C4 or name C40 or name C5 or name O1P or name O2 or name O2P \ or name O3 or name O3P or name O4 or name O4P or name O5 or name P )))) selection = (chain 'F' and (resid 1 through 501 or resid 503 or (resid 504 and (name N or na \ me C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or \ name C16 or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 \ or name C34 or name C35 or name C4 or name C5 or name O1P or name O2 or name O2P \ or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or resid \ 505 through 506)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 78 through 104) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.440 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 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 : 0.011 0.526 15218 Z= 0.621 Angle : 1.215 53.710 20744 Z= 0.468 Chirality : 0.045 0.217 2147 Planarity : 0.009 0.092 2582 Dihedral : 17.606 169.193 5330 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.38 % Favored : 96.50 % Rotamer: Outliers : 0.21 % Allowed : 3.63 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.18), residues: 1773 helix: -0.36 (0.15), residues: 933 sheet: -1.68 (0.58), residues: 61 loop : -0.64 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.004 ARG B 230 TYR 0.019 0.004 TYR E 156 PHE 0.042 0.002 PHE D 87 TRP 0.029 0.002 TRP E 147 HIS 0.007 0.001 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00840 / 0.42 (15200) covalent geometry : angle 1.09206 / 0.46 (20734) SS BOND : bond 0.00314 / 0.18 ( 2) SS BOND : angle 1.38754 / 0.81 ( 4) hydrogen bonds : bond 0.13448 / 8.72 ( 739) hydrogen bonds : angle 6.03654 / 4.26 ( 2109) metal coordination : bond 0.18856 / 14.55 ( 8) metal coordination : angle 31.33780 / 17.84 ( 6) Misc. bond : bond 0.21226 / 11.52 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 327 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 68 LEU cc_start: 0.6307 (tp) cc_final: 0.5986 (tt) REVERT: A 76 ARG cc_start: 0.6714 (ttt180) cc_final: 0.6386 (mtp85) REVERT: A 89 GLN cc_start: 0.7314 (mt0) cc_final: 0.7075 (tp40) REVERT: A 113 ASN cc_start: 0.7524 (m-40) cc_final: 0.7261 (m-40) REVERT: A 184 ILE cc_start: 0.6547 (mt) cc_final: 0.6302 (mt) REVERT: B 34 MET cc_start: 0.8460 (mmm) cc_final: 0.8236 (mmt) REVERT: B 84 MET cc_start: 0.8076 (mmm) cc_final: 0.7647 (mmt) REVERT: B 133 MET cc_start: 0.7778 (mmm) cc_final: 0.7340 (mmm) REVERT: B 137 LEU cc_start: 0.7340 (mt) cc_final: 0.7057 (mt) REVERT: B 180 LEU cc_start: 0.7848 (mt) cc_final: 0.7586 (tp) REVERT: B 306 ARG cc_start: 0.6934 (mtm180) cc_final: 0.6719 (mmt180) REVERT: B 317 ILE cc_start: 0.6793 (mp) cc_final: 0.6348 (mt) REVERT: B 342 VAL cc_start: 0.8098 (p) cc_final: 0.7794 (m) REVERT: B 393 SER cc_start: 0.8428 (t) cc_final: 0.8010 (p) REVERT: B 431 HIS cc_start: 0.6475 (m-70) cc_final: 0.6152 (m170) REVERT: C 64 MET cc_start: 0.7671 (mtt) cc_final: 0.7460 (mtm) REVERT: C 70 ARG cc_start: 0.7513 (ptt90) cc_final: 0.7180 (ptt90) REVERT: C 79 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7443 (mt-10) REVERT: C 86 ARG cc_start: 0.6599 (ttm110) cc_final: 0.6259 (mtm-85) REVERT: C 141 SER cc_start: 0.8326 (t) cc_final: 0.8101 (t) REVERT: F 137 LEU cc_start: 0.7106 (mt) cc_final: 0.6530 (mt) REVERT: F 270 MET cc_start: 0.8622 (ptm) cc_final: 0.8288 (ptp) REVERT: F 282 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7393 (mt-10) REVERT: F 325 ILE cc_start: 0.8047 (mm) cc_final: 0.7820 (tt) REVERT: F 352 SER cc_start: 0.7327 (t) cc_final: 0.7039 (m) REVERT: F 426 GLU cc_start: 0.7482 (tt0) cc_final: 0.6491 (tp30) REVERT: F 431 HIS cc_start: 0.6176 (m-70) cc_final: 0.5720 (m-70) REVERT: G 136 MET cc_start: 0.6401 (tpp) cc_final: 0.5615 (mtm) REVERT: G 164 PRO cc_start: 0.6686 (Cg_exo) cc_final: 0.6364 (Cg_endo) REVERT: G 223 ASP cc_start: 0.7174 (t0) cc_final: 0.6893 (t70) REVERT: G 257 MET cc_start: 0.6780 (mmp) cc_final: 0.6569 (mmt) REVERT: G 267 TYR cc_start: 0.8117 (t80) cc_final: 0.7883 (t80) outliers start: 3 outliers final: 1 residues processed: 330 average time/residue: 0.1123 time to fit residues: 56.1634 Evaluate side-chains 228 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 GLN B 217 HIS C 113 HIS C 171 HIS F 58 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.140264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.128217 restraints weight = 15847.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.098746 restraints weight = 42308.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.099251 restraints weight = 40038.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.098141 restraints weight = 33047.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.098397 restraints weight = 26837.984| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.294 15218 Z= 0.186 Angle : 0.777 31.191 20744 Z= 0.340 Chirality : 0.047 0.239 2147 Planarity : 0.005 0.050 2582 Dihedral : 17.115 147.979 2274 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.26 % Favored : 97.63 % Rotamer: Outliers : 1.88 % Allowed : 8.23 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.47 (0.20), residues: 1773 helix: 1.00 (0.17), residues: 942 sheet: -1.95 (0.49), residues: 77 loop : -0.19 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 77 TYR 0.020 0.002 TYR F 302 PHE 0.037 0.002 PHE D 87 TRP 0.019 0.002 TRP F 157 HIS 0.009 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.18 (15200) covalent geometry : angle 0.71196 / 0.34 (20734) SS BOND : bond 0.00294 / 0.18 ( 2) SS BOND : angle 0.44027 / 0.22 ( 4) hydrogen bonds : bond 0.05548 / 3.76 ( 739) hydrogen bonds : angle 4.54591 / 3.23 ( 2109) metal coordination : bond 0.03021 / 2.06 ( 8) metal coordination : angle 18.28666 / 10.38 ( 6) Misc. bond : bond 0.19454 / 14.09 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 0.466 Fit side-chains REVERT: A 63 LEU cc_start: 0.7630 (mt) cc_final: 0.7359 (mm) REVERT: A 113 ASN cc_start: 0.7436 (m-40) cc_final: 0.7193 (m-40) REVERT: B 133 MET cc_start: 0.8333 (mmm) cc_final: 0.7650 (mmm) REVERT: B 137 LEU cc_start: 0.8089 (mt) cc_final: 0.7824 (mt) REVERT: B 180 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8195 (tp) REVERT: B 260 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7306 (mt) REVERT: B 317 ILE cc_start: 0.7025 (OUTLIER) cc_final: 0.6500 (mt) REVERT: B 342 VAL cc_start: 0.8910 (p) cc_final: 0.8626 (m) REVERT: B 362 MET cc_start: 0.7577 (mtp) cc_final: 0.7238 (ttm) REVERT: B 378 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8432 (m) REVERT: C 86 ARG cc_start: 0.7065 (ttm110) cc_final: 0.6815 (mtm-85) REVERT: E 45 GLN cc_start: 0.6480 (mp10) cc_final: 0.5940 (mp10) REVERT: F 325 ILE cc_start: 0.8097 (mm) cc_final: 0.7813 (tt) REVERT: F 352 SER cc_start: 0.7850 (t) cc_final: 0.7396 (m) REVERT: G 74 GLU cc_start: 0.7064 (mm-30) cc_final: 0.6664 (mt-10) REVERT: G 104 GLU cc_start: 0.6459 (mt-10) cc_final: 0.6251 (mt-10) REVERT: G 125 MET cc_start: 0.8750 (tpp) cc_final: 0.8407 (tpp) REVERT: G 136 MET cc_start: 0.6137 (tpp) cc_final: 0.5579 (mtm) REVERT: G 163 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7489 (mm-30) REVERT: G 222 HIS cc_start: 0.7086 (m90) cc_final: 0.6864 (m90) REVERT: G 246 MET cc_start: 0.8150 (mmt) cc_final: 0.7638 (mmt) REVERT: G 257 MET cc_start: 0.7723 (mmp) cc_final: 0.7437 (mmt) outliers start: 27 outliers final: 16 residues processed: 253 average time/residue: 0.1125 time to fit residues: 43.4589 Evaluate side-chains 233 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 213 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 261 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 17 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 143 optimal weight: 0.2980 chunk 47 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 chunk 121 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.142778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.131028 restraints weight = 15923.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.101993 restraints weight = 38582.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.101450 restraints weight = 37503.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.101589 restraints weight = 33240.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.101636 restraints weight = 28099.372| |-----------------------------------------------------------------------------| r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.277 15218 Z= 0.120 Angle : 0.646 26.745 20744 Z= 0.285 Chirality : 0.043 0.183 2147 Planarity : 0.005 0.043 2582 Dihedral : 15.179 150.588 2274 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.71 % Favored : 97.18 % Rotamer: Outliers : 1.95 % Allowed : 9.00 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.20), residues: 1773 helix: 1.45 (0.17), residues: 938 sheet: -1.86 (0.50), residues: 77 loop : -0.02 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.016 0.001 TYR B 359 PHE 0.023 0.001 PHE D 87 TRP 0.015 0.001 TRP F 157 HIS 0.005 0.001 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (15200) covalent geometry : angle 0.59742 / 0.28 (20734) SS BOND : bond 0.00207 / 0.13 ( 2) SS BOND : angle 0.30072 / 0.16 ( 4) hydrogen bonds : bond 0.04516 / 3.05 ( 739) hydrogen bonds : angle 4.14354 / 2.94 ( 2109) metal coordination : bond 0.01427 / 0.90 ( 8) metal coordination : angle 14.43823 / 8.37 ( 6) Misc. bond : bond 0.16502 / 11.94 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 231 time to evaluate : 0.548 Fit side-chains REVERT: A 70 LYS cc_start: 0.7682 (mttt) cc_final: 0.7127 (mtmm) REVERT: B 84 MET cc_start: 0.8667 (mmm) cc_final: 0.8316 (mmt) REVERT: B 180 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8194 (tp) REVERT: B 260 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7272 (mt) REVERT: B 279 ASN cc_start: 0.8571 (t0) cc_final: 0.8219 (t0) REVERT: B 317 ILE cc_start: 0.6954 (OUTLIER) cc_final: 0.6462 (mt) REVERT: B 342 VAL cc_start: 0.8864 (p) cc_final: 0.8623 (m) REVERT: B 362 MET cc_start: 0.7535 (mtp) cc_final: 0.7195 (ttm) REVERT: C 246 MET cc_start: 0.7784 (mmm) cc_final: 0.7249 (mmm) REVERT: E 52 VAL cc_start: 0.2551 (OUTLIER) cc_final: 0.2262 (t) REVERT: F 140 MET cc_start: 0.6553 (mtp) cc_final: 0.6236 (mtm) REVERT: F 325 ILE cc_start: 0.8037 (mm) cc_final: 0.7750 (tt) REVERT: F 352 SER cc_start: 0.7868 (t) cc_final: 0.7384 (m) REVERT: F 431 HIS cc_start: 0.5856 (m-70) cc_final: 0.5504 (m-70) REVERT: G 64 MET cc_start: 0.8687 (mtm) cc_final: 0.8483 (mtp) REVERT: G 125 MET cc_start: 0.8800 (tpp) cc_final: 0.8531 (tpp) REVERT: G 136 MET cc_start: 0.6179 (tpp) cc_final: 0.5533 (mtm) REVERT: G 163 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7483 (mm-30) REVERT: G 246 MET cc_start: 0.8157 (mmt) cc_final: 0.7728 (mmt) REVERT: G 257 MET cc_start: 0.7759 (mmp) cc_final: 0.7520 (mmt) outliers start: 28 outliers final: 15 residues processed: 250 average time/residue: 0.1096 time to fit residues: 42.4545 Evaluate side-chains 238 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 219 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 268 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 40 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 HIS ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.139384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.127724 restraints weight = 16032.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.100991 restraints weight = 39896.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.099826 restraints weight = 45315.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.099914 restraints weight = 34230.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.100444 restraints weight = 25533.156| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.338 15218 Z= 0.157 Angle : 0.671 24.449 20744 Z= 0.296 Chirality : 0.044 0.189 2147 Planarity : 0.005 0.039 2582 Dihedral : 14.409 148.980 2274 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.65 % Favored : 97.24 % Rotamer: Outliers : 2.65 % Allowed : 8.58 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.20), residues: 1773 helix: 1.29 (0.17), residues: 948 sheet: -1.86 (0.49), residues: 78 loop : -0.05 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 163 TYR 0.017 0.001 TYR F 399 PHE 0.027 0.002 PHE D 87 TRP 0.015 0.001 TRP A 147 HIS 0.008 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.15 (15200) covalent geometry : angle 0.63247 / 0.30 (20734) SS BOND : bond 0.00198 / 0.12 ( 2) SS BOND : angle 0.32872 / 0.16 ( 4) hydrogen bonds : bond 0.05009 / 3.40 ( 739) hydrogen bonds : angle 4.18292 / 2.97 ( 2109) metal coordination : bond 0.01337 / 0.84 ( 8) metal coordination : angle 13.18910 / 7.61 ( 6) Misc. bond : bond 0.18480 / 13.53 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 220 time to evaluate : 0.512 Fit side-chains REVERT: A 47 LEU cc_start: 0.5977 (OUTLIER) cc_final: 0.5601 (mm) REVERT: B 34 MET cc_start: 0.8939 (mmm) cc_final: 0.8608 (mmm) REVERT: B 180 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8291 (tp) REVERT: B 260 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7292 (mt) REVERT: B 279 ASN cc_start: 0.8544 (t0) cc_final: 0.8206 (t0) REVERT: B 317 ILE cc_start: 0.7189 (OUTLIER) cc_final: 0.6634 (mt) REVERT: B 342 VAL cc_start: 0.8847 (OUTLIER) cc_final: 0.8575 (m) REVERT: B 362 MET cc_start: 0.7514 (mtp) cc_final: 0.7253 (ttm) REVERT: C 246 MET cc_start: 0.7728 (mmm) cc_final: 0.7183 (mmm) REVERT: E 45 GLN cc_start: 0.6644 (mp10) cc_final: 0.6374 (mp10) REVERT: F 325 ILE cc_start: 0.7926 (mm) cc_final: 0.7720 (tt) REVERT: F 352 SER cc_start: 0.7929 (t) cc_final: 0.7451 (m) REVERT: F 431 HIS cc_start: 0.5880 (m-70) cc_final: 0.5556 (m-70) REVERT: G 83 ASP cc_start: 0.6435 (OUTLIER) cc_final: 0.6165 (t0) REVERT: G 125 MET cc_start: 0.8770 (tpp) cc_final: 0.8478 (tpp) REVERT: G 136 MET cc_start: 0.6268 (tpp) cc_final: 0.5817 (mtm) REVERT: G 163 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7496 (mm-30) outliers start: 38 outliers final: 24 residues processed: 245 average time/residue: 0.1108 time to fit residues: 41.7951 Evaluate side-chains 244 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain G residue 268 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 77 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.140091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.127663 restraints weight = 15908.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.102833 restraints weight = 43754.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.100863 restraints weight = 54031.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.100258 restraints weight = 39738.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.101113 restraints weight = 29650.297| |-----------------------------------------------------------------------------| r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.301 15218 Z= 0.138 Angle : 0.627 22.733 20744 Z= 0.281 Chirality : 0.043 0.181 2147 Planarity : 0.005 0.038 2582 Dihedral : 13.850 152.288 2273 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.82 % Favored : 97.12 % Rotamer: Outliers : 2.16 % Allowed : 9.62 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.20), residues: 1773 helix: 1.34 (0.17), residues: 948 sheet: -1.87 (0.50), residues: 78 loop : -0.04 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 248 TYR 0.017 0.001 TYR B 359 PHE 0.028 0.002 PHE D 87 TRP 0.014 0.001 TRP F 157 HIS 0.006 0.001 HIS F 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (15200) covalent geometry : angle 0.59287 / 0.28 (20734) SS BOND : bond 0.00188 / 0.11 ( 2) SS BOND : angle 0.27518 / 0.15 ( 4) hydrogen bonds : bond 0.04722 / 3.21 ( 739) hydrogen bonds : angle 4.08722 / 2.90 ( 2109) metal coordination : bond 0.01197 / 0.75 ( 8) metal coordination : angle 12.01186 / 6.94 ( 6) Misc. bond : bond 0.16934 / 12.36 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 228 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: A 70 LYS cc_start: 0.7777 (mttt) cc_final: 0.7574 (mttp) REVERT: B 10 GLU cc_start: 0.5518 (pt0) cc_final: 0.5205 (pt0) REVERT: B 34 MET cc_start: 0.8889 (mmm) cc_final: 0.8568 (mmm) REVERT: B 180 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8169 (tp) REVERT: B 260 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7179 (mt) REVERT: B 274 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8267 (mm) REVERT: B 279 ASN cc_start: 0.8512 (t0) cc_final: 0.8194 (t0) REVERT: B 317 ILE cc_start: 0.7214 (OUTLIER) cc_final: 0.6618 (mt) REVERT: B 342 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8689 (m) REVERT: B 362 MET cc_start: 0.7690 (mtp) cc_final: 0.7246 (ttm) REVERT: C 246 MET cc_start: 0.7803 (mmm) cc_final: 0.7174 (mmm) REVERT: E 45 GLN cc_start: 0.6514 (mp10) cc_final: 0.6163 (mp10) REVERT: E 149 CYS cc_start: 0.1035 (OUTLIER) cc_final: 0.0179 (t) REVERT: F 140 MET cc_start: 0.6509 (mtp) cc_final: 0.6217 (mtm) REVERT: F 239 LYS cc_start: 0.7064 (mtpt) cc_final: 0.6857 (mtpt) REVERT: F 352 SER cc_start: 0.7949 (t) cc_final: 0.7445 (m) REVERT: F 431 HIS cc_start: 0.5920 (m-70) cc_final: 0.5533 (m-70) REVERT: G 125 MET cc_start: 0.8820 (tpp) cc_final: 0.8560 (tpp) REVERT: G 136 MET cc_start: 0.6470 (tpp) cc_final: 0.5941 (mtm) outliers start: 31 outliers final: 22 residues processed: 249 average time/residue: 0.1113 time to fit residues: 42.6714 Evaluate side-chains 249 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 149 CYS Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 217 HIS Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 268 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 144 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 105 optimal weight: 0.2980 chunk 130 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.140773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.129185 restraints weight = 15928.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.103529 restraints weight = 38106.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.101353 restraints weight = 50835.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.101463 restraints weight = 38919.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.102290 restraints weight = 28319.948| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.316 15218 Z= 0.124 Angle : 0.610 21.735 20744 Z= 0.271 Chirality : 0.042 0.177 2147 Planarity : 0.004 0.038 2582 Dihedral : 13.519 152.999 2273 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.59 % Favored : 97.35 % Rotamer: Outliers : 2.30 % Allowed : 10.67 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.20), residues: 1773 helix: 1.44 (0.17), residues: 949 sheet: -1.74 (0.51), residues: 78 loop : 0.05 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 94 TYR 0.015 0.001 TYR G 267 PHE 0.027 0.001 PHE D 87 TRP 0.015 0.001 TRP F 157 HIS 0.005 0.001 HIS F 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (15200) covalent geometry : angle 0.57972 / 0.27 (20734) SS BOND : bond 0.00163 / 0.10 ( 2) SS BOND : angle 0.28943 / 0.16 ( 4) hydrogen bonds : bond 0.04518 / 3.07 ( 739) hydrogen bonds : angle 3.97504 / 2.82 ( 2109) metal coordination : bond 0.01019 / 0.62 ( 8) metal coordination : angle 11.15086 / 6.49 ( 6) Misc. bond : bond 0.16948 / 12.41 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 222 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 47 LEU cc_start: 0.5669 (OUTLIER) cc_final: 0.5248 (mm) REVERT: A 186 LEU cc_start: 0.5950 (mt) cc_final: 0.5479 (tp) REVERT: B 34 MET cc_start: 0.8850 (mmm) cc_final: 0.8540 (mmm) REVERT: B 180 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8177 (tp) REVERT: B 279 ASN cc_start: 0.8439 (t0) cc_final: 0.8149 (t0) REVERT: B 317 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.6645 (mt) REVERT: B 342 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8666 (m) REVERT: B 362 MET cc_start: 0.7598 (mtp) cc_final: 0.7325 (ttm) REVERT: C 246 MET cc_start: 0.7708 (mmm) cc_final: 0.7151 (mmm) REVERT: E 45 GLN cc_start: 0.6452 (mp10) cc_final: 0.6204 (mp10) REVERT: F 352 SER cc_start: 0.7991 (t) cc_final: 0.7481 (m) REVERT: F 431 HIS cc_start: 0.5927 (m-70) cc_final: 0.5527 (m-70) REVERT: G 125 MET cc_start: 0.8756 (tpp) cc_final: 0.8487 (tpp) REVERT: G 136 MET cc_start: 0.6416 (tpp) cc_final: 0.5968 (mtm) outliers start: 33 outliers final: 23 residues processed: 245 average time/residue: 0.1120 time to fit residues: 42.0223 Evaluate side-chains 243 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 217 HIS Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain G residue 268 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 65 optimal weight: 0.3980 chunk 109 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 140 optimal weight: 0.0370 chunk 121 optimal weight: 0.7980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.142206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.130540 restraints weight = 15825.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.103780 restraints weight = 39477.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.102809 restraints weight = 36529.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.102144 restraints weight = 31621.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.102531 restraints weight = 26788.750| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.299 15218 Z= 0.112 Angle : 0.602 26.281 20744 Z= 0.264 Chirality : 0.041 0.170 2147 Planarity : 0.004 0.040 2582 Dihedral : 13.062 153.492 2273 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 2.02 % Allowed : 11.02 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.20), residues: 1773 helix: 1.57 (0.17), residues: 943 sheet: -1.71 (0.52), residues: 78 loop : 0.09 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.014 0.001 TYR B 359 PHE 0.026 0.001 PHE D 87 TRP 0.014 0.001 TRP F 157 HIS 0.004 0.001 HIS E 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (15200) covalent geometry : angle 0.56391 / 0.26 (20734) SS BOND : bond 0.00184 / 0.11 ( 2) SS BOND : angle 0.20731 / 0.12 ( 4) hydrogen bonds : bond 0.04248 / 2.88 ( 739) hydrogen bonds : angle 3.88568 / 2.75 ( 2109) metal coordination : bond 0.01005 / 0.63 ( 8) metal coordination : angle 12.45600 / 7.45 ( 6) Misc. bond : bond 0.15985 / 11.68 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 221 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: A 47 LEU cc_start: 0.5384 (OUTLIER) cc_final: 0.5001 (mm) REVERT: A 123 LEU cc_start: 0.7730 (tp) cc_final: 0.7510 (tp) REVERT: A 186 LEU cc_start: 0.6115 (mt) cc_final: 0.5481 (tp) REVERT: B 34 MET cc_start: 0.8796 (mmm) cc_final: 0.8528 (mmm) REVERT: B 180 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8174 (tp) REVERT: B 260 LEU cc_start: 0.8053 (mp) cc_final: 0.7588 (mt) REVERT: B 279 ASN cc_start: 0.8542 (t0) cc_final: 0.8225 (t0) REVERT: B 317 ILE cc_start: 0.6944 (OUTLIER) cc_final: 0.6577 (mp) REVERT: B 342 VAL cc_start: 0.8830 (p) cc_final: 0.8536 (m) REVERT: B 362 MET cc_start: 0.7731 (mtp) cc_final: 0.7322 (ttm) REVERT: C 246 MET cc_start: 0.7734 (mmm) cc_final: 0.7198 (mmm) REVERT: E 45 GLN cc_start: 0.6530 (mp10) cc_final: 0.6185 (mp10) REVERT: E 125 MET cc_start: 0.5061 (pmm) cc_final: 0.4493 (ttm) REVERT: F 140 MET cc_start: 0.6632 (mtp) cc_final: 0.6358 (mtm) REVERT: F 238 GLN cc_start: 0.7526 (mt0) cc_final: 0.7250 (mt0) REVERT: F 352 SER cc_start: 0.7937 (t) cc_final: 0.7448 (m) REVERT: F 431 HIS cc_start: 0.5811 (m-70) cc_final: 0.5301 (m-70) REVERT: G 125 MET cc_start: 0.8763 (tpp) cc_final: 0.8491 (tpp) REVERT: G 136 MET cc_start: 0.6486 (tpp) cc_final: 0.5814 (mtm) outliers start: 29 outliers final: 22 residues processed: 242 average time/residue: 0.1132 time to fit residues: 42.0167 Evaluate side-chains 243 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 217 HIS Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 253 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 109 optimal weight: 0.0970 chunk 36 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.140558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.128618 restraints weight = 15894.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.107278 restraints weight = 40605.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.102509 restraints weight = 54294.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.101927 restraints weight = 40685.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.102233 restraints weight = 32114.431| |-----------------------------------------------------------------------------| r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 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 : 0.005 0.349 15218 Z= 0.131 Angle : 0.628 26.788 20744 Z= 0.275 Chirality : 0.042 0.169 2147 Planarity : 0.004 0.039 2582 Dihedral : 12.876 152.331 2273 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.76 % Favored : 97.18 % Rotamer: Outliers : 2.16 % Allowed : 10.60 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.20), residues: 1773 helix: 1.50 (0.17), residues: 944 sheet: -1.65 (0.57), residues: 70 loop : 0.03 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 77 TYR 0.017 0.001 TYR G 267 PHE 0.024 0.001 PHE D 87 TRP 0.013 0.001 TRP F 157 HIS 0.006 0.001 HIS F 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (15200) covalent geometry : angle 0.59223 / 0.27 (20734) SS BOND : bond 0.00150 / 0.09 ( 2) SS BOND : angle 0.22269 / 0.11 ( 4) hydrogen bonds : bond 0.04610 / 3.14 ( 739) hydrogen bonds : angle 3.93946 / 2.78 ( 2109) metal coordination : bond 0.01365 / 0.86 ( 8) metal coordination : angle 12.36607 / 7.45 ( 6) Misc. bond : bond 0.17595 / 12.96 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 222 time to evaluate : 0.513 Fit side-chains REVERT: A 47 LEU cc_start: 0.5684 (OUTLIER) cc_final: 0.5268 (mm) REVERT: A 70 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7463 (mtmm) REVERT: A 123 LEU cc_start: 0.7822 (tp) cc_final: 0.7589 (tp) REVERT: A 186 LEU cc_start: 0.5886 (mt) cc_final: 0.5423 (tp) REVERT: B 34 MET cc_start: 0.8809 (mmm) cc_final: 0.8481 (mmm) REVERT: B 180 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8278 (tp) REVERT: B 260 LEU cc_start: 0.8094 (mp) cc_final: 0.7635 (mt) REVERT: B 279 ASN cc_start: 0.8539 (t0) cc_final: 0.8221 (t0) REVERT: B 317 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.6833 (mp) REVERT: B 342 VAL cc_start: 0.8869 (p) cc_final: 0.8601 (m) REVERT: B 362 MET cc_start: 0.7623 (mtp) cc_final: 0.7264 (ttm) REVERT: C 246 MET cc_start: 0.7705 (mmm) cc_final: 0.7139 (mmm) REVERT: E 45 GLN cc_start: 0.6497 (mp10) cc_final: 0.6210 (mp10) REVERT: F 239 LYS cc_start: 0.7126 (mtpt) cc_final: 0.6872 (mtpt) REVERT: F 352 SER cc_start: 0.7983 (t) cc_final: 0.7513 (m) REVERT: F 431 HIS cc_start: 0.5938 (m-70) cc_final: 0.5442 (m-70) REVERT: G 125 MET cc_start: 0.8741 (tpp) cc_final: 0.8481 (tpp) REVERT: G 136 MET cc_start: 0.6561 (tpp) cc_final: 0.6056 (mtm) outliers start: 31 outliers final: 24 residues processed: 244 average time/residue: 0.1104 time to fit residues: 41.6309 Evaluate side-chains 246 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 217 HIS Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain G residue 83 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 148 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 144 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.140927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.128547 restraints weight = 15969.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.100605 restraints weight = 44463.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.100716 restraints weight = 40688.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.099613 restraints weight = 32465.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.099520 restraints weight = 28601.349| |-----------------------------------------------------------------------------| r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.331 15218 Z= 0.129 Angle : 0.612 25.137 20744 Z= 0.272 Chirality : 0.042 0.164 2147 Planarity : 0.004 0.040 2582 Dihedral : 12.800 152.302 2273 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.88 % Favored : 97.07 % Rotamer: Outliers : 2.02 % Allowed : 11.16 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.20), residues: 1773 helix: 1.51 (0.17), residues: 942 sheet: -1.69 (0.57), residues: 70 loop : 0.07 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 94 TYR 0.017 0.001 TYR B 359 PHE 0.025 0.001 PHE D 87 TRP 0.013 0.001 TRP F 157 HIS 0.006 0.001 HIS F 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (15200) covalent geometry : angle 0.57884 / 0.27 (20734) SS BOND : bond 0.00186 / 0.11 ( 2) SS BOND : angle 0.20655 / 0.10 ( 4) hydrogen bonds : bond 0.04530 / 3.08 ( 739) hydrogen bonds : angle 3.92634 / 2.78 ( 2109) metal coordination : bond 0.01242 / 0.78 ( 8) metal coordination : angle 11.73643 / 7.07 ( 6) Misc. bond : bond 0.17303 / 12.72 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 228 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 70 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.7107 (mtmm) REVERT: A 186 LEU cc_start: 0.6155 (mt) cc_final: 0.5485 (tp) REVERT: B 34 MET cc_start: 0.8751 (mmm) cc_final: 0.8391 (mmm) REVERT: B 180 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8295 (tp) REVERT: B 260 LEU cc_start: 0.8148 (mp) cc_final: 0.7691 (mt) REVERT: B 279 ASN cc_start: 0.8537 (t0) cc_final: 0.8180 (t0) REVERT: B 317 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6606 (mp) REVERT: B 342 VAL cc_start: 0.8817 (p) cc_final: 0.8475 (m) REVERT: B 362 MET cc_start: 0.7729 (mtp) cc_final: 0.7346 (ttm) REVERT: C 246 MET cc_start: 0.7754 (mmm) cc_final: 0.7205 (mmm) REVERT: F 140 MET cc_start: 0.6666 (mtp) cc_final: 0.6430 (mtm) REVERT: F 270 MET cc_start: 0.8519 (ptm) cc_final: 0.8280 (ptm) REVERT: F 352 SER cc_start: 0.7934 (t) cc_final: 0.7494 (m) REVERT: F 431 HIS cc_start: 0.5943 (m-70) cc_final: 0.5371 (m-70) REVERT: G 125 MET cc_start: 0.8752 (tpp) cc_final: 0.8478 (tpp) REVERT: G 136 MET cc_start: 0.6501 (tpp) cc_final: 0.5866 (mtm) outliers start: 29 outliers final: 24 residues processed: 249 average time/residue: 0.1039 time to fit residues: 39.6466 Evaluate side-chains 246 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 219 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 217 HIS Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain G residue 83 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 87 optimal weight: 9.9990 chunk 70 optimal weight: 0.1980 chunk 4 optimal weight: 7.9990 chunk 148 optimal weight: 0.0870 chunk 174 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 62 GLN ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 272 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.140376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.128269 restraints weight = 15924.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.101236 restraints weight = 42577.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.100411 restraints weight = 39976.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.099631 restraints weight = 33371.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.099955 restraints weight = 26329.152| |-----------------------------------------------------------------------------| r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.345 15218 Z= 0.137 Angle : 0.624 24.884 20744 Z= 0.279 Chirality : 0.042 0.163 2147 Planarity : 0.004 0.039 2582 Dihedral : 12.832 151.447 2273 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.88 % Favored : 97.07 % Rotamer: Outliers : 1.95 % Allowed : 11.37 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.20), residues: 1773 helix: 1.47 (0.17), residues: 943 sheet: -1.50 (0.52), residues: 90 loop : 0.07 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 129 TYR 0.017 0.001 TYR B 359 PHE 0.024 0.002 PHE D 87 TRP 0.013 0.001 TRP F 157 HIS 0.006 0.001 HIS F 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.13 (15200) covalent geometry : angle 0.59259 / 0.28 (20734) SS BOND : bond 0.00180 / 0.11 ( 2) SS BOND : angle 0.20024 / 0.10 ( 4) hydrogen bonds : bond 0.04664 / 3.17 ( 739) hydrogen bonds : angle 3.95764 / 2.81 ( 2109) metal coordination : bond 0.01304 / 0.83 ( 8) metal coordination : angle 11.51598 / 6.96 ( 6) Misc. bond : bond 0.17821 / 13.12 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 70 LYS cc_start: 0.7386 (mttp) cc_final: 0.7006 (mtmm) REVERT: A 186 LEU cc_start: 0.6093 (mt) cc_final: 0.5519 (tp) REVERT: B 34 MET cc_start: 0.8757 (mmm) cc_final: 0.8407 (mmm) REVERT: B 180 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8294 (tp) REVERT: B 279 ASN cc_start: 0.8505 (t0) cc_final: 0.8145 (t0) REVERT: B 317 ILE cc_start: 0.7005 (OUTLIER) cc_final: 0.6637 (mp) REVERT: B 342 VAL cc_start: 0.8887 (p) cc_final: 0.8578 (m) REVERT: B 362 MET cc_start: 0.7703 (mtp) cc_final: 0.7326 (ttm) REVERT: C 246 MET cc_start: 0.7741 (mmm) cc_final: 0.7197 (mmm) REVERT: F 239 LYS cc_start: 0.7070 (mtpt) cc_final: 0.6844 (mtpt) REVERT: F 352 SER cc_start: 0.7938 (t) cc_final: 0.7488 (m) REVERT: F 431 HIS cc_start: 0.5958 (m-70) cc_final: 0.5387 (m-70) REVERT: G 125 MET cc_start: 0.8770 (tpp) cc_final: 0.8486 (tpp) REVERT: G 136 MET cc_start: 0.6563 (tpp) cc_final: 0.5865 (mtm) REVERT: G 207 MET cc_start: 0.7453 (tpp) cc_final: 0.6938 (tpp) outliers start: 28 outliers final: 25 residues processed: 239 average time/residue: 0.0933 time to fit residues: 34.1940 Evaluate side-chains 245 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 218 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 217 HIS Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 83 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 165 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 272 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.140718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.129216 restraints weight = 15819.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.102958 restraints weight = 37421.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.101142 restraints weight = 43724.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.100850 restraints weight = 42713.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.101367 restraints weight = 31846.904| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.317 15218 Z= 0.124 Angle : 0.605 24.614 20744 Z= 0.270 Chirality : 0.042 0.168 2147 Planarity : 0.004 0.039 2582 Dihedral : 12.741 151.192 2273 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.76 % Favored : 97.18 % Rotamer: Outliers : 1.88 % Allowed : 11.51 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.20), residues: 1773 helix: 1.51 (0.17), residues: 942 sheet: -1.63 (0.62), residues: 65 loop : 0.04 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 129 TYR 0.017 0.001 TYR B 359 PHE 0.025 0.001 PHE D 87 TRP 0.014 0.001 TRP F 157 HIS 0.005 0.001 HIS F 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (15200) covalent geometry : angle 0.57284 / 0.27 (20734) SS BOND : bond 0.00161 / 0.10 ( 2) SS BOND : angle 0.23144 / 0.11 ( 4) hydrogen bonds : bond 0.04495 / 3.05 ( 739) hydrogen bonds : angle 3.90437 / 2.76 ( 2109) metal coordination : bond 0.01293 / 0.83 ( 8) metal coordination : angle 11.44107 / 6.91 ( 6) Misc. bond : bond 0.17133 / 12.55 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2232.48 seconds wall clock time: 39 minutes 26.57 seconds (2366.57 seconds total)