Starting phenix.real_space_refine on Sun Aug 24 15:17:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmc_41384/08_2025/8tmc_41384.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmc_41384/08_2025/8tmc_41384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tmc_41384/08_2025/8tmc_41384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmc_41384/08_2025/8tmc_41384.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tmc_41384/08_2025/8tmc_41384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmc_41384/08_2025/8tmc_41384.map" } resolution = 3.3 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= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3661 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 6 5.21 5 S 64 5.16 5 C 11722 2.51 5 N 2942 2.21 5 O 3318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18052 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2871 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 15, 'TRANS': 329} Chain: "B" Number of atoms: 2879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2879 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain: "C" Number of atoms: 2838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2838 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 15, 'TRANS': 324} Chain: "D" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2899 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain: "E" Number of atoms: 2891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2891 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 15, 'TRANS': 331} Chain: "H" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1018 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "G" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.70, per 1000 atoms: 0.20 Number of scatterers: 18052 At special positions: 0 Unit cell: (111.24, 166.86, 160.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 Mg 6 11.99 O 3318 8.00 N 2942 7.00 C 11722 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " distance=2.03 Simple disulfide: pdb=" SG CYS G 24 " - pdb=" SG CYS G 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 678.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4188 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 16 sheets defined 47.9% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 50 through 56 removed outlier: 3.612A pdb=" N PHE A 53 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP A 55 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 80 removed outlier: 3.577A pdb=" N VAL A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 147 through 157 Processing helix chain 'A' and resid 165 through 202 Processing helix chain 'A' and resid 204 through 238 removed outlier: 3.693A pdb=" N VAL A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Proline residue: A 227 - end of helix Processing helix chain 'A' and resid 247 through 311 removed outlier: 3.667A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) Proline residue: A 303 - end of helix Processing helix chain 'A' and resid 325 through 348 Processing helix chain 'B' and resid 46 through 51 removed outlier: 4.233A pdb=" N VAL B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 56 removed outlier: 3.665A pdb=" N ASP B 55 " --> pdb=" O PRO B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 80 removed outlier: 4.340A pdb=" N VAL B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 117 through 120 Processing helix chain 'B' and resid 147 through 157 Processing helix chain 'B' and resid 165 through 202 removed outlier: 3.551A pdb=" N LEU B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 238 removed outlier: 3.577A pdb=" N ARG B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS B 215 " --> pdb=" O THR B 211 " (cutoff:3.500A) Proline residue: B 227 - end of helix removed outlier: 3.577A pdb=" N GLU B 230 " --> pdb=" O TRP B 226 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 247 through 312 Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 325 through 349 Processing helix chain 'C' and resid 47 through 56 Proline residue: C 52 - end of helix Processing helix chain 'C' and resid 69 through 81 removed outlier: 3.623A pdb=" N VAL C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 92 Processing helix chain 'C' and resid 147 through 156 Processing helix chain 'C' and resid 165 through 202 Processing helix chain 'C' and resid 205 through 238 removed outlier: 3.972A pdb=" N GLN C 209 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Proline residue: C 227 - end of helix removed outlier: 3.508A pdb=" N ASP C 238 " --> pdb=" O SER C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 299 removed outlier: 3.607A pdb=" N LEU C 276 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASP C 277 " --> pdb=" O SER C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 311 removed outlier: 4.124A pdb=" N TYR C 311 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 347 removed outlier: 4.210A pdb=" N LEU C 331 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL C 333 " --> pdb=" O VAL C 329 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N VAL C 336 " --> pdb=" O ALA C 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 removed outlier: 3.987A pdb=" N VAL D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 54 No H-bonds generated for 'chain 'D' and resid 52 through 54' Processing helix chain 'D' and resid 69 through 81 removed outlier: 3.626A pdb=" N VAL D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 147 through 157 Processing helix chain 'D' and resid 160 through 164 removed outlier: 3.541A pdb=" N LYS D 164 " --> pdb=" O ILE D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 202 removed outlier: 3.506A pdb=" N LEU D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 238 removed outlier: 4.328A pdb=" N VAL D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) Proline residue: D 227 - end of helix removed outlier: 3.895A pdb=" N ASP D 238 " --> pdb=" O SER D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 246 No H-bonds generated for 'chain 'D' and resid 244 through 246' Processing helix chain 'D' and resid 247 through 311 removed outlier: 3.786A pdb=" N ASP D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) Proline residue: D 303 - end of helix Processing helix chain 'D' and resid 326 through 348 Processing helix chain 'E' and resid 46 through 55 removed outlier: 3.536A pdb=" N SER E 49 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU E 51 " --> pdb=" O GLU E 48 " (cutoff:3.500A) Proline residue: E 52 - end of helix removed outlier: 3.762A pdb=" N ASP E 55 " --> pdb=" O PRO E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 81 removed outlier: 3.847A pdb=" N VAL E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 92 Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 165 through 202 Processing helix chain 'E' and resid 206 through 237 Proline residue: E 227 - end of helix Processing helix chain 'E' and resid 244 through 246 No H-bonds generated for 'chain 'E' and resid 244 through 246' Processing helix chain 'E' and resid 247 through 311 removed outlier: 3.575A pdb=" N PHE E 251 " --> pdb=" O THR E 247 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG E 252 " --> pdb=" O VAL E 248 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP E 253 " --> pdb=" O PRO E 249 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL E 254 " --> pdb=" O TYR E 250 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA E 298 " --> pdb=" O LEU E 294 " (cutoff:3.500A) Proline residue: E 303 - end of helix Processing helix chain 'E' and resid 327 through 348 removed outlier: 3.873A pdb=" N LEU E 331 " --> pdb=" O TYR E 327 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA E 332 " --> pdb=" O PRO E 328 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL E 333 " --> pdb=" O VAL E 329 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 34 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'F' and resid 31 through 35 Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.842A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 44 Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 44 removed outlier: 6.814A pdb=" N THR B 60 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N MET B 138 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE B 62 " --> pdb=" O MET B 138 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N GLN B 140 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE B 64 " --> pdb=" O GLN B 140 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLU B 121 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASP B 116 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 39 through 43 removed outlier: 4.570A pdb=" N GLU C 121 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP C 116 " --> pdb=" O GLU C 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 39 through 44 Processing sheet with id=AA5, first strand: chain 'E' and resid 39 through 44 Processing sheet with id=AA6, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA7, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.573A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N SER H 36 " --> pdb=" O SER H 102 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N CYS H 99 " --> pdb=" O TRP H 123 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TRP H 123 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG H 101 " --> pdb=" O ASP H 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.573A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N SER H 36 " --> pdb=" O SER H 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 106 through 107 removed outlier: 3.639A pdb=" N TYR H 114 " --> pdb=" O LYS H 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AB2, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.508A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 21 through 26 Processing sheet with id=AB4, first strand: chain 'F' and resid 60 through 63 removed outlier: 5.279A pdb=" N TRP F 50 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ARG F 41 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE F 37 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER F 36 " --> pdb=" O SER F 102 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR F 122 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE F 103 " --> pdb=" O MET F 120 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N MET F 120 " --> pdb=" O PHE F 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 106 through 107 Processing sheet with id=AB6, first strand: chain 'G' and resid 5 through 7 Processing sheet with id=AB7, first strand: chain 'G' and resid 11 through 14 removed outlier: 3.538A pdb=" N LEU G 12 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYR G 50 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) 1088 hydrogen bonds defined for protein. 3090 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5649 1.34 - 1.46: 3100 1.46 - 1.57: 9607 1.57 - 1.69: 0 1.69 - 1.81: 115 Bond restraints: 18471 Sorted by residual: bond pdb=" C LEU D 51 " pdb=" N PRO D 52 " ideal model delta sigma weight residual 1.337 1.355 -0.018 9.80e-03 1.04e+04 3.51e+00 bond pdb=" CG1 ILE B 192 " pdb=" CD1 ILE B 192 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.49e+00 bond pdb=" CG1 ILE B 296 " pdb=" CD1 ILE B 296 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.46e+00 bond pdb=" C MET E 302 " pdb=" N PRO E 303 " ideal model delta sigma weight residual 1.336 1.350 -0.014 1.20e-02 6.94e+03 1.39e+00 bond pdb=" CB ILE D 82 " pdb=" CG2 ILE D 82 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.32e+00 ... (remaining 18466 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 24504 1.84 - 3.68: 461 3.68 - 5.52: 65 5.52 - 7.36: 15 7.36 - 9.19: 6 Bond angle restraints: 25051 Sorted by residual: angle pdb=" N ILE C 297 " pdb=" CA ILE C 297 " pdb=" C ILE C 297 " ideal model delta sigma weight residual 113.53 108.91 4.62 9.80e-01 1.04e+00 2.22e+01 angle pdb=" C LEU A 235 " pdb=" N TYR A 236 " pdb=" CA TYR A 236 " ideal model delta sigma weight residual 122.06 115.81 6.25 1.86e+00 2.89e-01 1.13e+01 angle pdb=" N ARG D 322 " pdb=" CA ARG D 322 " pdb=" C ARG D 322 " ideal model delta sigma weight residual 113.28 108.23 5.05 1.57e+00 4.06e-01 1.03e+01 angle pdb=" CB MET B 313 " pdb=" CG MET B 313 " pdb=" SD MET B 313 " ideal model delta sigma weight residual 112.70 103.53 9.17 3.00e+00 1.11e-01 9.34e+00 angle pdb=" CB MET C 334 " pdb=" CG MET C 334 " pdb=" SD MET C 334 " ideal model delta sigma weight residual 112.70 103.77 8.93 3.00e+00 1.11e-01 8.86e+00 ... (remaining 25046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 9887 17.52 - 35.05: 962 35.05 - 52.57: 173 52.57 - 70.10: 35 70.10 - 87.62: 20 Dihedral angle restraints: 11077 sinusoidal: 4571 harmonic: 6506 Sorted by residual: dihedral pdb=" CB CYS L 24 " pdb=" SG CYS L 24 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 44.96 48.04 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" CA LEU D 321 " pdb=" C LEU D 321 " pdb=" N ARG D 322 " pdb=" CA ARG D 322 " ideal model delta harmonic sigma weight residual -180.00 -152.27 -27.73 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA ASN D 314 " pdb=" C ASN D 314 " pdb=" N PHE D 315 " pdb=" CA PHE D 315 " ideal model delta harmonic sigma weight residual -180.00 -155.61 -24.39 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 11074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2167 0.050 - 0.099: 546 0.099 - 0.149: 103 0.149 - 0.199: 6 0.199 - 0.248: 1 Chirality restraints: 2823 Sorted by residual: chirality pdb=" CB ILE F 37 " pdb=" CA ILE F 37 " pdb=" CG1 ILE F 37 " pdb=" CG2 ILE F 37 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CG LEU E 304 " pdb=" CB LEU E 304 " pdb=" CD1 LEU E 304 " pdb=" CD2 LEU E 304 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CA ILE A 64 " pdb=" N ILE A 64 " pdb=" C ILE A 64 " pdb=" CB ILE A 64 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 2820 not shown) Planarity restraints: 3137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 202 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO D 203 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 203 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 203 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS G 95 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.45e+00 pdb=" N PRO G 96 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO G 96 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 96 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 318 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO D 319 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 319 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 319 " -0.029 5.00e-02 4.00e+02 ... (remaining 3134 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 190 2.64 - 3.20: 17064 3.20 - 3.77: 28624 3.77 - 4.33: 39738 4.33 - 4.90: 65237 Nonbonded interactions: 150853 Sorted by model distance: nonbonded pdb=" O LYS E 111 " pdb=" OH TYR E 181 " model vdw 2.070 3.040 nonbonded pdb=" O TYR E 279 " pdb=" OG SER E 282 " model vdw 2.167 3.040 nonbonded pdb=" OG SER G 68 " pdb=" OD1 ASP G 71 " model vdw 2.176 3.040 nonbonded pdb=" NE2 GLN D 140 " pdb=" OD1 ASP D 145 " model vdw 2.193 3.120 nonbonded pdb=" O LYS A 111 " pdb=" OH TYR A 181 " model vdw 2.212 3.040 ... (remaining 150848 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 12 through 350) selection = (chain 'B' and resid 12 through 350) selection = (chain 'C' and resid 12 through 350) selection = (chain 'D' and resid 12 through 350) selection = (chain 'E' and resid 12 through 350) } ncs_group { reference = chain 'F' selection = (chain 'H' and resid 4 through 129) } ncs_group { reference = (chain 'G' and resid 1 through 108) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 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: 4.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.640 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 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 : 0.004 0.061 18475 Z= 0.170 Angle : 0.634 9.194 25059 Z= 0.335 Chirality : 0.044 0.248 2823 Planarity : 0.005 0.067 3137 Dihedral : 14.424 87.621 6877 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.68 % Favored : 95.14 % Rotamer: Outliers : 0.15 % Allowed : 0.30 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.18), residues: 2180 helix: 1.42 (0.17), residues: 942 sheet: 0.71 (0.25), residues: 443 loop : -1.48 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 165 TYR 0.025 0.001 TYR E 181 PHE 0.024 0.002 PHE E 79 TRP 0.018 0.001 TRP F 123 HIS 0.004 0.001 HIS E 94 Details of bonding type rmsd covalent geometry : bond 0.00389 (18471) covalent geometry : angle 0.63334 (25051) SS BOND : bond 0.00077 ( 4) SS BOND : angle 1.53294 ( 8) hydrogen bonds : bond 0.12214 ( 1074) hydrogen bonds : angle 6.34439 ( 3090) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 444 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7720 (pt0) cc_final: 0.7478 (pt0) REVERT: A 189 ASP cc_start: 0.6971 (t0) cc_final: 0.6714 (t0) REVERT: A 245 LYS cc_start: 0.8225 (mmtm) cc_final: 0.7806 (mmtm) REVERT: A 334 MET cc_start: 0.6156 (mtp) cc_final: 0.5749 (mtp) REVERT: B 20 THR cc_start: 0.8401 (m) cc_final: 0.8026 (m) REVERT: B 28 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6554 (mt-10) REVERT: B 163 LYS cc_start: 0.8054 (mmmm) cc_final: 0.7424 (mmtt) REVERT: B 165 ARG cc_start: 0.6926 (mmm-85) cc_final: 0.6712 (mmm-85) REVERT: B 186 GLU cc_start: 0.6776 (mm-30) cc_final: 0.6342 (mm-30) REVERT: B 202 ARG cc_start: 0.7069 (mtm-85) cc_final: 0.6241 (mtm-85) REVERT: B 306 PHE cc_start: 0.6911 (t80) cc_final: 0.6528 (t80) REVERT: C 30 GLU cc_start: 0.7719 (tt0) cc_final: 0.7445 (tt0) REVERT: C 96 ARG cc_start: 0.7376 (mtp180) cc_final: 0.7158 (mtp180) REVERT: C 104 ASN cc_start: 0.8495 (m-40) cc_final: 0.8277 (m-40) REVERT: C 193 ASP cc_start: 0.7660 (t0) cc_final: 0.7421 (t0) REVERT: E 28 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7472 (tt0) REVERT: H 93 ASP cc_start: 0.8572 (m-30) cc_final: 0.8045 (m-30) REVERT: F 70 ARG cc_start: 0.7982 (mtm110) cc_final: 0.7157 (ptt180) outliers start: 3 outliers final: 0 residues processed: 444 average time/residue: 0.1107 time to fit residues: 77.2186 Evaluate side-chains 395 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.4980 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS B 157 ASN C 134 ASN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN E 134 ASN E 140 GLN H 80 ASN L 39 GLN G 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.172665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.146361 restraints weight = 23984.518| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.24 r_work: 0.3420 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 18475 Z= 0.172 Angle : 0.610 13.962 25059 Z= 0.316 Chirality : 0.044 0.216 2823 Planarity : 0.005 0.053 3137 Dihedral : 4.509 28.807 2446 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.31 % Favored : 95.60 % Rotamer: Outliers : 1.39 % Allowed : 10.25 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.18), residues: 2180 helix: 2.02 (0.16), residues: 957 sheet: 0.69 (0.25), residues: 446 loop : -1.48 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 252 TYR 0.019 0.001 TYR L 50 PHE 0.023 0.001 PHE B 79 TRP 0.013 0.001 TRP F 123 HIS 0.005 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00399 (18471) covalent geometry : angle 0.60932 (25051) SS BOND : bond 0.00088 ( 4) SS BOND : angle 1.08250 ( 8) hydrogen bonds : bond 0.04627 ( 1074) hydrogen bonds : angle 4.88468 ( 3090) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 426 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8371 (pt0) cc_final: 0.7940 (pt0) REVERT: A 180 ASP cc_start: 0.8159 (t0) cc_final: 0.7942 (t0) REVERT: A 189 ASP cc_start: 0.7293 (t0) cc_final: 0.6995 (t0) REVERT: A 230 GLU cc_start: 0.6721 (mm-30) cc_final: 0.6273 (mm-30) REVERT: A 245 LYS cc_start: 0.8277 (mmtm) cc_final: 0.7842 (mmtm) REVERT: A 334 MET cc_start: 0.6644 (mtp) cc_final: 0.6259 (mtp) REVERT: B 28 GLU cc_start: 0.7300 (mt-10) cc_final: 0.7071 (mt-10) REVERT: B 37 GLU cc_start: 0.7155 (pm20) cc_final: 0.6891 (pm20) REVERT: B 79 PHE cc_start: 0.7262 (t80) cc_final: 0.7000 (t80) REVERT: B 133 LYS cc_start: 0.7822 (tptp) cc_final: 0.7501 (tptp) REVERT: B 186 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6830 (mm-30) REVERT: B 192 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8623 (mp) REVERT: B 230 GLU cc_start: 0.7486 (mt-10) cc_final: 0.6978 (mt-10) REVERT: B 296 ILE cc_start: 0.8499 (mp) cc_final: 0.8280 (mp) REVERT: C 104 ASN cc_start: 0.8656 (m-40) cc_final: 0.8453 (m-40) REVERT: C 193 ASP cc_start: 0.8101 (t0) cc_final: 0.7837 (t0) REVERT: C 289 GLU cc_start: 0.7641 (tt0) cc_final: 0.7421 (tt0) REVERT: C 334 MET cc_start: 0.6633 (ttt) cc_final: 0.6218 (ttt) REVERT: D 291 MET cc_start: 0.8451 (tpp) cc_final: 0.8174 (tpp) REVERT: D 313 MET cc_start: 0.5029 (mtt) cc_final: 0.4661 (mpp) REVERT: E 37 GLU cc_start: 0.7765 (pp20) cc_final: 0.7289 (pp20) REVERT: E 112 MET cc_start: 0.8923 (mtp) cc_final: 0.8596 (mtm) REVERT: E 125 GLU cc_start: 0.8300 (tt0) cc_final: 0.8006 (tt0) REVERT: H 9 GLU cc_start: 0.6644 (mp0) cc_final: 0.6198 (mp0) REVERT: H 93 ASP cc_start: 0.8524 (m-30) cc_final: 0.8221 (m-30) REVERT: L 80 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7711 (mm-40) REVERT: F 70 ARG cc_start: 0.8019 (mtm110) cc_final: 0.7093 (ptt180) outliers start: 28 outliers final: 17 residues processed: 436 average time/residue: 0.1172 time to fit residues: 80.0367 Evaluate side-chains 414 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 396 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 68 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 179 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 178 optimal weight: 3.9990 chunk 144 optimal weight: 0.0670 chunk 170 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 ASN C 134 ASN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN H 80 ASN L 39 GLN L 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.172646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.146357 restraints weight = 24191.837| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.25 r_work: 0.3415 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18475 Z= 0.154 Angle : 0.581 11.697 25059 Z= 0.301 Chirality : 0.043 0.205 2823 Planarity : 0.005 0.052 3137 Dihedral : 4.420 27.408 2446 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.94 % Favored : 95.96 % Rotamer: Outliers : 1.83 % Allowed : 12.78 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.18), residues: 2180 helix: 2.19 (0.17), residues: 951 sheet: 0.69 (0.25), residues: 437 loop : -1.51 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 96 TYR 0.022 0.001 TYR L 50 PHE 0.019 0.001 PHE H 71 TRP 0.012 0.001 TRP F 123 HIS 0.005 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00353 (18471) covalent geometry : angle 0.58121 (25051) SS BOND : bond 0.00075 ( 4) SS BOND : angle 0.79830 ( 8) hydrogen bonds : bond 0.04268 ( 1074) hydrogen bonds : angle 4.67648 ( 3090) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 410 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8206 (pt0) cc_final: 0.7730 (pt0) REVERT: A 189 ASP cc_start: 0.7257 (t0) cc_final: 0.6909 (t0) REVERT: A 205 LYS cc_start: 0.7744 (mmtt) cc_final: 0.7399 (mtpp) REVERT: A 230 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6312 (mm-30) REVERT: A 245 LYS cc_start: 0.8276 (mmtm) cc_final: 0.7815 (mmtm) REVERT: A 276 LEU cc_start: 0.7596 (mt) cc_final: 0.7316 (mt) REVERT: A 334 MET cc_start: 0.6719 (mtp) cc_final: 0.6351 (mtp) REVERT: B 78 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6615 (mp0) REVERT: B 79 PHE cc_start: 0.7346 (t80) cc_final: 0.7101 (t80) REVERT: B 133 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7436 (tptp) REVERT: B 186 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6799 (mm-30) REVERT: B 192 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8551 (mp) REVERT: B 260 GLN cc_start: 0.7194 (tt0) cc_final: 0.6958 (tt0) REVERT: B 296 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8266 (mp) REVERT: C 104 ASN cc_start: 0.8629 (m-40) cc_final: 0.8423 (m-40) REVERT: C 193 ASP cc_start: 0.8068 (t0) cc_final: 0.7819 (t0) REVERT: C 289 GLU cc_start: 0.7551 (tt0) cc_final: 0.7269 (tt0) REVERT: C 334 MET cc_start: 0.6772 (ttt) cc_final: 0.6421 (ttt) REVERT: D 232 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8368 (mm) REVERT: D 291 MET cc_start: 0.8499 (tpp) cc_final: 0.8054 (tpp) REVERT: E 37 GLU cc_start: 0.7885 (pp20) cc_final: 0.7252 (pp20) REVERT: E 237 ARG cc_start: 0.7678 (tpp80) cc_final: 0.7367 (tpp80) REVERT: E 291 MET cc_start: 0.8083 (tpp) cc_final: 0.7844 (tpp) REVERT: H 9 GLU cc_start: 0.6453 (mp0) cc_final: 0.5940 (mp0) REVERT: H 93 ASP cc_start: 0.8519 (m-30) cc_final: 0.7982 (m-30) REVERT: L 80 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7871 (mm-40) REVERT: F 70 ARG cc_start: 0.7903 (mtm110) cc_final: 0.6969 (ptt180) outliers start: 37 outliers final: 23 residues processed: 421 average time/residue: 0.1157 time to fit residues: 76.1220 Evaluate side-chains 426 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 398 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 282 SER Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 163 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 ASN C 95 GLN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN E 134 ASN H 80 ASN L 90 GLN G 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.171144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.144988 restraints weight = 24316.876| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.23 r_work: 0.3405 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18475 Z= 0.169 Angle : 0.587 9.221 25059 Z= 0.302 Chirality : 0.043 0.272 2823 Planarity : 0.005 0.052 3137 Dihedral : 4.420 26.437 2446 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.40 % Favored : 95.50 % Rotamer: Outliers : 2.82 % Allowed : 14.51 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.18), residues: 2180 helix: 2.18 (0.17), residues: 956 sheet: 0.70 (0.25), residues: 433 loop : -1.52 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 54 TYR 0.021 0.001 TYR L 50 PHE 0.015 0.001 PHE C 306 TRP 0.011 0.001 TRP F 123 HIS 0.006 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00399 (18471) covalent geometry : angle 0.58670 (25051) SS BOND : bond 0.00175 ( 4) SS BOND : angle 0.73866 ( 8) hydrogen bonds : bond 0.04214 ( 1074) hydrogen bonds : angle 4.61945 ( 3090) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 405 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8223 (pt0) cc_final: 0.7710 (pt0) REVERT: A 189 ASP cc_start: 0.7309 (t0) cc_final: 0.6950 (t0) REVERT: A 230 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6392 (mm-30) REVERT: A 245 LYS cc_start: 0.8271 (mmtm) cc_final: 0.7792 (mmtm) REVERT: A 276 LEU cc_start: 0.7615 (mt) cc_final: 0.7310 (mt) REVERT: A 334 MET cc_start: 0.6829 (mtp) cc_final: 0.6514 (mtp) REVERT: B 37 GLU cc_start: 0.7120 (pm20) cc_final: 0.6857 (pm20) REVERT: B 78 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6557 (mp0) REVERT: B 133 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7439 (tptp) REVERT: B 156 TYR cc_start: 0.6279 (m-10) cc_final: 0.6076 (m-10) REVERT: B 165 ARG cc_start: 0.7089 (mmm-85) cc_final: 0.6880 (mmm-85) REVERT: B 186 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6869 (mm-30) REVERT: B 192 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8583 (mp) REVERT: B 193 ASP cc_start: 0.7921 (t0) cc_final: 0.7562 (t0) REVERT: B 296 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8313 (mp) REVERT: B 306 PHE cc_start: 0.7276 (t80) cc_final: 0.6881 (t80) REVERT: C 104 ASN cc_start: 0.8634 (m-40) cc_final: 0.8418 (m-40) REVERT: C 193 ASP cc_start: 0.8077 (t0) cc_final: 0.7816 (t0) REVERT: C 289 GLU cc_start: 0.7613 (tt0) cc_final: 0.7319 (tt0) REVERT: D 232 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8371 (mm) REVERT: D 291 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7579 (ttp) REVERT: D 313 MET cc_start: 0.4905 (mtt) cc_final: 0.4590 (mpp) REVERT: E 37 GLU cc_start: 0.7905 (pp20) cc_final: 0.7589 (pp20) REVERT: E 70 THR cc_start: 0.8096 (p) cc_final: 0.7826 (m) REVERT: E 112 MET cc_start: 0.8873 (mtp) cc_final: 0.8630 (mtm) REVERT: E 125 GLU cc_start: 0.8232 (tt0) cc_final: 0.7957 (tt0) REVERT: H 9 GLU cc_start: 0.6445 (mp0) cc_final: 0.5894 (mp0) REVERT: H 38 HIS cc_start: 0.8399 (m170) cc_final: 0.7977 (m90) REVERT: H 93 ASP cc_start: 0.8497 (m-30) cc_final: 0.7986 (m-30) REVERT: H 120 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7982 (mtm) REVERT: L 80 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7903 (mm-40) REVERT: F 70 ARG cc_start: 0.7914 (mtm110) cc_final: 0.6984 (ptt180) outliers start: 57 outliers final: 34 residues processed: 429 average time/residue: 0.1112 time to fit residues: 74.8510 Evaluate side-chains 436 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 395 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 282 SER Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 135 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN H 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.170570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.144176 restraints weight = 24159.273| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.23 r_work: 0.3389 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3384 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3384 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18475 Z= 0.178 Angle : 0.588 9.219 25059 Z= 0.303 Chirality : 0.043 0.185 2823 Planarity : 0.005 0.054 3137 Dihedral : 4.446 25.814 2446 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.17 % Favored : 95.73 % Rotamer: Outliers : 2.77 % Allowed : 15.26 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.18), residues: 2180 helix: 2.17 (0.17), residues: 957 sheet: 0.70 (0.25), residues: 435 loop : -1.55 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 216 TYR 0.019 0.001 TYR L 50 PHE 0.022 0.001 PHE C 306 TRP 0.011 0.001 TRP H 50 HIS 0.006 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00421 (18471) covalent geometry : angle 0.58754 (25051) SS BOND : bond 0.00141 ( 4) SS BOND : angle 0.77216 ( 8) hydrogen bonds : bond 0.04213 ( 1074) hydrogen bonds : angle 4.61336 ( 3090) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 399 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7203 (t0) cc_final: 0.6847 (m-30) REVERT: A 30 GLU cc_start: 0.8298 (pt0) cc_final: 0.7754 (pt0) REVERT: A 189 ASP cc_start: 0.7283 (t0) cc_final: 0.6967 (t0) REVERT: A 205 LYS cc_start: 0.7857 (mmtt) cc_final: 0.7419 (mtpp) REVERT: A 230 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6478 (mm-30) REVERT: A 245 LYS cc_start: 0.8223 (mmtm) cc_final: 0.7738 (mmtm) REVERT: A 276 LEU cc_start: 0.7652 (mt) cc_final: 0.7351 (mt) REVERT: A 334 MET cc_start: 0.6920 (mtp) cc_final: 0.6632 (mtp) REVERT: B 78 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6630 (mp0) REVERT: B 133 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7441 (tptp) REVERT: B 165 ARG cc_start: 0.7136 (mmm-85) cc_final: 0.6914 (mmm-85) REVERT: B 186 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6846 (mm-30) REVERT: B 192 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8580 (mp) REVERT: B 193 ASP cc_start: 0.7882 (t0) cc_final: 0.7533 (t0) REVERT: B 260 GLN cc_start: 0.7180 (tt0) cc_final: 0.6928 (tt0) REVERT: B 291 MET cc_start: 0.7090 (ttt) cc_final: 0.6830 (ttm) REVERT: B 296 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8326 (mp) REVERT: B 306 PHE cc_start: 0.7432 (t80) cc_final: 0.7074 (t80) REVERT: C 104 ASN cc_start: 0.8641 (m-40) cc_final: 0.8439 (m-40) REVERT: C 193 ASP cc_start: 0.8091 (t0) cc_final: 0.7823 (t0) REVERT: C 289 GLU cc_start: 0.7544 (tt0) cc_final: 0.7188 (tt0) REVERT: D 232 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8370 (mm) REVERT: E 37 GLU cc_start: 0.7945 (pp20) cc_final: 0.7633 (pp20) REVERT: E 70 THR cc_start: 0.8176 (p) cc_final: 0.7880 (m) REVERT: E 125 GLU cc_start: 0.8249 (tt0) cc_final: 0.7984 (tt0) REVERT: E 232 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8438 (mm) REVERT: H 38 HIS cc_start: 0.8368 (m170) cc_final: 0.7945 (m90) REVERT: H 93 ASP cc_start: 0.8448 (m-30) cc_final: 0.7999 (m-30) REVERT: H 120 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7841 (mtm) REVERT: L 12 LEU cc_start: 0.6726 (tp) cc_final: 0.6445 (tp) REVERT: L 80 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7892 (mm-40) REVERT: F 70 ARG cc_start: 0.7899 (mtm110) cc_final: 0.6921 (ptt180) outliers start: 56 outliers final: 37 residues processed: 428 average time/residue: 0.1109 time to fit residues: 74.7689 Evaluate side-chains 433 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 389 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 282 SER Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 341 MET Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 105 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 133 optimal weight: 2.9990 chunk 147 optimal weight: 0.0170 chunk 149 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 45 optimal weight: 0.0370 chunk 167 optimal weight: 0.1980 chunk 2 optimal weight: 0.6980 chunk 180 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN H 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.174008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.147838 restraints weight = 23962.121| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.24 r_work: 0.3437 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3429 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3429 r_free = 0.3429 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3429 r_free = 0.3429 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3429 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18475 Z= 0.121 Angle : 0.558 9.113 25059 Z= 0.287 Chirality : 0.042 0.213 2823 Planarity : 0.004 0.053 3137 Dihedral : 4.323 24.812 2446 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.99 % Favored : 95.92 % Rotamer: Outliers : 2.43 % Allowed : 17.24 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.19), residues: 2180 helix: 2.37 (0.17), residues: 958 sheet: 0.75 (0.25), residues: 434 loop : -1.51 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 252 TYR 0.017 0.001 TYR L 50 PHE 0.022 0.001 PHE C 306 TRP 0.011 0.001 TRP H 50 HIS 0.006 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00268 (18471) covalent geometry : angle 0.55767 (25051) SS BOND : bond 0.00082 ( 4) SS BOND : angle 0.63426 ( 8) hydrogen bonds : bond 0.03855 ( 1074) hydrogen bonds : angle 4.44297 ( 3090) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 398 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8247 (pt0) cc_final: 0.7688 (pt0) REVERT: A 85 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8744 (mm) REVERT: A 189 ASP cc_start: 0.7265 (t0) cc_final: 0.6955 (t0) REVERT: A 205 LYS cc_start: 0.7887 (mmtt) cc_final: 0.7484 (mtpp) REVERT: A 230 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6399 (mm-30) REVERT: A 232 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8301 (mm) REVERT: A 245 LYS cc_start: 0.8160 (mmtm) cc_final: 0.7646 (mmtm) REVERT: A 276 LEU cc_start: 0.7561 (mt) cc_final: 0.7300 (mt) REVERT: A 291 MET cc_start: 0.6460 (tpp) cc_final: 0.5941 (tpp) REVERT: A 334 MET cc_start: 0.6872 (mtp) cc_final: 0.6553 (mtp) REVERT: B 78 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6566 (mp0) REVERT: B 79 PHE cc_start: 0.7235 (t80) cc_final: 0.6807 (t80) REVERT: B 133 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7423 (tptp) REVERT: B 165 ARG cc_start: 0.7163 (mmm-85) cc_final: 0.6949 (mmm-85) REVERT: B 186 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6905 (mm-30) REVERT: B 192 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8573 (mp) REVERT: B 193 ASP cc_start: 0.7854 (t0) cc_final: 0.7490 (t0) REVERT: B 230 GLU cc_start: 0.7530 (mt-10) cc_final: 0.6981 (mt-10) REVERT: B 260 GLN cc_start: 0.7114 (tt0) cc_final: 0.6902 (tt0) REVERT: B 296 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8384 (mp) REVERT: B 306 PHE cc_start: 0.7374 (t80) cc_final: 0.6990 (t80) REVERT: C 193 ASP cc_start: 0.8079 (t0) cc_final: 0.7797 (t0) REVERT: C 289 GLU cc_start: 0.7689 (tt0) cc_final: 0.7335 (tt0) REVERT: D 86 VAL cc_start: 0.9085 (t) cc_final: 0.8769 (m) REVERT: D 191 GLU cc_start: 0.6640 (tp30) cc_final: 0.6224 (tp30) REVERT: D 226 TRP cc_start: 0.8279 (m100) cc_final: 0.7831 (m100) REVERT: D 232 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8349 (mm) REVERT: D 313 MET cc_start: 0.4816 (mtt) cc_final: 0.4548 (mpp) REVERT: E 37 GLU cc_start: 0.7904 (pp20) cc_final: 0.7587 (pp20) REVERT: E 70 THR cc_start: 0.8144 (p) cc_final: 0.7823 (m) REVERT: E 232 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8343 (mm) REVERT: H 9 GLU cc_start: 0.6440 (mp0) cc_final: 0.5848 (mp0) REVERT: H 38 HIS cc_start: 0.8277 (m170) cc_final: 0.7847 (m90) REVERT: H 93 ASP cc_start: 0.8406 (m-30) cc_final: 0.7984 (m-30) REVERT: H 120 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7836 (mtm) REVERT: L 80 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7921 (mm-40) REVERT: F 70 ARG cc_start: 0.7805 (mtm110) cc_final: 0.6751 (ptt180) outliers start: 49 outliers final: 31 residues processed: 425 average time/residue: 0.1072 time to fit residues: 72.3949 Evaluate side-chains 421 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 381 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 282 SER Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 105 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 68 optimal weight: 0.0970 chunk 159 optimal weight: 0.0970 chunk 66 optimal weight: 0.5980 chunk 175 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 126 optimal weight: 0.0570 chunk 101 optimal weight: 1.9990 chunk 153 optimal weight: 0.0980 chunk 53 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 overall best weight: 0.1894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN H 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.175588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.149495 restraints weight = 24211.769| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.25 r_work: 0.3450 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18475 Z= 0.116 Angle : 0.554 10.670 25059 Z= 0.283 Chirality : 0.042 0.164 2823 Planarity : 0.004 0.052 3137 Dihedral : 4.249 24.254 2446 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.72 % Favored : 96.24 % Rotamer: Outliers : 2.43 % Allowed : 18.08 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.19), residues: 2180 helix: 2.45 (0.17), residues: 958 sheet: 0.74 (0.25), residues: 433 loop : -1.43 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 252 TYR 0.016 0.001 TYR L 50 PHE 0.019 0.001 PHE H 71 TRP 0.010 0.001 TRP F 50 HIS 0.005 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00254 (18471) covalent geometry : angle 0.55346 (25051) SS BOND : bond 0.00470 ( 4) SS BOND : angle 0.73040 ( 8) hydrogen bonds : bond 0.03741 ( 1074) hydrogen bonds : angle 4.37314 ( 3090) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 400 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8214 (pt0) cc_final: 0.7700 (pt0) REVERT: A 85 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8742 (mm) REVERT: A 189 ASP cc_start: 0.7262 (t0) cc_final: 0.6977 (t0) REVERT: A 205 LYS cc_start: 0.7820 (mmtt) cc_final: 0.7410 (mtpp) REVERT: A 230 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6373 (mm-30) REVERT: A 232 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8254 (mm) REVERT: A 245 LYS cc_start: 0.8076 (mmtm) cc_final: 0.7556 (mmtm) REVERT: A 334 MET cc_start: 0.6920 (mtp) cc_final: 0.6606 (mtp) REVERT: B 27 PHE cc_start: 0.7755 (t80) cc_final: 0.7372 (t80) REVERT: B 38 GLU cc_start: 0.6656 (mm-30) cc_final: 0.6325 (mm-30) REVERT: B 78 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6573 (mp0) REVERT: B 79 PHE cc_start: 0.7260 (t80) cc_final: 0.6833 (t80) REVERT: B 133 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7430 (tptp) REVERT: B 165 ARG cc_start: 0.7077 (mmm-85) cc_final: 0.6862 (mmm-85) REVERT: B 186 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6910 (mm-30) REVERT: B 192 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8592 (mp) REVERT: B 193 ASP cc_start: 0.7850 (t0) cc_final: 0.7510 (t0) REVERT: B 204 GLU cc_start: 0.6757 (mt-10) cc_final: 0.6393 (mt-10) REVERT: B 296 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8344 (mp) REVERT: B 306 PHE cc_start: 0.7365 (t80) cc_final: 0.6941 (t80) REVERT: B 346 LYS cc_start: 0.8074 (mmmm) cc_final: 0.7858 (mmmt) REVERT: C 193 ASP cc_start: 0.8056 (t0) cc_final: 0.7770 (t0) REVERT: D 160 ILE cc_start: 0.8018 (tt) cc_final: 0.7719 (mt) REVERT: D 191 GLU cc_start: 0.6645 (tp30) cc_final: 0.6181 (tp30) REVERT: D 226 TRP cc_start: 0.8269 (m100) cc_final: 0.7839 (m100) REVERT: D 232 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8252 (mm) REVERT: D 313 MET cc_start: 0.4936 (mtt) cc_final: 0.4606 (mpp) REVERT: E 37 GLU cc_start: 0.7890 (pp20) cc_final: 0.7573 (pp20) REVERT: H 9 GLU cc_start: 0.6410 (mp0) cc_final: 0.5821 (mp0) REVERT: H 38 HIS cc_start: 0.8235 (m170) cc_final: 0.7806 (m90) REVERT: H 93 ASP cc_start: 0.8408 (m-30) cc_final: 0.7952 (m-30) REVERT: H 120 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7852 (mtm) REVERT: L 80 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7940 (mm-40) REVERT: F 70 ARG cc_start: 0.7896 (mtm110) cc_final: 0.6930 (ptt180) outliers start: 49 outliers final: 31 residues processed: 428 average time/residue: 0.1151 time to fit residues: 76.3507 Evaluate side-chains 425 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 386 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 282 SER Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 105 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 103 optimal weight: 2.9990 chunk 156 optimal weight: 0.3980 chunk 148 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 199 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.170803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.144340 restraints weight = 24137.533| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.23 r_work: 0.3393 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18475 Z= 0.190 Angle : 0.607 11.275 25059 Z= 0.310 Chirality : 0.044 0.196 2823 Planarity : 0.005 0.053 3137 Dihedral : 4.410 24.253 2446 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.17 % Favored : 95.78 % Rotamer: Outliers : 2.72 % Allowed : 18.62 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.18), residues: 2180 helix: 2.24 (0.17), residues: 958 sheet: 0.64 (0.25), residues: 432 loop : -1.48 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 101 TYR 0.022 0.002 TYR C 236 PHE 0.015 0.002 PHE H 71 TRP 0.017 0.001 TRP F 39 HIS 0.007 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00449 (18471) covalent geometry : angle 0.60650 (25051) SS BOND : bond 0.00685 ( 4) SS BOND : angle 0.84051 ( 8) hydrogen bonds : bond 0.04146 ( 1074) hydrogen bonds : angle 4.53568 ( 3090) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 400 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8244 (pt0) cc_final: 0.7652 (pt0) REVERT: A 189 ASP cc_start: 0.7284 (t0) cc_final: 0.7013 (t0) REVERT: A 198 GLU cc_start: 0.7750 (tt0) cc_final: 0.7501 (tt0) REVERT: A 205 LYS cc_start: 0.7972 (mmtt) cc_final: 0.7575 (mtpp) REVERT: A 230 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6469 (mm-30) REVERT: A 232 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8309 (mm) REVERT: A 276 LEU cc_start: 0.7681 (mt) cc_final: 0.7408 (mt) REVERT: A 334 MET cc_start: 0.6863 (mtp) cc_final: 0.6582 (mtp) REVERT: B 10 LYS cc_start: 0.7077 (mtpp) cc_final: 0.6811 (mtpt) REVERT: B 38 GLU cc_start: 0.6697 (mm-30) cc_final: 0.6415 (mm-30) REVERT: B 79 PHE cc_start: 0.7320 (t80) cc_final: 0.6891 (t80) REVERT: B 133 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7392 (tptp) REVERT: B 156 TYR cc_start: 0.6284 (m-10) cc_final: 0.6056 (m-10) REVERT: B 165 ARG cc_start: 0.7160 (mmm-85) cc_final: 0.6936 (mmm-85) REVERT: B 186 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7093 (mm-30) REVERT: B 192 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8604 (mp) REVERT: B 193 ASP cc_start: 0.7924 (t0) cc_final: 0.7546 (t0) REVERT: B 230 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7008 (mt-10) REVERT: B 291 MET cc_start: 0.7173 (ttt) cc_final: 0.6900 (ttm) REVERT: B 292 LYS cc_start: 0.7512 (mttp) cc_final: 0.7280 (tttt) REVERT: B 296 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8422 (mp) REVERT: B 306 PHE cc_start: 0.7442 (t80) cc_final: 0.7057 (t80) REVERT: C 193 ASP cc_start: 0.8050 (t0) cc_final: 0.7775 (t0) REVERT: D 232 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8379 (mm) REVERT: E 170 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8607 (tt) REVERT: E 232 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8459 (mm) REVERT: H 38 HIS cc_start: 0.8359 (m170) cc_final: 0.7925 (m90) REVERT: H 93 ASP cc_start: 0.8430 (m-30) cc_final: 0.7963 (m-30) REVERT: H 120 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7898 (mtm) REVERT: F 70 ARG cc_start: 0.7974 (mtm110) cc_final: 0.6999 (ptt180) outliers start: 55 outliers final: 36 residues processed: 428 average time/residue: 0.1125 time to fit residues: 75.1168 Evaluate side-chains 428 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 384 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 282 SER Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 105 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 99 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 188 optimal weight: 0.0980 chunk 121 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 213 optimal weight: 0.0570 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN D 126 GLN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN L 80 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.171162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.144848 restraints weight = 24088.655| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.21 r_work: 0.3398 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18475 Z= 0.167 Angle : 0.598 10.938 25059 Z= 0.306 Chirality : 0.043 0.186 2823 Planarity : 0.005 0.052 3137 Dihedral : 4.423 24.130 2446 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.22 % Favored : 95.73 % Rotamer: Outliers : 2.67 % Allowed : 18.97 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.18), residues: 2180 helix: 2.26 (0.17), residues: 958 sheet: 0.66 (0.25), residues: 434 loop : -1.53 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 252 TYR 0.020 0.001 TYR B 255 PHE 0.018 0.001 PHE B 27 TRP 0.020 0.001 TRP F 39 HIS 0.006 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00394 (18471) covalent geometry : angle 0.59753 (25051) SS BOND : bond 0.00103 ( 4) SS BOND : angle 0.79523 ( 8) hydrogen bonds : bond 0.04060 ( 1074) hydrogen bonds : angle 4.52754 ( 3090) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 379 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8256 (pt0) cc_final: 0.7704 (pt0) REVERT: A 189 ASP cc_start: 0.7251 (t0) cc_final: 0.6975 (t0) REVERT: A 198 GLU cc_start: 0.7743 (tt0) cc_final: 0.7461 (tt0) REVERT: A 205 LYS cc_start: 0.7889 (mmtt) cc_final: 0.7511 (mtpp) REVERT: A 230 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6478 (mm-30) REVERT: A 232 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8282 (mm) REVERT: A 276 LEU cc_start: 0.7660 (mt) cc_final: 0.7367 (mt) REVERT: A 334 MET cc_start: 0.6862 (mtp) cc_final: 0.6591 (mtp) REVERT: B 10 LYS cc_start: 0.7168 (mtpp) cc_final: 0.6912 (mtpt) REVERT: B 38 GLU cc_start: 0.6694 (mm-30) cc_final: 0.6430 (mm-30) REVERT: B 79 PHE cc_start: 0.7264 (t80) cc_final: 0.6853 (t80) REVERT: B 133 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7380 (tptp) REVERT: B 165 ARG cc_start: 0.7156 (mmm-85) cc_final: 0.6927 (mmm-85) REVERT: B 186 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7065 (mm-30) REVERT: B 192 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8605 (mp) REVERT: B 193 ASP cc_start: 0.7921 (t0) cc_final: 0.7530 (t0) REVERT: B 204 GLU cc_start: 0.6780 (mt-10) cc_final: 0.6446 (mt-10) REVERT: B 291 MET cc_start: 0.7177 (ttt) cc_final: 0.6927 (ttm) REVERT: B 292 LYS cc_start: 0.7553 (mttp) cc_final: 0.7230 (tttp) REVERT: B 296 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8397 (mp) REVERT: C 193 ASP cc_start: 0.8071 (t0) cc_final: 0.7786 (t0) REVERT: D 226 TRP cc_start: 0.8313 (m100) cc_final: 0.7892 (m100) REVERT: D 232 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8359 (mm) REVERT: H 38 HIS cc_start: 0.8374 (m170) cc_final: 0.7955 (m90) REVERT: H 93 ASP cc_start: 0.8421 (m-30) cc_final: 0.7984 (m-30) REVERT: H 120 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7961 (mtm) REVERT: F 50 TRP cc_start: 0.8532 (t60) cc_final: 0.8171 (t60) REVERT: F 70 ARG cc_start: 0.7966 (mtm110) cc_final: 0.7015 (ptt180) outliers start: 54 outliers final: 40 residues processed: 407 average time/residue: 0.1078 time to fit residues: 69.1042 Evaluate side-chains 429 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 383 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 282 SER Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 61 SER Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 138 optimal weight: 2.9990 chunk 49 optimal weight: 0.0060 chunk 144 optimal weight: 0.0670 chunk 189 optimal weight: 1.9990 chunk 161 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 184 optimal weight: 0.5980 chunk 87 optimal weight: 0.0170 overall best weight: 0.2572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 ASN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.174273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.148145 restraints weight = 24145.390| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.24 r_work: 0.3440 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18475 Z= 0.122 Angle : 0.576 10.899 25059 Z= 0.293 Chirality : 0.042 0.169 2823 Planarity : 0.004 0.051 3137 Dihedral : 4.303 23.597 2446 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.22 % Favored : 95.73 % Rotamer: Outliers : 2.23 % Allowed : 19.56 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.19), residues: 2180 helix: 2.41 (0.17), residues: 958 sheet: 0.74 (0.26), residues: 426 loop : -1.44 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 237 TYR 0.020 0.001 TYR B 255 PHE 0.014 0.001 PHE E 79 TRP 0.020 0.001 TRP F 39 HIS 0.005 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00274 (18471) covalent geometry : angle 0.57547 (25051) SS BOND : bond 0.00102 ( 4) SS BOND : angle 0.73469 ( 8) hydrogen bonds : bond 0.03769 ( 1074) hydrogen bonds : angle 4.38205 ( 3090) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 384 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.8188 (pt0) cc_final: 0.7582 (pt0) REVERT: A 189 ASP cc_start: 0.7231 (t0) cc_final: 0.6947 (t0) REVERT: A 205 LYS cc_start: 0.7860 (mmtt) cc_final: 0.7473 (mtpp) REVERT: A 230 GLU cc_start: 0.6982 (mm-30) cc_final: 0.6440 (mm-30) REVERT: A 232 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8264 (mm) REVERT: A 276 LEU cc_start: 0.7636 (mt) cc_final: 0.7344 (mt) REVERT: A 334 MET cc_start: 0.6840 (mtp) cc_final: 0.6515 (mtp) REVERT: B 10 LYS cc_start: 0.7057 (mtpp) cc_final: 0.6719 (mtpt) REVERT: B 24 ARG cc_start: 0.6822 (mtt-85) cc_final: 0.6607 (mtt-85) REVERT: B 38 GLU cc_start: 0.6746 (mm-30) cc_final: 0.6506 (mm-30) REVERT: B 79 PHE cc_start: 0.7233 (t80) cc_final: 0.6819 (t80) REVERT: B 133 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7357 (tptp) REVERT: B 186 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7000 (mm-30) REVERT: B 192 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8571 (mp) REVERT: B 193 ASP cc_start: 0.7875 (t0) cc_final: 0.7488 (t0) REVERT: B 204 GLU cc_start: 0.6790 (mt-10) cc_final: 0.6438 (mt-10) REVERT: B 230 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6938 (mt-10) REVERT: B 292 LYS cc_start: 0.7411 (mttp) cc_final: 0.7067 (tttp) REVERT: B 296 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8374 (mp) REVERT: C 193 ASP cc_start: 0.8038 (t0) cc_final: 0.7763 (t0) REVERT: C 334 MET cc_start: 0.7536 (ttp) cc_final: 0.7320 (ttm) REVERT: D 226 TRP cc_start: 0.8277 (m100) cc_final: 0.7896 (m100) REVERT: D 232 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8277 (mm) REVERT: E 232 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8425 (mm) REVERT: H 38 HIS cc_start: 0.8295 (m170) cc_final: 0.7891 (m90) REVERT: H 93 ASP cc_start: 0.8336 (m-30) cc_final: 0.7921 (m-30) REVERT: H 120 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7890 (mtm) REVERT: L 56 TYR cc_start: 0.8342 (t80) cc_final: 0.8084 (t80) REVERT: F 70 ARG cc_start: 0.7944 (mtm110) cc_final: 0.6999 (ptt180) outliers start: 45 outliers final: 35 residues processed: 407 average time/residue: 0.1158 time to fit residues: 73.2736 Evaluate side-chains 415 residues out of total 2019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 373 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 140 GLN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 282 SER Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 0.4980 chunk 213 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 179 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 126 GLN B 157 ASN ** E 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.171254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.144671 restraints weight = 24144.438| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.24 r_work: 0.3399 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18475 Z= 0.180 Angle : 0.617 13.091 25059 Z= 0.313 Chirality : 0.044 0.227 2823 Planarity : 0.005 0.053 3137 Dihedral : 4.425 23.721 2446 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.27 % Favored : 95.69 % Rotamer: Outliers : 2.43 % Allowed : 19.71 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.18), residues: 2180 helix: 2.25 (0.17), residues: 958 sheet: 0.66 (0.25), residues: 449 loop : -1.57 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 237 TYR 0.018 0.001 TYR C 236 PHE 0.014 0.001 PHE H 71 TRP 0.016 0.001 TRP F 39 HIS 0.005 0.001 HIS B 212 Details of bonding type rmsd covalent geometry : bond 0.00429 (18471) covalent geometry : angle 0.61710 (25051) SS BOND : bond 0.00214 ( 4) SS BOND : angle 0.83127 ( 8) hydrogen bonds : bond 0.04095 ( 1074) hydrogen bonds : angle 4.49754 ( 3090) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3927.27 seconds wall clock time: 68 minutes 6.67 seconds (4086.67 seconds total)