Starting phenix.real_space_refine on Fri Jul 3 18:22:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8asi_15616/07_2026/8asi_15616.cif Found real_map, /net/cci-nas-00/data/ceres_data/8asi_15616/07_2026/8asi_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8asi_15616/07_2026/8asi_15616.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8asi_15616/07_2026/8asi_15616.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8asi_15616/07_2026/8asi_15616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8asi_15616/07_2026/8asi_15616.map" model { file = "/net/cci-nas-00/data/ceres_data/8asi_15616/07_2026/8asi_15616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8asi_15616/07_2026/8asi_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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14720 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1342 Classifications: {'peptide': 179} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 168} Chain: "B" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3477 Classifications: {'peptide': 433} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 404} Chain: "C" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1944 Classifications: {'peptide': 254} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 233} Chain: "D" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 222 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "E" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1357 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 170} Chain: "F" Number of atoms: 3471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3471 Classifications: {'peptide': 432} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 403} Chain: "G" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1944 Classifications: {'peptide': 254} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 233} Chain: "H" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 203 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "A" Number of atoms: 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: 2.61, per 1000 atoms: 0.18 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: 1.42 Conformation dependent library (CDL) restraints added in 533.0 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 201 " pdb="FE2 FES A 201 " - pdb=" ND1 HIS A 152 " pdb="FE2 FES A 201 " - pdb=" ND1 HIS A 131 " pdb="FE1 FES A 201 " - pdb=" SG CYS A 149 " pdb="FE1 FES A 201 " - pdb=" SG CYS A 129 " pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" 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: 0.44 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: 1.84 Time building geometry restraints manager: 1.64 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 - 34.09: 8341 34.09 - 68.18: 178 68.18 - 102.27: 50 102.27 - 136.36: 14 136.36 - 170.45: 7 Dihedral angle restraints: 8590 sinusoidal: 3485 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 8587 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 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: 13.250 Find NCS groups from input model: 0.200 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: 0.000 Load rotamer database and sin/cos tables:5.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 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 : 17.523 170.451 5330 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 are 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/Z covalent geometry : bond 0.00888 / 0.44 (15200) covalent geometry : angle 1.27255 / 0.58 (20734) SS BOND : bond 0.00519 / 0.32 ( 2) SS BOND : angle 1.39786 / 0.69 ( 4) hydrogen bonds : bond 0.14398 / 9.56 ( 751) hydrogen bonds : angle 6.41406 / 4.61 ( 2142) metal coordination : bond 0.11554 / 8.48 ( 8) metal coordination : angle 15.91242 / 8.09 ( 6) Misc. bond : bond 0.38101 / 24.36 ( 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 : 0.335 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: 0.4560 time to fit residues: 144.0082 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 : 0.419 ------------------------------------------------------------------------------- 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... 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 = 0.3605 r_free = 0.3605 target = 0.148827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.096984 restraints weight = 16063.961| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.88 r_work: 0.2744 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.272 15221 Z= 0.164 Angle : 0.733 15.737 20744 Z= 0.335 Chirality : 0.047 0.239 2147 Planarity : 0.005 0.048 2582 Dihedral : 17.028 167.120 2275 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.95 % Allowed : 8.16 % 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 are not related in a simple way. whole: 0.72 (0.20), residues: 1773 helix: 1.03 (0.17), residues: 926 sheet: -1.93 (0.52), residues: 72 loop : 0.21 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 248 TYR 0.015 0.002 TYR B 199 PHE 0.041 0.002 PHE D 88 TRP 0.018 0.002 TRP F 157 HIS 0.009 0.002 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (15200) covalent geometry : angle 0.72197 / 0.33 (20734) SS BOND : bond 0.00447 / 0.26 ( 2) SS BOND : angle 0.88503 / 0.47 ( 4) hydrogen bonds : bond 0.05514 / 3.72 ( 751) hydrogen bonds : angle 4.47190 / 3.21 ( 2142) metal coordination : bond 0.01030 / 0.62 ( 8) metal coordination : angle 7.31565 / 3.66 ( 6) Misc. bond : bond 0.14905 / 8.59 ( 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 266 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 238 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9341 (mtp) cc_final: 0.9059 (mtp) REVERT: A 180 ASP cc_start: 0.5653 (OUTLIER) cc_final: 0.5379 (p0) REVERT: B 1 MET cc_start: 0.2428 (OUTLIER) cc_final: 0.1226 (ppp) REVERT: B 6 HIS cc_start: 0.7704 (p-80) cc_final: 0.7403 (p-80) REVERT: B 20 HIS cc_start: 0.8722 (t-90) cc_final: 0.8434 (t70) REVERT: B 239 LYS cc_start: 0.8121 (mttt) cc_final: 0.7829 (mtpt) REVERT: B 416 LYS cc_start: 0.8344 (mmtt) cc_final: 0.7835 (mmtp) REVERT: C 180 ARG cc_start: 0.8356 (ttp-110) cc_final: 0.7978 (ttp-110) REVERT: C 189 ASP cc_start: 0.6673 (p0) cc_final: 0.5776 (t0) REVERT: C 212 MET cc_start: 0.7634 (ttp) cc_final: 0.7372 (ttt) REVERT: C 214 ASP cc_start: 0.7696 (m-30) cc_final: 0.7426 (m-30) REVERT: F 137 LEU cc_start: 0.8678 (mt) cc_final: 0.8309 (mt) REVERT: F 239 LYS cc_start: 0.8315 (mttt) cc_final: 0.7979 (mttm) REVERT: F 252 ASP cc_start: 0.8183 (m-30) cc_final: 0.7970 (m-30) REVERT: F 270 MET cc_start: 0.9101 (ptp) cc_final: 0.8890 (ptp) REVERT: F 313 TRP cc_start: 0.5550 (m-90) cc_final: 0.3960 (m-10) REVERT: G 74 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7854 (mt-10) REVERT: G 136 MET cc_start: 0.6631 (tpp) cc_final: 0.6200 (tpt) REVERT: G 198 LYS cc_start: 0.7905 (ttpt) cc_final: 0.7700 (ttpp) REVERT: G 246 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.7947 (mpp) outliers start: 28 outliers final: 11 residues processed: 252 average time/residue: 0.4316 time to fit residues: 122.1428 Evaluate side-chains 219 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 205 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 180 LEU 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 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: 0.0470 chunk 91 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 0.0010 chunk 143 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 61 optimal weight: 0.0270 chunk 52 optimal weight: 4.9990 overall best weight: 0.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3638 r_free = 0.3638 target = 0.151749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.100448 restraints weight = 16092.314| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.87 r_work: 0.2795 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.294 15221 Z= 0.117 Angle : 0.632 15.136 20744 Z= 0.281 Chirality : 0.042 0.177 2147 Planarity : 0.005 0.046 2582 Dihedral : 15.416 170.562 2275 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.16 % Allowed : 9.83 % Favored : 88.01 % 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 are not related in a simple way. whole: 1.18 (0.20), residues: 1773 helix: 1.39 (0.17), residues: 942 sheet: -1.60 (0.56), residues: 72 loop : 0.41 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 12 TYR 0.012 0.001 TYR F 399 PHE 0.026 0.001 PHE D 88 TRP 0.016 0.001 TRP A 147 HIS 0.021 0.001 HIS B 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (15200) covalent geometry : angle 0.62596 / 0.28 (20734) SS BOND : bond 0.00920 / 0.51 ( 2) SS BOND : angle 0.95060 / 0.55 ( 4) hydrogen bonds : bond 0.04550 / 3.06 ( 751) hydrogen bonds : angle 4.14794 / 2.98 ( 2142) metal coordination : bond 0.00502 / 0.33 ( 8) metal coordination : angle 5.02299 / 2.52 ( 6) Misc. bond : bond 0.13615 / 7.40 ( 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 271 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 240 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.9335 (mtp) cc_final: 0.8997 (mtp) REVERT: A 180 ASP cc_start: 0.5997 (OUTLIER) cc_final: 0.5553 (p0) REVERT: B 1 MET cc_start: 0.2329 (OUTLIER) cc_final: 0.1588 (ttp) REVERT: B 20 HIS cc_start: 0.8751 (t-90) cc_final: 0.8456 (t70) REVERT: B 239 LYS cc_start: 0.8119 (mttt) cc_final: 0.7826 (mtpt) REVERT: B 260 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7810 (mp) REVERT: B 317 ILE cc_start: 0.6806 (OUTLIER) cc_final: 0.6385 (mt) REVERT: B 416 LYS cc_start: 0.8216 (mmtt) cc_final: 0.7744 (mmtp) REVERT: B 423 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7810 (p) REVERT: B 431 HIS cc_start: 0.7083 (m90) cc_final: 0.6862 (m170) REVERT: C 74 GLU cc_start: 0.7473 (tt0) cc_final: 0.6733 (mm-30) REVERT: C 180 ARG cc_start: 0.8367 (ttp-110) cc_final: 0.7987 (ttp-110) REVERT: C 189 ASP cc_start: 0.6798 (p0) cc_final: 0.6155 (t0) REVERT: C 207 MET cc_start: 0.8779 (ttm) cc_final: 0.8325 (ttm) REVERT: C 212 MET cc_start: 0.7600 (ttp) cc_final: 0.7324 (ttt) REVERT: C 214 ASP cc_start: 0.7444 (m-30) cc_final: 0.7189 (m-30) REVERT: F 137 LEU cc_start: 0.8680 (mt) cc_final: 0.8318 (mt) REVERT: F 239 LYS cc_start: 0.8255 (mttt) cc_final: 0.7821 (mttm) REVERT: F 270 MET cc_start: 0.9123 (ptp) cc_final: 0.8862 (ptp) REVERT: F 313 TRP cc_start: 0.5427 (m-90) cc_final: 0.3906 (m-10) REVERT: F 432 TYR cc_start: 0.5497 (m-80) cc_final: 0.4891 (t80) REVERT: G 74 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7838 (mt-10) REVERT: G 136 MET cc_start: 0.6530 (tpp) cc_final: 0.6281 (tpt) REVERT: G 232 ASP cc_start: 0.8964 (m-30) cc_final: 0.8648 (m-30) REVERT: G 271 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8372 (ttmm) outliers start: 31 outliers final: 9 residues processed: 256 average time/residue: 0.4282 time to fit residues: 123.3299 Evaluate side-chains 234 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 219 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 260 LEU 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 C residue 83 ASP 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: 6.9990 chunk 46 optimal weight: 0.0010 chunk 63 optimal weight: 6.9990 chunk 152 optimal weight: 0.0870 chunk 21 optimal weight: 0.2980 chunk 56 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 20 optimal weight: 0.0980 chunk 153 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.2364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 177 GLN C 171 HIS C 183 GLN F 221 ASN F 316 GLN F 383 GLN G 118 ASN G 142 GLN G 179 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.153303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.102278 restraints weight = 16051.279| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.05 r_work: 0.2809 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.251 15221 Z= 0.108 Angle : 0.594 13.900 20744 Z= 0.265 Chirality : 0.041 0.160 2147 Planarity : 0.004 0.044 2582 Dihedral : 14.213 168.762 2273 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.09 % Allowed : 10.32 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.20), residues: 1773 helix: 1.55 (0.17), residues: 946 sheet: -1.41 (0.55), residues: 77 loop : 0.46 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 49 TYR 0.013 0.001 TYR G 88 PHE 0.022 0.001 PHE D 88 TRP 0.019 0.001 TRP A 147 HIS 0.005 0.001 HIS G 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (15200) covalent geometry : angle 0.58834 / 0.26 (20734) SS BOND : bond 0.00330 / 0.19 ( 2) SS BOND : angle 0.67753 / 0.33 ( 4) hydrogen bonds : bond 0.04121 / 2.79 ( 751) hydrogen bonds : angle 3.92923 / 2.84 ( 2142) metal coordination : bond 0.00616 / 0.42 ( 8) metal coordination : angle 4.64964 / 2.30 ( 6) Misc. bond : bond 0.12599 / 6.59 ( 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 248 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.9344 (mtp) cc_final: 0.8960 (mtp) REVERT: A 180 ASP cc_start: 0.5949 (OUTLIER) cc_final: 0.5629 (p0) REVERT: B 1 MET cc_start: 0.2171 (OUTLIER) cc_final: 0.1739 (ttp) REVERT: B 20 HIS cc_start: 0.8754 (t-90) cc_final: 0.8463 (t70) REVERT: B 180 LEU cc_start: 0.8807 (tp) cc_final: 0.8389 (tp) REVERT: B 239 LYS cc_start: 0.8144 (mttt) cc_final: 0.7854 (mtpt) REVERT: B 317 ILE cc_start: 0.6825 (OUTLIER) cc_final: 0.6373 (mt) REVERT: B 416 LYS cc_start: 0.8202 (mmtt) cc_final: 0.7749 (mmtp) REVERT: B 423 THR cc_start: 0.8025 (OUTLIER) cc_final: 0.7771 (p) REVERT: C 74 GLU cc_start: 0.7478 (tt0) cc_final: 0.6739 (mm-30) REVERT: C 180 ARG cc_start: 0.8343 (ttp-110) cc_final: 0.7846 (ttp-110) REVERT: C 189 ASP cc_start: 0.6824 (p0) cc_final: 0.6061 (t0) REVERT: C 207 MET cc_start: 0.8804 (ttm) cc_final: 0.8345 (ttm) REVERT: C 212 MET cc_start: 0.7611 (ttp) cc_final: 0.7392 (ttt) REVERT: C 214 ASP cc_start: 0.7499 (m-30) cc_final: 0.7229 (m-30) REVERT: F 137 LEU cc_start: 0.8718 (mt) cc_final: 0.8343 (mt) REVERT: F 239 LYS cc_start: 0.8234 (mttt) cc_final: 0.7772 (mttp) REVERT: F 270 MET cc_start: 0.9055 (ptp) cc_final: 0.8778 (ptp) REVERT: F 313 TRP cc_start: 0.5154 (m-90) cc_final: 0.3765 (m-10) REVERT: F 414 ILE cc_start: 0.8196 (pt) cc_final: 0.7867 (mp) REVERT: F 432 TYR cc_start: 0.5497 (m-80) cc_final: 0.5045 (m-80) REVERT: G 48 GLN cc_start: 0.8235 (mt0) cc_final: 0.8015 (mt0) REVERT: G 74 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7779 (mt-10) REVERT: G 136 MET cc_start: 0.6575 (tpp) cc_final: 0.6319 (tpt) REVERT: G 271 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8384 (ttmm) outliers start: 30 outliers final: 11 residues processed: 233 average time/residue: 0.4239 time to fit residues: 110.6911 Evaluate side-chains 237 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 221 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 423 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 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: 0.0870 chunk 10 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 49 optimal weight: 0.0970 chunk 110 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 177 GLN C 183 GLN G 84 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 = 0.3640 r_free = 0.3640 target = 0.151927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.100833 restraints weight = 15905.144| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.96 r_work: 0.2797 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.244 15221 Z= 0.110 Angle : 0.602 15.218 20744 Z= 0.264 Chirality : 0.042 0.159 2147 Planarity : 0.004 0.042 2582 Dihedral : 13.566 166.608 2273 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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 are not related in a simple way. whole: 1.39 (0.20), residues: 1773 helix: 1.64 (0.17), residues: 943 sheet: -1.37 (0.55), residues: 77 loop : 0.39 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 49 TYR 0.013 0.001 TYR F 399 PHE 0.022 0.001 PHE D 88 TRP 0.023 0.001 TRP A 147 HIS 0.006 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (15200) covalent geometry : angle 0.59619 / 0.26 (20734) SS BOND : bond 0.00303 / 0.17 ( 2) SS BOND : angle 0.88828 / 0.45 ( 4) hydrogen bonds : bond 0.04236 / 2.88 ( 751) hydrogen bonds : angle 3.87055 / 2.80 ( 2142) metal coordination : bond 0.00742 / 0.53 ( 8) metal coordination : angle 4.70013 / 2.11 ( 6) Misc. bond : bond 0.11930 / 6.12 ( 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 259 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 224 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.9334 (mtp) cc_final: 0.8986 (mtp) REVERT: A 47 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7720 (mm) REVERT: A 68 LEU cc_start: 0.8082 (tt) cc_final: 0.7822 (tt) REVERT: A 70 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8064 (mttp) REVERT: A 180 ASP cc_start: 0.6213 (OUTLIER) cc_final: 0.5978 (p0) REVERT: B 1 MET cc_start: 0.2090 (OUTLIER) cc_final: 0.1615 (ttp) REVERT: B 20 HIS cc_start: 0.8734 (t-90) cc_final: 0.8450 (t70) REVERT: B 180 LEU cc_start: 0.8815 (tp) cc_final: 0.8362 (tp) REVERT: B 239 LYS cc_start: 0.8141 (mttt) cc_final: 0.7853 (mtpt) REVERT: B 317 ILE cc_start: 0.6791 (OUTLIER) cc_final: 0.6368 (mt) REVERT: B 416 LYS cc_start: 0.8116 (mmtt) cc_final: 0.7781 (mmtp) REVERT: C 29 GLU cc_start: 0.7770 (tt0) cc_final: 0.7487 (mm-30) REVERT: C 74 GLU cc_start: 0.7425 (tt0) cc_final: 0.6641 (mm-30) REVERT: C 180 ARG cc_start: 0.8272 (ttp-110) cc_final: 0.8009 (ttp-110) REVERT: C 189 ASP cc_start: 0.6621 (p0) cc_final: 0.5927 (t0) REVERT: C 207 MET cc_start: 0.8842 (ttp) cc_final: 0.8444 (ttm) REVERT: C 214 ASP cc_start: 0.7499 (m-30) cc_final: 0.7224 (m-30) REVERT: E 125 MET cc_start: 0.6195 (OUTLIER) cc_final: 0.5717 (ptm) REVERT: F 137 LEU cc_start: 0.8724 (mt) cc_final: 0.8349 (mt) REVERT: F 239 LYS cc_start: 0.8173 (mttt) cc_final: 0.7768 (mttm) REVERT: F 270 MET cc_start: 0.9082 (ptp) cc_final: 0.8741 (ptp) REVERT: F 313 TRP cc_start: 0.5135 (m-90) cc_final: 0.3763 (m-10) REVERT: F 416 LYS cc_start: 0.8036 (mmtm) cc_final: 0.7574 (mmpt) REVERT: G 74 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: G 136 MET cc_start: 0.6805 (tpp) cc_final: 0.6441 (tpt) REVERT: G 253 PHE cc_start: 0.8302 (m-80) cc_final: 0.7075 (t80) REVERT: G 271 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8367 (ttmm) outliers start: 35 outliers final: 14 residues processed: 239 average time/residue: 0.4026 time to fit residues: 108.8229 Evaluate side-chains 232 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL 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 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 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 74 GLU Chi-restraints excluded: chain G residue 93 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: 0.9980 chunk 164 optimal weight: 0.1980 chunk 105 optimal weight: 0.0970 chunk 130 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 146 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 177 GLN B 383 GLN C 183 GLN F 316 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.152497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.103492 restraints weight = 15938.426| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.67 r_work: 0.2815 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.235 15221 Z= 0.107 Angle : 0.592 14.941 20744 Z= 0.259 Chirality : 0.041 0.164 2147 Planarity : 0.004 0.046 2582 Dihedral : 13.260 165.530 2273 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.58 % Allowed : 11.44 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.20), residues: 1773 helix: 1.71 (0.17), residues: 945 sheet: -1.21 (0.56), residues: 77 loop : 0.38 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 49 TYR 0.013 0.001 TYR B 432 PHE 0.020 0.001 PHE D 88 TRP 0.021 0.001 TRP A 147 HIS 0.005 0.001 HIS G 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (15200) covalent geometry : angle 0.58640 / 0.26 (20734) SS BOND : bond 0.00265 / 0.15 ( 2) SS BOND : angle 0.73048 / 0.36 ( 4) hydrogen bonds : bond 0.04084 / 2.77 ( 751) hydrogen bonds : angle 3.81097 / 2.76 ( 2142) metal coordination : bond 0.00665 / 0.47 ( 8) metal coordination : angle 4.63035 / 2.10 ( 6) Misc. bond : bond 0.11700 / 6.00 ( 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 257 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.9331 (mtp) cc_final: 0.8958 (mtp) REVERT: A 47 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7684 (mm) REVERT: A 68 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7789 (tt) REVERT: A 70 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7979 (mttp) REVERT: A 137 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7516 (mm) REVERT: B 20 HIS cc_start: 0.8718 (t-90) cc_final: 0.8416 (t70) REVERT: B 154 MET cc_start: 0.9297 (mmp) cc_final: 0.9043 (mmm) REVERT: B 180 LEU cc_start: 0.8763 (tp) cc_final: 0.8330 (tp) REVERT: B 239 LYS cc_start: 0.8072 (mttt) cc_final: 0.7779 (mtpt) REVERT: B 317 ILE cc_start: 0.6835 (OUTLIER) cc_final: 0.6420 (mt) REVERT: B 416 LYS cc_start: 0.8066 (mmtt) cc_final: 0.7715 (mmtp) REVERT: C 29 GLU cc_start: 0.7745 (tt0) cc_final: 0.7435 (mm-30) REVERT: C 74 GLU cc_start: 0.7374 (tt0) cc_final: 0.6568 (mm-30) REVERT: C 180 ARG cc_start: 0.8217 (ttp-110) cc_final: 0.7950 (ttp-110) REVERT: C 189 ASP cc_start: 0.6620 (p0) cc_final: 0.5910 (t0) REVERT: C 214 ASP cc_start: 0.7463 (m-30) cc_final: 0.7188 (m-30) REVERT: F 137 LEU cc_start: 0.8648 (mt) cc_final: 0.8250 (mt) REVERT: F 239 LYS cc_start: 0.8103 (mttt) cc_final: 0.7704 (mttm) REVERT: F 245 TRP cc_start: 0.8592 (t-100) cc_final: 0.8238 (t-100) REVERT: F 270 MET cc_start: 0.9041 (ptp) cc_final: 0.8723 (ptp) REVERT: F 313 TRP cc_start: 0.5081 (m-90) cc_final: 0.3748 (m-10) REVERT: F 350 ASP cc_start: 0.8539 (t0) cc_final: 0.8238 (t70) REVERT: F 416 LYS cc_start: 0.8001 (mmtm) cc_final: 0.7543 (mmpt) REVERT: G 74 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7853 (mt-10) REVERT: G 136 MET cc_start: 0.6807 (tpp) cc_final: 0.6311 (tpt) REVERT: G 253 PHE cc_start: 0.8223 (m-80) cc_final: 0.7022 (t80) REVERT: G 271 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8321 (ttmm) outliers start: 37 outliers final: 19 residues processed: 236 average time/residue: 0.4038 time to fit residues: 107.6398 Evaluate side-chains 233 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 A residue 72 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 260 LEU 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 C residue 190 THR Chi-restraints excluded: chain C residue 262 LEU 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 249 ILE Chi-restraints excluded: chain F residue 327 ASP Chi-restraints excluded: chain G residue 74 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 65 optimal weight: 0.9980 chunk 109 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 140 optimal weight: 0.1980 chunk 121 optimal weight: 0.5980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 183 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 = 0.3639 r_free = 0.3639 target = 0.151724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.102634 restraints weight = 15868.837| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.70 r_work: 0.2792 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.237 15221 Z= 0.112 Angle : 0.598 15.683 20744 Z= 0.261 Chirality : 0.042 0.171 2147 Planarity : 0.004 0.045 2582 Dihedral : 13.101 164.720 2273 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.72 % Allowed : 11.44 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.20), residues: 1773 helix: 1.70 (0.17), residues: 945 sheet: -0.87 (0.58), residues: 78 loop : 0.36 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 94 TYR 0.014 0.001 TYR B 432 PHE 0.018 0.001 PHE D 88 TRP 0.025 0.001 TRP A 147 HIS 0.006 0.001 HIS F 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (15200) covalent geometry : angle 0.59276 / 0.26 (20734) SS BOND : bond 0.00300 / 0.17 ( 2) SS BOND : angle 0.83103 / 0.41 ( 4) hydrogen bonds : bond 0.04241 / 2.88 ( 751) hydrogen bonds : angle 3.80514 / 2.76 ( 2142) metal coordination : bond 0.00780 / 0.55 ( 8) metal coordination : angle 4.55725 / 2.06 ( 6) Misc. bond : bond 0.11331 / 5.67 ( 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 249 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.9321 (mtp) cc_final: 0.8996 (mtp) REVERT: A 47 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7645 (mm) REVERT: A 68 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7800 (tt) REVERT: A 70 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7904 (mtmp) REVERT: B 20 HIS cc_start: 0.8706 (t-90) cc_final: 0.8438 (t70) REVERT: B 154 MET cc_start: 0.9325 (mmp) cc_final: 0.9001 (mmm) REVERT: B 180 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8353 (tp) REVERT: B 239 LYS cc_start: 0.8056 (mttt) cc_final: 0.7765 (mtpt) REVERT: B 317 ILE cc_start: 0.6592 (OUTLIER) cc_final: 0.6204 (mt) REVERT: B 416 LYS cc_start: 0.7966 (mmtt) cc_final: 0.7664 (mmtp) REVERT: C 29 GLU cc_start: 0.7735 (tt0) cc_final: 0.7385 (mm-30) REVERT: C 74 GLU cc_start: 0.7390 (tt0) cc_final: 0.6542 (mm-30) REVERT: C 180 ARG cc_start: 0.8114 (ttp-110) cc_final: 0.7757 (ttp-110) REVERT: C 189 ASP cc_start: 0.6626 (p0) cc_final: 0.5916 (t0) REVERT: C 214 ASP cc_start: 0.7452 (m-30) cc_final: 0.7176 (m-30) REVERT: F 137 LEU cc_start: 0.8641 (mt) cc_final: 0.8249 (mt) REVERT: F 239 LYS cc_start: 0.8070 (mttt) cc_final: 0.7682 (mttm) REVERT: F 245 TRP cc_start: 0.8525 (t-100) cc_final: 0.8188 (t-100) REVERT: F 270 MET cc_start: 0.9039 (ptp) cc_final: 0.8649 (ptp) REVERT: F 272 ASN cc_start: 0.8927 (m-40) cc_final: 0.8685 (m-40) REVERT: F 313 TRP cc_start: 0.5082 (m-90) cc_final: 0.3714 (m-10) REVERT: F 394 LEU cc_start: 0.8484 (tt) cc_final: 0.8161 (tm) REVERT: F 416 LYS cc_start: 0.7936 (mmtm) cc_final: 0.7472 (mmpt) REVERT: G 74 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7877 (mt-10) REVERT: G 136 MET cc_start: 0.6808 (tpp) cc_final: 0.6354 (tpt) REVERT: G 253 PHE cc_start: 0.8246 (m-80) cc_final: 0.7020 (t80) REVERT: G 271 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8304 (ttmm) outliers start: 39 outliers final: 18 residues processed: 226 average time/residue: 0.4128 time to fit residues: 105.3636 Evaluate side-chains 234 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 A residue 72 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 317 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 262 LEU 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 249 ILE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 93 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: 6.9990 chunk 56 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 316 GLN G 84 GLN G 222 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.148907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.101326 restraints weight = 15873.743| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.70 r_work: 0.2711 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.272 15221 Z= 0.169 Angle : 0.684 18.390 20744 Z= 0.299 Chirality : 0.045 0.177 2147 Planarity : 0.005 0.044 2582 Dihedral : 13.421 167.224 2273 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.44 % Allowed : 11.92 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.20), residues: 1773 helix: 1.39 (0.17), residues: 948 sheet: -0.88 (0.61), residues: 70 loop : 0.21 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 114 TYR 0.019 0.002 TYR F 399 PHE 0.022 0.002 PHE F 105 TRP 0.028 0.002 TRP A 147 HIS 0.013 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (15200) covalent geometry : angle 0.68071 / 0.30 (20734) SS BOND : bond 0.00348 / 0.20 ( 2) SS BOND : angle 1.51375 / 0.75 ( 4) hydrogen bonds : bond 0.05265 / 3.58 ( 751) hydrogen bonds : angle 4.03024 / 2.91 ( 2142) metal coordination : bond 0.01158 / 0.75 ( 8) metal coordination : angle 3.80641 / 1.73 ( 6) Misc. bond : bond 0.12343 / 6.73 ( 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 249 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.9407 (mtp) cc_final: 0.9183 (mtp) REVERT: A 47 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7603 (mm) REVERT: A 68 LEU cc_start: 0.8062 (tt) cc_final: 0.7831 (tt) REVERT: B 10 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7119 (mt-10) REVERT: B 20 HIS cc_start: 0.8731 (t-90) cc_final: 0.8433 (t70) REVERT: B 154 MET cc_start: 0.9401 (mmp) cc_final: 0.9075 (mmm) REVERT: B 180 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8551 (tp) REVERT: B 239 LYS cc_start: 0.8169 (mttt) cc_final: 0.7862 (mtpt) REVERT: B 317 ILE cc_start: 0.6662 (OUTLIER) cc_final: 0.6257 (mt) REVERT: B 416 LYS cc_start: 0.8013 (mmtt) cc_final: 0.7691 (mmtp) REVERT: C 180 ARG cc_start: 0.8252 (ttp-110) cc_final: 0.7876 (ttp-110) REVERT: C 189 ASP cc_start: 0.6620 (p0) cc_final: 0.5897 (t0) REVERT: C 214 ASP cc_start: 0.7518 (m-30) cc_final: 0.7229 (m-30) REVERT: F 6 HIS cc_start: 0.8259 (p-80) cc_final: 0.8014 (p90) REVERT: F 137 LEU cc_start: 0.8714 (mt) cc_final: 0.8302 (mt) REVERT: F 238 GLN cc_start: 0.7986 (mt0) cc_final: 0.7719 (mt0) REVERT: F 239 LYS cc_start: 0.8084 (mttt) cc_final: 0.7708 (mttm) REVERT: F 270 MET cc_start: 0.9119 (ptp) cc_final: 0.8789 (ptp) REVERT: F 272 ASN cc_start: 0.8948 (m-40) cc_final: 0.8691 (m-40) REVERT: F 313 TRP cc_start: 0.5311 (m-90) cc_final: 0.3842 (m-10) REVERT: F 383 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7964 (mp10) REVERT: G 74 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7717 (mt-10) REVERT: G 136 MET cc_start: 0.6841 (tpp) cc_final: 0.6508 (tpt) REVERT: G 253 PHE cc_start: 0.8389 (m-80) cc_final: 0.7089 (t80) REVERT: G 271 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.7934 (ttpp) outliers start: 35 outliers final: 21 residues processed: 231 average time/residue: 0.4426 time to fit residues: 113.9280 Evaluate side-chains 232 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 72 ILE Chi-restraints excluded: chain B residue 1 MET 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 305 LEU 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 C residue 190 THR Chi-restraints excluded: chain C residue 262 LEU 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 178 THR Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 321 ILE Chi-restraints excluded: chain F residue 383 GLN Chi-restraints excluded: chain G residue 93 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: 0.0170 chunk 11 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 68 optimal weight: 0.2980 chunk 91 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 238 GLN C 46 GLN G 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.150641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.103736 restraints weight = 15880.290| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.62 r_work: 0.2754 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.252 15221 Z= 0.135 Angle : 0.634 17.019 20744 Z= 0.277 Chirality : 0.043 0.185 2147 Planarity : 0.005 0.046 2582 Dihedral : 13.217 169.707 2273 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.02 % Allowed : 12.62 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.20), residues: 1773 helix: 1.49 (0.17), residues: 943 sheet: -0.95 (0.58), residues: 80 loop : 0.23 (0.23), residues: 750 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 0.020 0.001 PHE B 216 TRP 0.029 0.001 TRP A 147 HIS 0.007 0.001 HIS B 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.13 (15200) covalent geometry : angle 0.63023 / 0.28 (20734) SS BOND : bond 0.00368 / 0.21 ( 2) SS BOND : angle 1.08468 / 0.53 ( 4) hydrogen bonds : bond 0.04743 / 3.22 ( 751) hydrogen bonds : angle 3.92462 / 2.84 ( 2142) metal coordination : bond 0.00843 / 0.56 ( 8) metal coordination : angle 4.06692 / 1.86 ( 6) Misc. bond : bond 0.11400 / 6.01 ( 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 245 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.9388 (mtp) cc_final: 0.9130 (mtp) REVERT: A 47 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7610 (mm) REVERT: A 68 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7835 (tt) REVERT: B 10 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7058 (mt-10) REVERT: B 20 HIS cc_start: 0.8707 (t-90) cc_final: 0.8390 (t70) REVERT: B 154 MET cc_start: 0.9365 (mmp) cc_final: 0.9034 (mmm) REVERT: B 180 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8492 (tp) REVERT: B 239 LYS cc_start: 0.8116 (mttt) cc_final: 0.7806 (mtpt) REVERT: B 317 ILE cc_start: 0.6617 (OUTLIER) cc_final: 0.6219 (mt) REVERT: B 416 LYS cc_start: 0.8018 (mmtt) cc_final: 0.7740 (mmtp) REVERT: C 180 ARG cc_start: 0.8160 (ttp-110) cc_final: 0.7801 (ttp-110) REVERT: C 189 ASP cc_start: 0.6601 (p0) cc_final: 0.5887 (t0) REVERT: C 214 ASP cc_start: 0.7522 (m-30) cc_final: 0.7233 (m-30) REVERT: F 137 LEU cc_start: 0.8664 (mt) cc_final: 0.8245 (mt) REVERT: F 238 GLN cc_start: 0.7932 (mt0) cc_final: 0.7703 (mt0) REVERT: F 239 LYS cc_start: 0.8043 (mttt) cc_final: 0.7684 (mttm) REVERT: F 270 MET cc_start: 0.9081 (ptp) cc_final: 0.8672 (ptp) REVERT: F 272 ASN cc_start: 0.8920 (m-40) cc_final: 0.8663 (m-40) REVERT: F 313 TRP cc_start: 0.5197 (m-90) cc_final: 0.3727 (m-10) REVERT: F 394 LEU cc_start: 0.8438 (tt) cc_final: 0.8164 (tm) REVERT: G 74 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7714 (mt-10) REVERT: G 136 MET cc_start: 0.6803 (tpp) cc_final: 0.6500 (tpt) REVERT: G 253 PHE cc_start: 0.8322 (m-80) cc_final: 0.7066 (t80) REVERT: G 271 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.7885 (ttpp) outliers start: 29 outliers final: 18 residues processed: 229 average time/residue: 0.4458 time to fit residues: 114.7854 Evaluate side-chains 230 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 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 180 LEU 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 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 G residue 93 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: 0.9980 chunk 70 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 148 optimal weight: 0.0670 chunk 174 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 238 GLN C 46 GLN ** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN G 118 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.151102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.104079 restraints weight = 15870.296| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.65 r_work: 0.2766 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.240 15221 Z= 0.116 Angle : 0.614 15.907 20744 Z= 0.268 Chirality : 0.042 0.187 2147 Planarity : 0.004 0.045 2582 Dihedral : 13.001 169.689 2273 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.74 % Allowed : 13.18 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.20), residues: 1773 helix: 1.58 (0.17), residues: 945 sheet: -0.92 (0.58), residues: 80 loop : 0.26 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 180 TYR 0.015 0.001 TYR B 432 PHE 0.017 0.001 PHE B 216 TRP 0.030 0.001 TRP A 147 HIS 0.005 0.001 HIS G 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (15200) covalent geometry : angle 0.60981 / 0.27 (20734) SS BOND : bond 0.00333 / 0.19 ( 2) SS BOND : angle 0.86083 / 0.42 ( 4) hydrogen bonds : bond 0.04445 / 3.02 ( 751) hydrogen bonds : angle 3.86071 / 2.80 ( 2142) metal coordination : bond 0.00749 / 0.52 ( 8) metal coordination : angle 4.18944 / 1.90 ( 6) Misc. bond : bond 0.11284 / 5.80 ( 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 243 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.9299 (mtp) cc_final: 0.9031 (mtp) REVERT: A 47 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7611 (mm) REVERT: B 1 MET cc_start: 0.2890 (OUTLIER) cc_final: 0.1796 (ttp) REVERT: B 10 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7134 (mt-10) REVERT: B 20 HIS cc_start: 0.8697 (t-90) cc_final: 0.8423 (t70) REVERT: B 154 MET cc_start: 0.9336 (mmp) cc_final: 0.8961 (mmm) REVERT: B 180 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8460 (tp) REVERT: B 239 LYS cc_start: 0.8075 (mttt) cc_final: 0.7738 (mtpt) REVERT: B 317 ILE cc_start: 0.6591 (OUTLIER) cc_final: 0.6200 (mt) REVERT: B 416 LYS cc_start: 0.7881 (mmtt) cc_final: 0.7582 (mmtm) REVERT: C 180 ARG cc_start: 0.8089 (ttp-110) cc_final: 0.7833 (ttp-110) REVERT: C 189 ASP cc_start: 0.6603 (p0) cc_final: 0.5863 (t0) REVERT: C 214 ASP cc_start: 0.7507 (m-30) cc_final: 0.7220 (m-30) REVERT: F 6 HIS cc_start: 0.8223 (p-80) cc_final: 0.7968 (p90) REVERT: F 137 LEU cc_start: 0.8632 (mt) cc_final: 0.8225 (mt) REVERT: F 239 LYS cc_start: 0.8110 (mttt) cc_final: 0.7804 (mttm) REVERT: F 270 MET cc_start: 0.9036 (ptp) cc_final: 0.8659 (ptp) REVERT: F 272 ASN cc_start: 0.8923 (m-40) cc_final: 0.8665 (m-40) REVERT: F 313 TRP cc_start: 0.5160 (m-90) cc_final: 0.3711 (m-10) REVERT: G 74 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7693 (mt-10) REVERT: G 136 MET cc_start: 0.6831 (tpp) cc_final: 0.6546 (tpt) REVERT: G 253 PHE cc_start: 0.8264 (m-80) cc_final: 0.7055 (t80) REVERT: G 271 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.7869 (ttpp) outliers start: 25 outliers final: 17 residues processed: 228 average time/residue: 0.4360 time to fit residues: 111.9849 Evaluate side-chains 229 residues out of total 1434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 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 180 LEU 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 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 212 MET 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: 0.0770 chunk 58 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 165 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 155 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 46 GLN ** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.149291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.101991 restraints weight = 15778.363| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.63 r_work: 0.2738 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.241 15221 Z= 0.141 Angle : 0.650 17.164 20744 Z= 0.282 Chirality : 0.043 0.189 2147 Planarity : 0.005 0.046 2582 Dihedral : 13.052 171.389 2273 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.74 % Allowed : 13.32 % 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 are not related in a simple way. whole: 1.18 (0.20), residues: 1773 helix: 1.48 (0.17), residues: 945 sheet: -0.89 (0.58), residues: 80 loop : 0.20 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 103 TYR 0.024 0.001 TYR B 147 PHE 0.028 0.002 PHE G 258 TRP 0.030 0.001 TRP A 147 HIS 0.008 0.001 HIS F 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (15200) covalent geometry : angle 0.64684 / 0.28 (20734) SS BOND : bond 0.00383 / 0.22 ( 2) SS BOND : angle 1.18744 / 0.59 ( 4) hydrogen bonds : bond 0.04810 / 3.27 ( 751) hydrogen bonds : angle 3.93403 / 2.85 ( 2142) metal coordination : bond 0.00839 / 0.53 ( 8) metal coordination : angle 3.82566 / 1.73 ( 6) Misc. bond : bond 0.11140 / 5.89 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4715.98 seconds wall clock time: 80 minutes 51.66 seconds (4851.66 seconds total)