Starting phenix.real_space_refine on Sat Aug 23 23:52:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8asi_15616/08_2025/8asi_15616.cif Found real_map, /net/cci-nas-00/data/ceres_data/8asi_15616/08_2025/8asi_15616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8asi_15616/08_2025/8asi_15616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8asi_15616/08_2025/8asi_15616.map" model { file = "/net/cci-nas-00/data/ceres_data/8asi_15616/08_2025/8asi_15616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8asi_15616/08_2025/8asi_15616.cif" } resolution = 2.9 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 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 87 Unusual residues: {'FES': 1, 'PEE': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 19 Chain: "B" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 269 Unusual residues: {'HEM': 2, 'PEE': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 72 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: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 280 Unusual residues: {'HEM': 2, 'PEE': 4, 'U10': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 69 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 34.336 79.448 51.034 1.00 77.73 S ATOM 1053 SG CYS A 149 37.178 80.949 52.834 1.00 72.20 S ATOM 7913 SG CYS E 129 71.785 34.949 77.937 1.00 98.47 S ATOM 8053 SG CYS E 149 69.114 33.393 76.251 1.00 97.18 S Time building chain proxies: 3.95, per 1000 atoms: 0.27 Number of scatterers: 14720 At special positions: 0 Unit cell: (120.695, 114.836, 117.18, 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=2.02 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=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 699.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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=" ND1 HIS E 152 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 149 " pdb="FE2 FES E 201 " - pdb=" ND1 HIS E 131 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 129 " 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: 76 helices and 13 sheets defined 57.5% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 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: 3.857A 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 removed outlier: 3.750A pdb=" N VAL B 56 " --> pdb=" O ALA B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 87 removed outlier: 3.707A pdb=" N VAL B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 119 removed outlier: 3.876A 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 168 removed outlier: 4.112A pdb=" N PHE B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY B 167 " --> pdb=" O THR B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 182 Processing helix chain 'B' and resid 187 through 218 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: 6.774A pdb=" N ILE B 249 " --> pdb=" O TRP B 245 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 261 " --> pdb=" O ALA B 257 " (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: 4.123A 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: 3.931A pdb=" N ILE B 340 " --> pdb=" O MET B 336 " (cutoff:3.500A) removed outlier: 3.740A 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: 3.577A pdb=" N TYR B 366 " --> pdb=" O MET B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 406 removed outlier: 3.714A pdb=" N PHE B 404 " --> pdb=" O TRP B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 415 removed outlier: 4.072A pdb=" N ALA B 413 " --> pdb=" O PRO B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 432 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 225 through 242 Processing helix chain 'C' and resid 244 through 276 removed outlier: 3.611A 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 79 through 79 No H-bonds generated for 'chain 'D' and resid 79 through 79' Processing helix chain 'D' and resid 80 through 103 removed outlier: 3.739A pdb=" N ARG D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 37 removed outlier: 3.572A 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 55 through 57 No H-bonds generated for 'chain 'E' and resid 55 through 57' Processing helix chain 'E' and resid 78 through 88 removed outlier: 3.814A pdb=" N VAL E 88 " --> pdb=" O LEU E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'F' and resid 13 through 21 Processing helix chain 'F' and resid 24 through 35 Processing helix chain 'F' and resid 42 through 45 Processing helix chain 'F' and resid 46 through 66 Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'F' and resid 89 through 118 removed outlier: 3.944A pdb=" N SER F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 149 removed outlier: 3.571A pdb=" N LEU F 149 " --> pdb=" O MET F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 168 removed outlier: 4.003A pdb=" N PHE F 166 " --> pdb=" O ILE F 162 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY F 167 " --> pdb=" O THR F 163 " (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: 3.580A pdb=" N LYS F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 270 removed outlier: 6.766A pdb=" N ILE F 249 " --> pdb=" O TRP F 245 " (cutoff:3.500A) removed outlier: 3.780A 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: 4.092A 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: 4.333A pdb=" N ILE F 340 " --> pdb=" O MET F 336 " (cutoff:3.500A) removed outlier: 3.838A 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: 3.636A pdb=" N TYR F 366 " --> pdb=" O MET F 362 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA F 382 " --> pdb=" O THR F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 406 removed outlier: 3.734A pdb=" N PHE F 404 " --> pdb=" O TRP F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 415 removed outlier: 3.582A pdb=" N GLY F 412 " --> pdb=" O LEU F 408 " (cutoff:3.500A) removed outlier: 3.896A 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 90 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: 3.918A pdb=" N GLY G 276 " --> pdb=" O ARG G 272 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL G 277 " --> pdb=" O LEU G 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 105 removed outlier: 4.111A pdb=" N PHE H 102 " --> pdb=" O LEU H 98 " (cutoff:3.500A) removed outlier: 4.048A 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: 5.915A 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: 3.647A 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: 6.595A 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 50 through 53 Processing sheet with id=AA9, first strand: chain 'E' and resid 62 through 67 Processing sheet with id=AB1, first strand: chain 'E' and resid 145 through 149 removed outlier: 3.687A pdb=" N SER E 154 " --> pdb=" O CYS E 149 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N HIS E 155 " --> pdb=" O ARG E 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 36 through 38 Processing sheet with id=AB3, first strand: chain 'G' and resid 93 through 95 Processing sheet with id=AB4, first strand: chain 'G' and resid 177 through 179 751 hydrogen bonds defined for protein. 2142 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: 2.44 Time building geometry restraints manager: 1.92 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: 6181 1.39 - 1.59: 8841 1.59 - 1.80: 87 1.80 - 2.00: 60 2.00 - 2.20: 31 Bond restraints: 15200 Sorted by residual: bond pdb=" C18 PEE B 507 " pdb=" C19 PEE B 507 " ideal model delta sigma weight residual 1.523 1.318 0.205 2.00e-02 2.50e+03 1.05e+02 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 8.88e+01 bond pdb=" C38 PEE F 507 " pdb=" C39 PEE F 507 " ideal model delta sigma weight residual 1.523 1.336 0.187 2.00e-02 2.50e+03 8.76e+01 bond pdb=" C38 PEE A 203 " pdb=" C39 PEE A 203 " ideal model delta sigma weight residual 1.523 1.339 0.184 2.00e-02 2.50e+03 8.50e+01 bond pdb=" C38 PEE B 507 " pdb=" C39 PEE B 507 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.40e+01 ... (remaining 15195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.96: 20677 8.96 - 17.93: 52 17.93 - 26.89: 4 26.89 - 35.86: 0 35.86 - 44.82: 1 Bond angle restraints: 20734 Sorted by residual: angle pdb=" C17 PEE B 507 " pdb=" C18 PEE B 507 " pdb=" C19 PEE B 507 " ideal model delta sigma weight residual 113.68 158.50 -44.82 3.00e+00 1.11e-01 2.23e+02 angle pdb=" C25 PEE A 203 " pdb=" C26 PEE A 203 " pdb=" C27 PEE A 203 " ideal model delta sigma weight residual 112.90 136.75 -23.85 3.00e+00 1.11e-01 6.32e+01 angle pdb=" C38 PEE F 507 " pdb=" C39 PEE F 507 " pdb=" C40 PEE F 507 " ideal model delta sigma weight residual 112.47 90.37 22.10 3.00e+00 1.11e-01 5.43e+01 angle pdb=" CG MET C 207 " pdb=" SD MET C 207 " pdb=" CE MET C 207 " ideal model delta sigma weight residual 100.90 86.04 14.86 2.20e+00 2.07e-01 4.56e+01 angle pdb=" C38 PEE B 503 " pdb=" C39 PEE B 503 " pdb=" C40 PEE B 503 " ideal model delta sigma weight residual 112.47 92.48 19.99 3.00e+00 1.11e-01 4.44e+01 ... (remaining 20729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.61: 8403 34.61 - 69.22: 204 69.22 - 103.82: 59 103.82 - 138.43: 30 138.43 - 173.04: 14 Dihedral angle restraints: 8710 sinusoidal: 3605 harmonic: 5105 Sorted by residual: dihedral pdb=" C6 U10 F 503 " pdb=" C7 U10 F 503 " pdb=" C8 U10 F 503 " pdb=" C9 U10 F 503 " ideal model delta sinusoidal sigma weight residual 101.51 -103.09 -155.39 1 2.00e+01 2.50e-03 4.58e+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 240.00 174.57 65.43 2 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" C3M U10 F 503 " pdb=" C3 U10 F 503 " pdb=" O3 U10 F 503 " pdb=" C4 U10 F 503 " ideal model delta sinusoidal sigma weight residual 244.38 122.40 121.98 1 2.00e+01 2.50e-03 3.67e+01 ... (remaining 8707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1780 0.070 - 0.139: 327 0.139 - 0.209: 34 0.209 - 0.278: 4 0.278 - 0.348: 2 Chirality restraints: 2147 Sorted by residual: chirality pdb=" C2 PEE B 503 " pdb=" C1 PEE B 503 " pdb=" C3 PEE B 503 " pdb=" O2 PEE B 503 " both_signs ideal model delta sigma weight residual False -2.33 -1.98 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CB VAL A 25 " pdb=" CA VAL A 25 " pdb=" CG1 VAL A 25 " pdb=" CG2 VAL A 25 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CB VAL B 108 " pdb=" CA VAL B 108 " pdb=" CG1 VAL B 108 " pdb=" CG2 VAL B 108 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 2144 not shown) Planarity restraints: 2582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC C 301 " 0.044 2.00e-02 2.50e+03 9.83e-02 2.17e+02 pdb=" C2C HEC C 301 " -0.267 2.00e-02 2.50e+03 pdb=" C3C HEC C 301 " 0.068 2.00e-02 2.50e+03 pdb=" C4C HEC C 301 " 0.014 2.00e-02 2.50e+03 pdb=" CAC HEC C 301 " 0.035 2.00e-02 2.50e+03 pdb=" CHC HEC C 301 " 0.037 2.00e-02 2.50e+03 pdb=" CHD HEC C 301 " -0.012 2.00e-02 2.50e+03 pdb=" CMC HEC C 301 " 0.077 2.00e-02 2.50e+03 pdb=" NC HEC C 301 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC G 301 " 0.023 2.00e-02 2.50e+03 6.68e-02 1.00e+02 pdb=" C2C HEC G 301 " -0.183 2.00e-02 2.50e+03 pdb=" C3C HEC G 301 " 0.035 2.00e-02 2.50e+03 pdb=" C4C HEC G 301 " 0.008 2.00e-02 2.50e+03 pdb=" CAC HEC G 301 " 0.030 2.00e-02 2.50e+03 pdb=" CHC HEC G 301 " 0.030 2.00e-02 2.50e+03 pdb=" CHD HEC G 301 " -0.006 2.00e-02 2.50e+03 pdb=" CMC HEC G 301 " 0.053 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=" CA GLY A 21 " 0.035 2.00e-02 2.50e+03 6.96e-02 4.84e+01 pdb=" C GLY A 21 " -0.120 2.00e-02 2.50e+03 pdb=" O GLY A 21 " 0.044 2.00e-02 2.50e+03 pdb=" N ALA A 22 " 0.041 2.00e-02 2.50e+03 ... (remaining 2579 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 29 2.52 - 3.12: 11251 3.12 - 3.71: 23788 3.71 - 4.31: 34332 4.31 - 4.90: 55890 Nonbonded interactions: 125290 Sorted by model distance: nonbonded pdb=" NE2 HIS G 62 " pdb="FE HEC G 301 " model vdw 1.929 3.080 nonbonded pdb=" NE2 HIS B 198 " pdb="FE HEM B 502 " model vdw 2.007 3.080 nonbonded pdb=" NE2 HIS C 62 " pdb="FE HEC C 301 " model vdw 2.022 3.080 nonbonded pdb=" NE2 HIS F 198 " pdb="FE HEM F 502 " model vdw 2.026 3.080 nonbonded pdb=" NE2 HIS F 111 " pdb="FE HEM F 501 " model vdw 2.156 3.080 ... (remaining 125285 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 202) selection = (chain 'E' 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 C4 or name C5 \ or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4 \ P or name O5 or name P )))) } ncs_group { reference = (chain 'B' and (resid 1 through 432 or resid 501 through 502 or resid 504 or (re \ sid 505 and (name N or name C1 or name C10 or name C11 or name C12 or name C13 o \ r 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 O \ 1P 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 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 C1 \ 7 or name C18 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 n \ ame C31 or name 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 C41 or name C42 or name C \ 43 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 502 or resid 504 or (resid 505 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 \ 506 and (name N or name C1 or name C10 or name C11 or name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 o \ r name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C3 \ 5 or name C36 or name C4 or name C5 or name O1P or name O2 or name O2P or name O \ 3 or name O3P or name O4 or name O4P or name O5 or name P )) or resid 507)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 79 through 105) 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.930 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 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 : 0.014 0.756 15221 Z= 0.960 Angle : 1.301 44.822 20744 Z= 0.582 Chirality : 0.054 0.348 2147 Planarity : 0.010 0.098 2582 Dihedral : 20.468 173.040 5450 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.54 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % 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 aren not related in a simple way. whole: -0.83 (0.18), residues: 1773 helix: -0.46 (0.15), residues: 912 sheet: -1.38 (0.60), residues: 62 loop : -0.39 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.004 ARG B 355 TYR 0.035 0.005 TYR F 280 PHE 0.099 0.003 PHE D 88 TRP 0.034 0.003 TRP B 348 HIS 0.012 0.002 HIS B 291 Details of bonding type rmsd covalent geometry : bond 0.00888 (15200) covalent geometry : angle 1.27255 (20734) SS BOND : bond 0.00519 ( 2) SS BOND : angle 1.39786 ( 4) hydrogen bonds : bond 0.14398 ( 751) hydrogen bonds : angle 6.41406 ( 2142) metal coordination : bond 0.11554 ( 8) metal coordination : angle 15.91242 ( 6) Misc. bond : bond 0.38101 ( 11) *********************** 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 283 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.600 Fit side-chains REVERT: A 38 MET cc_start: 0.9055 (mtp) cc_final: 0.8736 (mtp) REVERT: A 63 LEU cc_start: 0.7711 (mt) cc_final: 0.7334 (tp) REVERT: B 6 HIS cc_start: 0.7923 (p-80) cc_final: 0.7555 (p-80) REVERT: B 92 MET cc_start: 0.7963 (mmt) cc_final: 0.7684 (tpt) REVERT: B 133 MET cc_start: 0.8676 (mmm) cc_final: 0.8314 (mmm) REVERT: B 239 LYS cc_start: 0.7953 (mttt) cc_final: 0.7676 (mtpt) REVERT: B 393 SER cc_start: 0.8531 (t) cc_final: 0.8024 (p) REVERT: B 416 LYS cc_start: 0.8407 (mmtt) cc_final: 0.7907 (mmtp) REVERT: C 52 GLN cc_start: 0.7976 (tt0) cc_final: 0.7390 (tt0) REVERT: C 56 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7457 (mp0) REVERT: C 101 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7203 (mt-10) REVERT: C 180 ARG cc_start: 0.8099 (ttp-110) cc_final: 0.7859 (ttp-110) REVERT: C 189 ASP cc_start: 0.6504 (p0) cc_final: 0.5970 (t0) REVERT: C 212 MET cc_start: 0.6956 (ttp) cc_final: 0.6619 (ttt) REVERT: C 214 ASP cc_start: 0.7295 (m-30) cc_final: 0.6744 (t0) REVERT: F 34 MET cc_start: 0.8800 (mmm) cc_final: 0.8452 (mmt) REVERT: F 92 MET cc_start: 0.7809 (tpt) cc_final: 0.7567 (tpt) REVERT: F 137 LEU cc_start: 0.7860 (mt) cc_final: 0.7465 (mt) REVERT: F 239 LYS cc_start: 0.8042 (mttt) cc_final: 0.7681 (mtmt) REVERT: F 313 TRP cc_start: 0.5592 (m-90) cc_final: 0.4408 (m-10) REVERT: F 394 LEU cc_start: 0.8446 (tp) cc_final: 0.8242 (tt) REVERT: F 428 PHE cc_start: 0.8466 (t80) cc_final: 0.8199 (t80) REVERT: G 136 MET cc_start: 0.6413 (tpp) cc_final: 0.6118 (tpt) outliers start: 0 outliers final: 1 residues processed: 283 average time/residue: 0.5757 time to fit residues: 180.8333 Evaluate side-chains 211 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 106 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN B 217 HIS B 276 HIS C 145 ASN C 183 GLN F 319 ASN F 383 GLN G 84 GLN G 118 ASN G 179 ASN G 183 GLN G 222 HIS G 227 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.148711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.097232 restraints weight = 16076.155| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.86 r_work: 0.2739 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.297 15221 Z= 0.163 Angle : 0.748 17.575 20744 Z= 0.337 Chirality : 0.047 0.239 2147 Planarity : 0.005 0.047 2582 Dihedral : 22.656 179.721 2395 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.02 % Allowed : 8.09 % Favored : 89.89 % 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 aren not related in a simple way. whole: 0.68 (0.20), residues: 1773 helix: 1.01 (0.17), residues: 924 sheet: -1.94 (0.52), residues: 72 loop : 0.17 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 49 TYR 0.016 0.002 TYR F 399 PHE 0.043 0.002 PHE D 88 TRP 0.017 0.002 TRP F 157 HIS 0.009 0.002 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00375 (15200) covalent geometry : angle 0.73625 (20734) SS BOND : bond 0.00503 ( 2) SS BOND : angle 0.84953 ( 4) hydrogen bonds : bond 0.05664 ( 751) hydrogen bonds : angle 4.51631 ( 2142) metal coordination : bond 0.01246 ( 8) metal coordination : angle 7.71252 ( 6) Misc. bond : bond 0.15860 ( 11) *********************** 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 267 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 238 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9328 (mtp) cc_final: 0.9033 (mtp) REVERT: A 180 ASP cc_start: 0.5587 (OUTLIER) cc_final: 0.5315 (p0) REVERT: B 1 MET cc_start: 0.2319 (OUTLIER) cc_final: 0.1113 (ppp) REVERT: B 6 HIS cc_start: 0.7762 (p-80) cc_final: 0.7452 (p-80) REVERT: B 20 HIS cc_start: 0.8640 (t-90) cc_final: 0.8341 (t70) REVERT: B 239 LYS cc_start: 0.7979 (mttt) cc_final: 0.7685 (mtpt) REVERT: B 343 MET cc_start: 0.9008 (ttp) cc_final: 0.8805 (ttp) REVERT: B 416 LYS cc_start: 0.8308 (mmtt) cc_final: 0.7787 (mmtp) REVERT: C 180 ARG cc_start: 0.8303 (ttp-110) cc_final: 0.7929 (ttp-110) REVERT: C 189 ASP cc_start: 0.6675 (p0) cc_final: 0.5761 (t0) REVERT: C 212 MET cc_start: 0.7657 (ttp) cc_final: 0.7376 (ttt) REVERT: C 214 ASP cc_start: 0.7443 (m-30) cc_final: 0.7230 (m-30) REVERT: F 137 LEU cc_start: 0.8563 (mt) cc_final: 0.8207 (mt) REVERT: F 239 LYS cc_start: 0.8210 (mttt) cc_final: 0.7861 (mttm) REVERT: F 313 TRP cc_start: 0.5460 (m-90) cc_final: 0.3880 (m-10) REVERT: G 136 MET cc_start: 0.6571 (tpp) cc_final: 0.6309 (tpt) REVERT: G 198 LYS cc_start: 0.7831 (ttpt) cc_final: 0.7629 (ttpp) REVERT: G 246 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7870 (mpp) outliers start: 29 outliers final: 12 residues processed: 252 average time/residue: 0.5008 time to fit residues: 141.4894 Evaluate side-chains 222 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 207 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 321 ILE Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain G residue 212 MET Chi-restraints excluded: chain G residue 246 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 17 optimal weight: 0.0060 chunk 91 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 0.0670 chunk 143 optimal weight: 4.9990 chunk 47 optimal weight: 0.4980 chunk 79 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 52 optimal weight: 0.2980 overall best weight: 0.2934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN B 276 HIS C 142 GLN C 183 GLN F 383 GLN G 84 GLN G 118 ASN G 142 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.152045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.101168 restraints weight = 16128.916| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.93 r_work: 0.2797 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.286 15221 Z= 0.118 Angle : 0.632 14.932 20744 Z= 0.282 Chirality : 0.043 0.196 2147 Planarity : 0.005 0.046 2582 Dihedral : 21.235 171.065 2395 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.09 % Allowed : 9.69 % 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 aren not related in a simple way. whole: 1.19 (0.20), residues: 1773 helix: 1.40 (0.17), residues: 942 sheet: -1.59 (0.56), residues: 72 loop : 0.42 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 12 TYR 0.012 0.001 TYR G 88 PHE 0.024 0.001 PHE D 88 TRP 0.016 0.001 TRP A 147 HIS 0.006 0.001 HIS B 276 Details of bonding type rmsd covalent geometry : bond 0.00250 (15200) covalent geometry : angle 0.62574 (20734) SS BOND : bond 0.01141 ( 2) SS BOND : angle 1.04230 ( 4) hydrogen bonds : bond 0.04467 ( 751) hydrogen bonds : angle 4.13256 ( 2142) metal coordination : bond 0.00574 ( 8) metal coordination : angle 5.00752 ( 6) Misc. bond : bond 0.13516 ( 11) *********************** 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 265 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 235 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.9335 (mtp) cc_final: 0.8969 (mtp) REVERT: A 180 ASP cc_start: 0.6009 (OUTLIER) cc_final: 0.5562 (p0) REVERT: B 1 MET cc_start: 0.2215 (OUTLIER) cc_final: 0.1656 (ttp) REVERT: B 20 HIS cc_start: 0.8772 (t-90) cc_final: 0.8480 (t70) REVERT: B 239 LYS cc_start: 0.8165 (mttt) cc_final: 0.7880 (mtpt) REVERT: B 260 LEU cc_start: 0.8167 (mt) cc_final: 0.7904 (mp) REVERT: B 317 ILE cc_start: 0.6827 (OUTLIER) cc_final: 0.6417 (mt) REVERT: B 416 LYS cc_start: 0.8232 (mmtt) cc_final: 0.7743 (mmtp) REVERT: B 423 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.8027 (p) REVERT: B 431 HIS cc_start: 0.7273 (OUTLIER) cc_final: 0.6902 (m-70) REVERT: C 29 GLU cc_start: 0.7657 (tt0) cc_final: 0.7455 (tp30) REVERT: C 74 GLU cc_start: 0.7490 (tt0) cc_final: 0.6761 (mm-30) REVERT: C 99 THR cc_start: 0.6151 (OUTLIER) cc_final: 0.5909 (p) REVERT: C 180 ARG cc_start: 0.8355 (ttp-110) cc_final: 0.7989 (ttp-110) REVERT: C 189 ASP cc_start: 0.6799 (p0) cc_final: 0.6167 (t0) REVERT: C 207 MET cc_start: 0.8835 (ttm) cc_final: 0.8386 (ttm) REVERT: C 212 MET cc_start: 0.7614 (ttp) cc_final: 0.7373 (ttt) REVERT: C 214 ASP cc_start: 0.7461 (m-30) cc_final: 0.7200 (m-30) REVERT: F 137 LEU cc_start: 0.8715 (mt) cc_final: 0.8357 (mt) REVERT: F 239 LYS cc_start: 0.8293 (mttt) cc_final: 0.7932 (mttm) REVERT: F 313 TRP cc_start: 0.5417 (m-90) cc_final: 0.3956 (m-10) REVERT: F 414 ILE cc_start: 0.8118 (pt) cc_final: 0.7769 (mp) REVERT: F 432 TYR cc_start: 0.5517 (m-80) cc_final: 0.4914 (t80) REVERT: G 74 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7879 (mt-10) REVERT: G 136 MET cc_start: 0.6548 (tpp) cc_final: 0.6275 (tpt) REVERT: G 232 ASP cc_start: 0.8962 (m-30) cc_final: 0.8688 (m-30) REVERT: G 271 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8398 (ttmm) outliers start: 30 outliers final: 9 residues processed: 251 average time/residue: 0.5204 time to fit residues: 145.9629 Evaluate side-chains 236 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 220 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 431 HIS Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 212 MET Chi-restraints excluded: chain G residue 271 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 40 optimal weight: 7.9990 chunk 46 optimal weight: 0.3980 chunk 63 optimal weight: 6.9990 chunk 152 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 153 optimal weight: 20.0000 chunk 89 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN C 171 HIS C 183 GLN F 316 GLN F 383 GLN G 118 ASN G 142 GLN G 179 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.150359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.099213 restraints weight = 16041.119| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.90 r_work: 0.2775 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.267 15221 Z= 0.124 Angle : 0.635 16.302 20744 Z= 0.280 Chirality : 0.043 0.174 2147 Planarity : 0.005 0.047 2582 Dihedral : 20.233 170.154 2393 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.86 % Allowed : 9.69 % Favored : 87.45 % 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 aren not related in a simple way. whole: 1.23 (0.20), residues: 1773 helix: 1.44 (0.17), residues: 940 sheet: -1.47 (0.57), residues: 72 loop : 0.41 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 39 TYR 0.014 0.001 TYR F 399 PHE 0.023 0.002 PHE D 88 TRP 0.019 0.001 TRP A 147 HIS 0.007 0.001 HIS F 212 Details of bonding type rmsd covalent geometry : bond 0.00282 (15200) covalent geometry : angle 0.63104 (20734) SS BOND : bond 0.00358 ( 2) SS BOND : angle 0.84229 ( 4) hydrogen bonds : bond 0.04626 ( 751) hydrogen bonds : angle 4.03663 ( 2142) metal coordination : bond 0.00755 ( 8) metal coordination : angle 4.29171 ( 6) Misc. bond : bond 0.12641 ( 11) *********************** 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 262 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 221 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.9350 (mtp) cc_final: 0.9052 (mtp) REVERT: A 180 ASP cc_start: 0.5934 (OUTLIER) cc_final: 0.5611 (p0) REVERT: B 1 MET cc_start: 0.2362 (OUTLIER) cc_final: 0.1778 (ttp) REVERT: B 20 HIS cc_start: 0.8781 (t-90) cc_final: 0.8521 (t70) REVERT: B 180 LEU cc_start: 0.8847 (tp) cc_final: 0.8496 (tp) REVERT: B 239 LYS cc_start: 0.8215 (mttt) cc_final: 0.7915 (mtpt) REVERT: B 317 ILE cc_start: 0.6825 (OUTLIER) cc_final: 0.6429 (mt) REVERT: B 416 LYS cc_start: 0.8186 (mmtt) cc_final: 0.7843 (mmtp) REVERT: B 423 THR cc_start: 0.8281 (OUTLIER) cc_final: 0.8012 (p) REVERT: B 431 HIS cc_start: 0.7174 (OUTLIER) cc_final: 0.6928 (m-70) REVERT: C 74 GLU cc_start: 0.7574 (tt0) cc_final: 0.6840 (mm-30) REVERT: C 180 ARG cc_start: 0.8346 (ttp-110) cc_final: 0.7883 (ttp-110) REVERT: C 189 ASP cc_start: 0.6693 (p0) cc_final: 0.5969 (t0) REVERT: C 207 MET cc_start: 0.8864 (ttm) cc_final: 0.8445 (ttm) REVERT: C 212 MET cc_start: 0.7615 (ttp) cc_final: 0.7352 (ttt) REVERT: C 214 ASP cc_start: 0.7504 (m-30) cc_final: 0.7233 (m-30) REVERT: F 137 LEU cc_start: 0.8782 (mt) cc_final: 0.8403 (mt) REVERT: F 239 LYS cc_start: 0.8279 (mttt) cc_final: 0.7874 (mttm) REVERT: F 313 TRP cc_start: 0.5325 (m-90) cc_final: 0.3860 (m-10) REVERT: F 432 TYR cc_start: 0.5512 (m-80) cc_final: 0.5041 (m-80) REVERT: G 136 MET cc_start: 0.6623 (tpp) cc_final: 0.6379 (tpt) REVERT: G 271 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8419 (ttmm) outliers start: 41 outliers final: 16 residues processed: 244 average time/residue: 0.5432 time to fit residues: 147.8093 Evaluate side-chains 233 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 211 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 431 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 271 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 77 optimal weight: 10.0000 chunk 10 optimal weight: 0.0370 chunk 84 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN B 383 GLN C 183 GLN G 118 ASN G 142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.149014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.100353 restraints weight = 15880.517| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.67 r_work: 0.2745 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.262 15221 Z= 0.136 Angle : 0.648 16.923 20744 Z= 0.284 Chirality : 0.044 0.178 2147 Planarity : 0.005 0.048 2582 Dihedral : 19.615 174.453 2393 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.44 % Allowed : 10.88 % 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 aren not related in a simple way. whole: 1.13 (0.20), residues: 1773 helix: 1.41 (0.17), residues: 946 sheet: -1.33 (0.55), residues: 77 loop : 0.27 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 114 TYR 0.015 0.001 TYR F 399 PHE 0.024 0.002 PHE D 88 TRP 0.020 0.001 TRP A 147 HIS 0.008 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00321 (15200) covalent geometry : angle 0.64354 (20734) SS BOND : bond 0.00382 ( 2) SS BOND : angle 1.04697 ( 4) hydrogen bonds : bond 0.04765 ( 751) hydrogen bonds : angle 4.00862 ( 2142) metal coordination : bond 0.00761 ( 8) metal coordination : angle 4.23057 ( 6) Misc. bond : bond 0.12281 ( 11) *********************** 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 249 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.9371 (mtp) cc_final: 0.9095 (mtp) REVERT: A 47 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7619 (mm) REVERT: A 70 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7995 (mttp) REVERT: A 180 ASP cc_start: 0.6111 (OUTLIER) cc_final: 0.5829 (p0) REVERT: B 1 MET cc_start: 0.2425 (OUTLIER) cc_final: 0.1740 (ttp) REVERT: B 20 HIS cc_start: 0.8676 (t-90) cc_final: 0.8399 (t70) REVERT: B 180 LEU cc_start: 0.8807 (tp) cc_final: 0.8451 (tp) REVERT: B 239 LYS cc_start: 0.8065 (mttt) cc_final: 0.7743 (mtpt) REVERT: B 317 ILE cc_start: 0.6527 (OUTLIER) cc_final: 0.6244 (mt) REVERT: B 416 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7702 (mmtp) REVERT: B 423 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7819 (p) REVERT: B 431 HIS cc_start: 0.7152 (OUTLIER) cc_final: 0.6892 (m-70) REVERT: C 29 GLU cc_start: 0.7790 (tt0) cc_final: 0.7450 (mm-30) REVERT: C 70 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7083 (ptt-90) REVERT: C 180 ARG cc_start: 0.8229 (ttp-110) cc_final: 0.7755 (ttp-110) REVERT: C 189 ASP cc_start: 0.6640 (p0) cc_final: 0.5924 (t0) REVERT: C 207 MET cc_start: 0.8829 (ttp) cc_final: 0.8395 (ttm) REVERT: C 212 MET cc_start: 0.7512 (ttp) cc_final: 0.7235 (ttt) REVERT: C 214 ASP cc_start: 0.7466 (m-30) cc_final: 0.7199 (m-30) REVERT: F 137 LEU cc_start: 0.8640 (mt) cc_final: 0.8234 (mt) REVERT: F 239 LYS cc_start: 0.8143 (mttt) cc_final: 0.7770 (mttm) REVERT: F 272 ASN cc_start: 0.8858 (m-40) cc_final: 0.8588 (m-40) REVERT: F 313 TRP cc_start: 0.5280 (m-90) cc_final: 0.3769 (m-10) REVERT: F 394 LEU cc_start: 0.8469 (tt) cc_final: 0.8161 (tm) REVERT: G 136 MET cc_start: 0.6783 (tpp) cc_final: 0.6278 (tpt) REVERT: G 253 PHE cc_start: 0.8296 (m-80) cc_final: 0.7038 (t80) REVERT: G 271 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.7898 (ttpp) outliers start: 35 outliers final: 20 residues processed: 229 average time/residue: 0.5587 time to fit residues: 142.5323 Evaluate side-chains 237 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 431 HIS Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 271 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 144 optimal weight: 0.9990 chunk 164 optimal weight: 7.9990 chunk 105 optimal weight: 0.0050 chunk 130 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 11 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN F 316 GLN F 383 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.149693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.102219 restraints weight = 15928.825| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.58 r_work: 0.2769 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.254 15221 Z= 0.120 Angle : 0.627 16.657 20744 Z= 0.273 Chirality : 0.042 0.173 2147 Planarity : 0.004 0.046 2582 Dihedral : 19.262 178.877 2393 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.37 % Allowed : 11.23 % Favored : 86.40 % 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 aren not related in a simple way. whole: 1.24 (0.20), residues: 1773 helix: 1.52 (0.17), residues: 941 sheet: -1.25 (0.56), residues: 77 loop : 0.30 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 86 TYR 0.014 0.001 TYR F 399 PHE 0.024 0.001 PHE D 88 TRP 0.022 0.001 TRP A 147 HIS 0.006 0.001 HIS F 212 Details of bonding type rmsd covalent geometry : bond 0.00277 (15200) covalent geometry : angle 0.62280 (20734) SS BOND : bond 0.00316 ( 2) SS BOND : angle 0.88977 ( 4) hydrogen bonds : bond 0.04502 ( 751) hydrogen bonds : angle 3.92432 ( 2142) metal coordination : bond 0.00731 ( 8) metal coordination : angle 4.34645 ( 6) Misc. bond : bond 0.11965 ( 11) *********************** 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 247 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 213 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.9345 (mtp) cc_final: 0.9054 (mtp) REVERT: A 47 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7680 (mm) REVERT: A 68 LEU cc_start: 0.8082 (tt) cc_final: 0.7790 (tt) REVERT: A 70 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.8040 (mttp) REVERT: B 1 MET cc_start: 0.2713 (OUTLIER) cc_final: 0.2131 (ttp) REVERT: B 10 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7020 (mt-10) REVERT: B 20 HIS cc_start: 0.8737 (t-90) cc_final: 0.8449 (t70) REVERT: B 180 LEU cc_start: 0.8838 (tp) cc_final: 0.8493 (tp) REVERT: B 239 LYS cc_start: 0.8122 (mttt) cc_final: 0.7823 (mtpt) REVERT: B 317 ILE cc_start: 0.6564 (OUTLIER) cc_final: 0.6254 (mt) REVERT: B 416 LYS cc_start: 0.8153 (mmtt) cc_final: 0.7780 (mmtp) REVERT: B 431 HIS cc_start: 0.7188 (OUTLIER) cc_final: 0.6892 (m-70) REVERT: C 29 GLU cc_start: 0.7766 (tt0) cc_final: 0.7444 (mm-30) REVERT: C 70 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7076 (ptt-90) REVERT: C 74 GLU cc_start: 0.7457 (tt0) cc_final: 0.6638 (mm-30) REVERT: C 180 ARG cc_start: 0.8254 (ttp-110) cc_final: 0.7759 (ttp-110) REVERT: C 189 ASP cc_start: 0.6635 (p0) cc_final: 0.5917 (t0) REVERT: C 212 MET cc_start: 0.7496 (ttp) cc_final: 0.7224 (ttt) REVERT: C 214 ASP cc_start: 0.7479 (m-30) cc_final: 0.7196 (m-30) REVERT: F 137 LEU cc_start: 0.8696 (mt) cc_final: 0.8275 (mt) REVERT: F 239 LYS cc_start: 0.8167 (mttt) cc_final: 0.7808 (mttm) REVERT: F 245 TRP cc_start: 0.8671 (t-100) cc_final: 0.8433 (t-100) REVERT: F 272 ASN cc_start: 0.8894 (m-40) cc_final: 0.8639 (m-40) REVERT: F 313 TRP cc_start: 0.5202 (m-90) cc_final: 0.3747 (m-10) REVERT: F 331 PHE cc_start: 0.9179 (t80) cc_final: 0.8968 (t80) REVERT: F 394 LEU cc_start: 0.8529 (tt) cc_final: 0.8215 (tm) REVERT: F 416 LYS cc_start: 0.7952 (mmtm) cc_final: 0.7454 (mmpt) REVERT: G 74 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7735 (mt-10) REVERT: G 136 MET cc_start: 0.6776 (tpp) cc_final: 0.6386 (tpt) REVERT: G 253 PHE cc_start: 0.8276 (m-80) cc_final: 0.7078 (t80) REVERT: G 271 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.7908 (ttpp) outliers start: 34 outliers final: 19 residues processed: 228 average time/residue: 0.5553 time to fit residues: 141.0774 Evaluate side-chains 234 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 431 HIS Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 212 MET Chi-restraints excluded: chain G residue 271 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 65 optimal weight: 0.1980 chunk 109 optimal weight: 0.0370 chunk 58 optimal weight: 0.7980 chunk 152 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 134 optimal weight: 0.0570 chunk 140 optimal weight: 0.8980 chunk 121 optimal weight: 0.0000 overall best weight: 0.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN F 221 ASN F 383 GLN G 84 GLN G 222 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.152734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.103509 restraints weight = 15885.764| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.81 r_work: 0.2807 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.232 15221 Z= 0.104 Angle : 0.589 14.379 20744 Z= 0.259 Chirality : 0.041 0.171 2147 Planarity : 0.004 0.043 2582 Dihedral : 18.686 169.286 2393 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.95 % Allowed : 11.79 % Favored : 86.26 % 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 aren not related in a simple way. whole: 1.40 (0.20), residues: 1773 helix: 1.67 (0.17), residues: 945 sheet: -1.08 (0.57), residues: 77 loop : 0.32 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 86 TYR 0.013 0.001 TYR G 88 PHE 0.021 0.001 PHE D 88 TRP 0.024 0.001 TRP A 147 HIS 0.005 0.001 HIS G 227 Details of bonding type rmsd covalent geometry : bond 0.00228 (15200) covalent geometry : angle 0.58302 (20734) SS BOND : bond 0.00276 ( 2) SS BOND : angle 0.64518 ( 4) hydrogen bonds : bond 0.03957 ( 751) hydrogen bonds : angle 3.80273 ( 2142) metal coordination : bond 0.00647 ( 8) metal coordination : angle 4.84694 ( 6) Misc. bond : bond 0.11585 ( 11) *********************** 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 252 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 224 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.9293 (mtp) cc_final: 0.8926 (mtp) REVERT: A 47 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7656 (mm) REVERT: A 68 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7753 (tt) REVERT: A 70 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7872 (mtmp) REVERT: B 1 MET cc_start: 0.2616 (OUTLIER) cc_final: 0.2024 (ttp) REVERT: B 20 HIS cc_start: 0.8667 (t-90) cc_final: 0.8387 (t70) REVERT: B 180 LEU cc_start: 0.8759 (tp) cc_final: 0.8340 (tp) REVERT: B 239 LYS cc_start: 0.8027 (mttt) cc_final: 0.7698 (mtpt) REVERT: B 317 ILE cc_start: 0.6566 (OUTLIER) cc_final: 0.6200 (mt) REVERT: B 416 LYS cc_start: 0.7908 (mmtt) cc_final: 0.7604 (mmtp) REVERT: B 431 HIS cc_start: 0.7127 (OUTLIER) cc_final: 0.6719 (m-70) REVERT: B 432 TYR cc_start: 0.6737 (m-80) cc_final: 0.6026 (m-80) REVERT: C 29 GLU cc_start: 0.7746 (tt0) cc_final: 0.7348 (mm-30) REVERT: C 74 GLU cc_start: 0.7303 (tt0) cc_final: 0.6436 (mm-30) REVERT: C 180 ARG cc_start: 0.8134 (ttp-110) cc_final: 0.7872 (ttp-110) REVERT: C 189 ASP cc_start: 0.6595 (p0) cc_final: 0.5863 (t0) REVERT: C 214 ASP cc_start: 0.7458 (m-30) cc_final: 0.7174 (m-30) REVERT: F 1 MET cc_start: 0.3077 (ppp) cc_final: 0.2877 (pp-130) REVERT: F 6 HIS cc_start: 0.8174 (p-80) cc_final: 0.7958 (p90) REVERT: F 137 LEU cc_start: 0.8599 (mt) cc_final: 0.8182 (mt) REVERT: F 239 LYS cc_start: 0.8045 (mttt) cc_final: 0.7663 (mttm) REVERT: F 245 TRP cc_start: 0.8503 (t-100) cc_final: 0.8226 (t-100) REVERT: F 272 ASN cc_start: 0.8836 (m-40) cc_final: 0.8615 (m-40) REVERT: F 313 TRP cc_start: 0.5097 (m-90) cc_final: 0.3661 (m-10) REVERT: F 394 LEU cc_start: 0.8435 (tt) cc_final: 0.8106 (tm) REVERT: F 416 LYS cc_start: 0.7938 (mmtm) cc_final: 0.7470 (mmpt) REVERT: G 48 GLN cc_start: 0.8013 (mt0) cc_final: 0.7801 (mt0) REVERT: G 74 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7626 (mt-10) REVERT: G 136 MET cc_start: 0.6714 (tpp) cc_final: 0.6345 (tpt) REVERT: G 253 PHE cc_start: 0.8209 (m-80) cc_final: 0.7048 (t80) REVERT: G 271 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8270 (ttmm) outliers start: 28 outliers final: 13 residues processed: 234 average time/residue: 0.5154 time to fit residues: 135.4421 Evaluate side-chains 231 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 431 HIS Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 271 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 20.0000 chunk 125 optimal weight: 1.9990 chunk 40 optimal weight: 0.0370 chunk 56 optimal weight: 0.7980 chunk 150 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 61 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN F 316 GLN G 84 GLN G 222 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.152111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.101210 restraints weight = 15891.878| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.04 r_work: 0.2794 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.233 15221 Z= 0.107 Angle : 0.593 14.643 20744 Z= 0.259 Chirality : 0.041 0.176 2147 Planarity : 0.004 0.044 2582 Dihedral : 18.379 170.232 2393 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.16 % Allowed : 12.55 % Favored : 85.29 % 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 aren not related in a simple way. whole: 1.44 (0.20), residues: 1773 helix: 1.71 (0.17), residues: 945 sheet: -0.85 (0.58), residues: 78 loop : 0.30 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 77 TYR 0.012 0.001 TYR B 302 PHE 0.019 0.001 PHE D 88 TRP 0.025 0.001 TRP A 147 HIS 0.005 0.001 HIS G 227 Details of bonding type rmsd covalent geometry : bond 0.00242 (15200) covalent geometry : angle 0.58781 (20734) SS BOND : bond 0.00272 ( 2) SS BOND : angle 0.70029 ( 4) hydrogen bonds : bond 0.04064 ( 751) hydrogen bonds : angle 3.78958 ( 2142) metal coordination : bond 0.00691 ( 8) metal coordination : angle 4.65098 ( 6) Misc. bond : bond 0.11326 ( 11) *********************** 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 240 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.9325 (mtp) cc_final: 0.9021 (mtp) REVERT: A 47 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7835 (mm) REVERT: A 68 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7858 (tt) REVERT: A 70 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.8026 (mtmp) REVERT: B 1 MET cc_start: 0.2607 (OUTLIER) cc_final: 0.2111 (ttp) REVERT: B 20 HIS cc_start: 0.8806 (t-90) cc_final: 0.8516 (t70) REVERT: B 133 MET cc_start: 0.9039 (mmm) cc_final: 0.8726 (mmp) REVERT: B 154 MET cc_start: 0.9375 (mmp) cc_final: 0.9105 (mmm) REVERT: B 180 LEU cc_start: 0.8885 (tp) cc_final: 0.8473 (tp) REVERT: B 239 LYS cc_start: 0.8300 (mttt) cc_final: 0.7988 (mtpt) REVERT: B 317 ILE cc_start: 0.6767 (OUTLIER) cc_final: 0.6368 (mt) REVERT: B 416 LYS cc_start: 0.8051 (mmtt) cc_final: 0.7810 (mmtp) REVERT: B 431 HIS cc_start: 0.7289 (OUTLIER) cc_final: 0.6881 (m-70) REVERT: C 74 GLU cc_start: 0.7470 (tt0) cc_final: 0.6686 (mm-30) REVERT: C 180 ARG cc_start: 0.8194 (ttp-110) cc_final: 0.7934 (ttp-110) REVERT: C 189 ASP cc_start: 0.6607 (p0) cc_final: 0.5884 (t0) REVERT: C 214 ASP cc_start: 0.7530 (m-30) cc_final: 0.7234 (m-30) REVERT: F 1 MET cc_start: 0.3361 (ppp) cc_final: 0.3101 (pp-130) REVERT: F 137 LEU cc_start: 0.8841 (mt) cc_final: 0.8454 (mt) REVERT: F 239 LYS cc_start: 0.8237 (mttt) cc_final: 0.7868 (mttm) REVERT: F 245 TRP cc_start: 0.8635 (t-100) cc_final: 0.8354 (t-100) REVERT: F 272 ASN cc_start: 0.8986 (m-40) cc_final: 0.8771 (m-40) REVERT: F 313 TRP cc_start: 0.5237 (m-90) cc_final: 0.3750 (m-10) REVERT: F 394 LEU cc_start: 0.8680 (tt) cc_final: 0.8364 (tm) REVERT: F 416 LYS cc_start: 0.8066 (mmtm) cc_final: 0.7619 (mmpt) REVERT: G 48 GLN cc_start: 0.8344 (mt0) cc_final: 0.8124 (mt0) REVERT: G 74 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7878 (mt-10) REVERT: G 136 MET cc_start: 0.6919 (tpp) cc_final: 0.6496 (tpt) REVERT: G 253 PHE cc_start: 0.8387 (m-80) cc_final: 0.7219 (t80) REVERT: G 271 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8431 (ttmm) outliers start: 31 outliers final: 16 residues processed: 224 average time/residue: 0.5027 time to fit residues: 127.1929 Evaluate side-chains 226 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 431 HIS Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 271 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 148 optimal weight: 0.9980 chunk 11 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 144 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 166 optimal weight: 20.0000 chunk 68 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 84 GLN G 222 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.150471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.102971 restraints weight = 15916.876| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.81 r_work: 0.2753 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.209 15221 Z= 0.128 Angle : 0.628 16.399 20744 Z= 0.274 Chirality : 0.043 0.185 2147 Planarity : 0.004 0.045 2582 Dihedral : 18.297 171.172 2393 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.02 % Allowed : 12.48 % Favored : 85.50 % 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 aren not related in a simple way. whole: 1.33 (0.20), residues: 1773 helix: 1.61 (0.17), residues: 945 sheet: -0.86 (0.58), residues: 80 loop : 0.26 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 103 TYR 0.015 0.001 TYR F 399 PHE 0.020 0.001 PHE B 216 TRP 0.029 0.001 TRP A 147 HIS 0.007 0.001 HIS F 212 Details of bonding type rmsd covalent geometry : bond 0.00304 (15200) covalent geometry : angle 0.62374 (20734) SS BOND : bond 0.00340 ( 2) SS BOND : angle 0.98428 ( 4) hydrogen bonds : bond 0.04557 ( 751) hydrogen bonds : angle 3.87969 ( 2142) metal coordination : bond 0.00782 ( 8) metal coordination : angle 4.27197 ( 6) Misc. bond : bond 0.10492 ( 11) *********************** 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 233 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.9351 (mtp) cc_final: 0.9073 (mtp) REVERT: A 47 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7574 (mm) REVERT: A 68 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7793 (tt) REVERT: A 70 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7908 (mtmp) REVERT: B 20 HIS cc_start: 0.8701 (t-90) cc_final: 0.8387 (t70) REVERT: B 154 MET cc_start: 0.9369 (mmp) cc_final: 0.9068 (mmm) REVERT: B 180 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8428 (tp) REVERT: B 239 LYS cc_start: 0.8064 (mttt) cc_final: 0.7717 (mtpt) REVERT: B 317 ILE cc_start: 0.6607 (OUTLIER) cc_final: 0.6234 (mt) REVERT: B 416 LYS cc_start: 0.7993 (mmtt) cc_final: 0.7658 (mmtp) REVERT: B 431 HIS cc_start: 0.7186 (OUTLIER) cc_final: 0.6830 (m-70) REVERT: C 74 GLU cc_start: 0.7434 (tt0) cc_final: 0.6620 (mm-30) REVERT: C 180 ARG cc_start: 0.8163 (ttp-110) cc_final: 0.7902 (ttp-110) REVERT: C 189 ASP cc_start: 0.6608 (p0) cc_final: 0.5880 (t0) REVERT: C 214 ASP cc_start: 0.7504 (m-30) cc_final: 0.7214 (m-30) REVERT: F 137 LEU cc_start: 0.8667 (mt) cc_final: 0.8240 (mt) REVERT: F 239 LYS cc_start: 0.8097 (mttt) cc_final: 0.7749 (mttm) REVERT: F 272 ASN cc_start: 0.8868 (m-40) cc_final: 0.8633 (m-40) REVERT: F 313 TRP cc_start: 0.5033 (m-90) cc_final: 0.3664 (m-10) REVERT: F 383 GLN cc_start: 0.8090 (mp-120) cc_final: 0.7795 (mp10) REVERT: F 416 LYS cc_start: 0.7926 (mmtm) cc_final: 0.7475 (mmpt) REVERT: G 74 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7697 (mt-10) REVERT: G 136 MET cc_start: 0.6840 (tpp) cc_final: 0.6468 (tpt) REVERT: G 253 PHE cc_start: 0.8294 (m-80) cc_final: 0.7118 (t80) REVERT: G 271 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.7888 (ttpp) outliers start: 29 outliers final: 19 residues processed: 216 average time/residue: 0.4987 time to fit residues: 120.8514 Evaluate side-chains 224 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 431 HIS Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 271 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 87 optimal weight: 0.6980 chunk 70 optimal weight: 0.0870 chunk 4 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN G 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.151171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.104272 restraints weight = 15903.974| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.71 r_work: 0.2766 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.211 15221 Z= 0.117 Angle : 0.615 15.691 20744 Z= 0.269 Chirality : 0.042 0.187 2147 Planarity : 0.004 0.046 2582 Dihedral : 18.096 172.055 2393 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.88 % Allowed : 13.18 % Favored : 84.94 % 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 aren not related in a simple way. whole: 1.34 (0.20), residues: 1773 helix: 1.62 (0.17), residues: 945 sheet: -0.85 (0.58), residues: 80 loop : 0.25 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 103 TYR 0.015 0.001 TYR B 432 PHE 0.018 0.001 PHE B 216 TRP 0.029 0.001 TRP A 147 HIS 0.006 0.001 HIS F 212 Details of bonding type rmsd covalent geometry : bond 0.00273 (15200) covalent geometry : angle 0.61038 (20734) SS BOND : bond 0.00323 ( 2) SS BOND : angle 0.88845 ( 4) hydrogen bonds : bond 0.04393 ( 751) hydrogen bonds : angle 3.85897 ( 2142) metal coordination : bond 0.00661 ( 8) metal coordination : angle 4.37180 ( 6) Misc. bond : bond 0.10113 ( 11) ********************** 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 230 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.9360 (mtp) cc_final: 0.9068 (mtp) REVERT: A 47 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7575 (mm) REVERT: A 68 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7784 (tt) REVERT: A 70 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7924 (mtmp) REVERT: B 20 HIS cc_start: 0.8679 (t-90) cc_final: 0.8401 (t70) REVERT: B 154 MET cc_start: 0.9372 (mmp) cc_final: 0.8857 (mmm) REVERT: B 180 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8381 (tp) REVERT: B 239 LYS cc_start: 0.8081 (mttt) cc_final: 0.7759 (mtpt) REVERT: B 317 ILE cc_start: 0.6607 (OUTLIER) cc_final: 0.6234 (mt) REVERT: B 416 LYS cc_start: 0.7872 (mmtt) cc_final: 0.7597 (mmtp) REVERT: B 431 HIS cc_start: 0.7135 (OUTLIER) cc_final: 0.6768 (m-70) REVERT: C 74 GLU cc_start: 0.7414 (tt0) cc_final: 0.6598 (mm-30) REVERT: C 180 ARG cc_start: 0.8124 (ttp-110) cc_final: 0.7872 (ttp-110) REVERT: C 189 ASP cc_start: 0.6609 (p0) cc_final: 0.5870 (t0) REVERT: C 214 ASP cc_start: 0.7511 (m-30) cc_final: 0.7222 (m-30) REVERT: F 6 HIS cc_start: 0.8185 (p-80) cc_final: 0.7907 (p90) REVERT: F 137 LEU cc_start: 0.8666 (mt) cc_final: 0.8258 (mt) REVERT: F 239 LYS cc_start: 0.8117 (mttt) cc_final: 0.7804 (mttm) REVERT: F 272 ASN cc_start: 0.8877 (m-40) cc_final: 0.8642 (m-40) REVERT: F 313 TRP cc_start: 0.5021 (m-90) cc_final: 0.3647 (m-10) REVERT: F 383 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7805 (mp10) REVERT: F 394 LEU cc_start: 0.8437 (tt) cc_final: 0.8142 (tm) REVERT: F 416 LYS cc_start: 0.7918 (mmtm) cc_final: 0.7469 (mmpt) REVERT: G 48 GLN cc_start: 0.8097 (mt0) cc_final: 0.7849 (mt0) REVERT: G 74 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7691 (mt-10) REVERT: G 136 MET cc_start: 0.6836 (tpp) cc_final: 0.6465 (tpt) REVERT: G 253 PHE cc_start: 0.8279 (m-80) cc_final: 0.7103 (t80) REVERT: G 271 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.7896 (ttpp) outliers start: 27 outliers final: 16 residues processed: 216 average time/residue: 0.5035 time to fit residues: 122.9460 Evaluate side-chains 221 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 431 HIS Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 383 GLN Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 199 THR Chi-restraints excluded: chain G residue 271 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 17 optimal weight: 6.9990 chunk 26 optimal weight: 0.0030 chunk 58 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 0.0030 chunk 72 optimal weight: 0.7980 chunk 165 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 155 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 84 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.151503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.105462 restraints weight = 15781.371| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.66 r_work: 0.2750 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.208 15221 Z= 0.119 Angle : 0.616 15.656 20744 Z= 0.270 Chirality : 0.042 0.188 2147 Planarity : 0.004 0.046 2582 Dihedral : 17.901 172.877 2393 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.74 % Allowed : 13.25 % Favored : 85.01 % 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 aren not related in a simple way. whole: 1.35 (0.20), residues: 1773 helix: 1.63 (0.17), residues: 943 sheet: -0.81 (0.59), residues: 80 loop : 0.27 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 103 TYR 0.016 0.001 TYR B 432 PHE 0.025 0.001 PHE G 258 TRP 0.029 0.001 TRP A 147 HIS 0.006 0.001 HIS F 212 Details of bonding type rmsd covalent geometry : bond 0.00280 (15200) covalent geometry : angle 0.61184 (20734) SS BOND : bond 0.00455 ( 2) SS BOND : angle 0.70050 ( 4) hydrogen bonds : bond 0.04423 ( 751) hydrogen bonds : angle 3.87264 ( 2142) metal coordination : bond 0.00734 ( 8) metal coordination : angle 4.28851 ( 6) Misc. bond : bond 0.09857 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5797.16 seconds wall clock time: 99 minutes 17.60 seconds (5957.60 seconds total)